DNA Strand

When our services have provided data that will be used in a manuscript, we would appreciate acknowledgement of the shared instrumentation grants and support from the Chao Comprehensive Cancer Center at UCI, Complexity, Cooperation and Community in Cancer and the Skin Biology Resource-Based Center at UCI.

The following publications have acknowledged these services and support:

How to Acknowledge the GRT in your Publications

To acknowledge the GRT Hub in your publications, copy and paste the language below:

"This work utilized resources of the UCI Genomics Research and Technology Hub (GRT Hub) parts of which are supported by NIH grants to the Comprehensive Cancer Center (P30CA-062203) and the UCI Skin Biology Resource Based Center (P30AR075047) at the University of California, Irvine, as well as to the GRT Hub for instrumentation (1S10OD010794-01and 1S10OD021718-01)."

Childs, J.E., Morabito, S., Das, S., Santelli, C., Pham, V., Kusche, K., Vera, V.A., Reese, F., Campbell, R.R., Matheos, D.P., Swarup, V., and Wood. M.A. Relapse to cocaine seeking is regulated by medial habenula NR4A2/NURR1 in mice. (2024) Cell Rep. 2024 Mar 26;43(3):113956.
Chea, S., Kreger, J., Lopez-Burks, M.E., Laclean, A.L., Lander, A.D., and Calof, A.L. Gastrulation-stage gene expression in Nipbl+/- mouse embryos foreshadows the development of syndromic birth defects. (2024) Sci Adv. 2024 Mar 22; 10(12): eadl4239.
Chen, Z., Snetkova, V., Bower, G., Jacinto, S., Clock, B., Dizehchi, A., Barozzi, I., Mannion, B.J., Alcaina-Caro, A., Lopez-Rioz, J., Dickel, D.E., Visel, Z., Pennacchio, L.A., and Kvon, E.Z. Increased enhancer-promoter interactions during developmental enhancer activation in mammals. (2024) Nat Genet. 2024 Mar 20. doi: 10.1038/s41588-024-01681-2
Kastenschmidt, J.M., Schroers-Martin, J.G., Sworder, B.J., Sureshcandra, S., Khodadoust, M.S., Liu, C.L., Olsen, M., Kurtz, D.M., Diehn, M., Wagar, L.E., and Alizadeh, A.A. A human lymphoma organoid model for evaluating and targeting the follicular lymphoma tumor immune microenvironment. (2024) Cell Stem Cell. 2024 Mar 7;31(3):410-420.e4.
Mendez Luque, L. F., Avelar-Barragan, J., Nguyen H., Nguyen J., Soyfer, Eli M., Liu, J., Chen, J. H., Mehrotra, N., Huang, X., Kosiorkek, H. E., Dueck, A., Himstead, A., Heide, E., Lem, M., El Alaoui, K., Mas, E., Scherber R. M., Mesa, R. A., Whiteson, K. L., Odegaard, A., and Fleischman, A. G. The NUTRIENT Trial (NUTRitional Intervention among myEloproliferative Neoplasms): Results from a Randomized Phase I Pilot Study for Feasibility and Adherence. Cancer Res Commun. 2024 Mar 5;4(3):660-670.
Kong, X., Nguyen, N.V., Li, Y., Sakr, J.S., Williams, K., Sharifi, S., Chau, J., Bayrakci, A., Mizuno, S., Takahashi, S., Kiyono, T., Tawil, R., Mortazavi, Ali., and Yokomori, K. Engineered FSHD mutations results in D4Z4 heterochromatin disruption and feedforward DUX4 network activation. (2024) iScience. 2024 Apr 19; 27(4): 109357.
Sanchez, A., Ortega, P., Sakhetemani, R., Manjunath, L., Oh, S., Bournique, E., Becker, A., Kim, K., Durfee, C., Temiz, N.A., Chen, X.S., Harris, R.S., Lawrence, M.S., and Buisson, R. Mesoscale DNA features impact APOBEC3A and APOBEC3B deaminase activity and shape tumor mutational landscapes. (2024) Nat Commun. 2024; 15: 2370.
Hicks, M.R., Saleh, K.K., Clock, B., Gibbs, D.E., Yang, M., Younesi, S., Gane, L., Guiterrez-Garcia, V., Xi, H., and Pyle, A.D. Regenerating human skeletal muscle forms an emerging niche in vivo to support PAX7 cells. (2024) Nat Cell Biol. 2024 Feb;26(2):306.
Watson, S.J., Arisdakessian, C., Petelo, M., Kellipuleole, K., Tachera, D.K., Okuhata, B.K. and Frank, K.L. Groundwater microbial communities reflect geothermal activity on volcanic island. (2024) Geobiology 22e12591
Liu, X., Liu, Z., Morgan, T.R., and Norden-Krichmar, T.M., Single-cell transcriptomics of peripheral blood mononuclear cells indicates impaired immune and inflammatory responses in alcohol-associated hepatitis. (2024) Hum Immunol
. 2024 Jan;85(1):110735.
Hachey, S.J., Hatch, C.J., Gaebler, D., Mocherla, A., Nee, K., Kessenbrock, K., and Hughes, C.C.W. Targeting tumor-stromal interactions in triple-negative breast cancer using a human vascularized micro-tumor model. (2024) Breast Cancer Res. 2024 Jan 5;26(1):5.
Listopad S, Magnan C, Day LZ, Asghar A, Stolz A, Tayek JA, Liu, Z-X, Jacobs JM, Morgan TR and Norden-Krichmar TM Identification of integrated proteomics and transcriptomics signature of alcohol-associated liver disease using machine learning. (2024) PLOS Digital Health 3(2): e0000447.
Liu, L., Yu, A.M., Wang, X., Soles, L.V., Teng, X., Chen, Y., Yoon, Y., Sarkan, K.S.K., Valdez, M.C., Linder, J., England, W., Spitale, R., Yu, Z., Marazzi, I., Qiao, F., Li, W., Seelig, G., and Shi, Y. The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery. (2023) Nat Struct Mol Biol. 2023 Dec;30(12):1947-1957.
Hollingsworth, E. W., Liu, T. A., Jacinto, S. H., Chen, C. X., Alcantara, J. A., and Kvon, E. Z. Rapid and quantitative functional interrogation of human enhancer variant activity in Live Mice. bioRxiv. 2023 Dec 10:2023.12.10.570890.
Holley, S. M., Reidling, J. C., Cepeda, C., Wu, J., Lim, R. G., Lau, A., Moore, C>, Miramontes, R., Fury, B., Orellana, I., Neel, M., Coleal-Bergum, D., Monuki, E. S., Bauer, G., Meshul, C. K., Levine, M. S., and Thompson, L. M. Transplated human neural stem cells rescue phenoypes in zQ175 Huntington's disease mice and innervate the striatum Mol Ther. 2023 Dec 6;31(12):3545-3563.
Pham, P.D., Lu, H., Han, H., Zhour, J.J. Madan, A., Wang, W., Murre, C. and Cho, K.W.Y.  Transcriptional network governing extraembryonic endoderm cell fate choice.  (2023)  Developmental Biology 502: 20-37
Charney, R.M., Prasad, M.S., Juan-Sing, C., Patel, L.J., Hernandez, J.C., Wu, J., and García-Castro, M.I. Mowat-Wilson syndrome factor ZEB2 controls early formation of human neural crest through BMP signaling modulation. (2023) Stem Cell Reports
. 2023 Nov 14;18(11):2254-2267.
Smith, J.G., Koronowski, K.B., Mortimer, T., Sato, T., Greco, C.M., Petrus, P., Verlande, A., Chen, S., Samad, M., Deyneka, E., Mathur, L., Blazev, R., Molendijk, J., Kumar, A., Deryagin, O., Vaca-Dempere, M., Sica, V., Liu, P., Orlando, V., Parker, B.L., Baldi, P., Patrick-Simon, W., Jang, C., Masri, S., Bentiah, S.A., Muñoz-Cánoves, P., and Sassone-Corsi, P. Liver and Muscle Circadian Clocks Cooperate to Support Glucose Tolerance in Mice. (2023) Cell Rep. Author manuscript; available in PMC 2023 Oct 23.
Milovic, A., Duong, J. V., and Barbour, A. G. The white-footed deermouse, an infection-tolerant reservoir for several zoonotic agents, tempers interferon responses to endotoxin in comparison to the mouse and rat. 2023 Oct 12:2023.06.06.543964.
Doratt, B.M., Sureshchandra, S., True, H., Rincon, M., Marshall, N.E., and Messaoudi, I. Mild/asymptomatic COVID-19 in unvaccinated pregnant mothers impairs neonatal immune responses. (2023) JCI Insight. 2023 Oct 9; 8(19): e172658.
Lewis, S.A., Doratt, B.M., Qiao, Q., Blanton, M., Grant, K.A., and Messaoudi, M. Integrated single cell analysis shows chronic alcohol drinking disrupts monocyte differentiation in the bone marrow. (2023) Stem Cell Reports. 2023 Sep 12; 18(9): 1884–1897
Le, N., Heras, J., Herrera, M.J., German, D.P., and Crummett, L.T. The genome of Anoplarchus purpurescens (Stichaeidae) reflects its carnivorous diet. (2023) Mol Genet Genomics. 2023 Nov;298(6):1419-1434
Harb, J. F>, Christensen, C. L., Kan, S., Rha, A. K., Andrade-Heckman, P., Pollard, L., Steet, R., Huang, J. Y., and Wang, R. Y. Base editing corrects the common Salla disease SLC17A5 c.115C>T variant. Mol Ther Nucleic Acids. 2023 Aug 26:34:102022.
Rankins, D. R., Herrera, M. J., Christensen M. P., Chen, A., Hood, N. Z., Heras, J., and German, D. P. When digestive physiology doesn't match "diet": Lumpenus sagitta (Stichaeidae) is an "omnivore" with a carnivorous gut. Comp Biochem Physiol A Mol Integr Physiol. 2023 Nov:285:111508.
Ziegler, M. E., Khabaz, K., Khoshab, N., Halaseh, F. F., Chnari, E., Chen, S., Baldi, P., Evans, G. R. D., and Widgerow, A. D. Combining Allograft Adipose and Fascia Matrix as an Off-the-Shelf Scaffold for Adipose Tissue Engineering Stimulates Angiogenic Responses and Activates a Proregenerative Macrophage Profile in a Rodent Model. Ann Plast Surg. 2023 Aug 1;91(2):294-300.
Barbour, A. G., Duong, J. V., and Long A. D. Lyme Disease Agent Reservoirs Peromyscus leucopus and P. maniculatus Have Natively Inactivated Genes for the High-Affinity Immunoglobulin Gamma Fc Receptor I (CD64). Pathogens
. 2023 Aug 18;12(8):1056.
Neubert, E.N., DeRogatis, J.M, Lewis, S.A. Viramontes, K.M., Ortega, P., Hernriquez, M.L., Buisson, R., Messaoudi, I. and Tinoco, R.  HMGB2 regulates the differentiation and stemness of exhausted CD8+ T cells during chronic viral infection and cancer  (2023)  Nature Communications 14: 5631
Nakahara, S., Male, A.G., Turner, J.A., Calhoun, V.D., Lim, K.O., Mueller, B.A., Bustillo, J.R., O’Leary, D.S., Voyvodic, J., Belger, A., Preda, A., Mathalon, D.H., Ford, J.M., Guiffanti, G., Macciardi, F., Potkin, S.G. and van Erpk T.G.M.  Auditory oddball hypoactivation in schizophrenia.  (2023)  Psychiatry Research Neuroimaging epub August 28
Kastenschmidt, J.M., Sureschandra, S., Jain, A.,  Hernandez-Davies, J.E.,  de Assis, R., Wagoner, Z.W., Sorn, A.M.,  Mitul, M.T., Benchorin, A.I., Levendosky, E., Ahuja, G., Zhong, Q., Trask, D., Boeckmann, J.,  Nakajima, R., Jasinskas, A., Saligrama, N., Davies, D.H. and Wagar, L.E.  Influenza vaccine format mediates distinct cellular and antibody response in human immune organoids.  (2023)  Immunity 56:1910-1926
Kim, J., Chun, Yl, Ramirez, CB., Hoffner, L.A., Jung, S., Jang, K.H.,  Rubtsova, V.I., Jang, C. and Lee, G.  MAPK13 stabilization via m6A mRNA modification limits anticancer efficacy of rapamycin.  (2023)  Journal of Biological Chemistry 299(9): 105175
Hakiem, O.R., Rizvi, S.M.A., Ramirez, C and Tan, M.  Euo is a developmental regulator that represses late genes and activates midcycle genes in Chlamydia trachomatis.  (2023)  Microbial Pathogenesis epub August 1
Lin, L, Jung, K-M., Lee, H-L, Le, J., Colleluori, G., Wood, C., Palese, F., Squire, E., Ramirez, J., Su, S., Torrens, A., fotio, Yl, Tang, L., Yu, C., Yang, Q., Huang, L., DiPatrizio, N., Jang, C., Cinti, S. and Piomelli, D. Adolescent exposure to low-dose THC disrupts energy balance and adipose organ homeostatsis in adulthood. (2023) Cell Metabolism 35: 1227-1241
Kumar, T., Nee, K., Wei, R., He, S., Nguyen, Q.H., Bai, S., Blake, K., Pein, M., Gong, Y., Sei, E., Hu, M., Cassent, A.K., Thennavan, A., Li, J., Tran, T., Chen, K., Nilges, B., Kashikar, N., Braubach, O., Cheikh, B.B., Nikuline, N., Chen, H., Teshome, M., Menegaz, B., Javaid, H., Nagi, C., Montalvan, J., Lev, T., Mallya, S., Tifrea, D.F., Edwards, R., Lin, E., Parajuli, R., Hanson, S., Winoccur, S., Thompson, A., Lim, B., Lawson, D.A., Kessenbrock, K and Navin, N.  A spatially resolved single-cell genomic atlas of the adult human breast.  (2023)  Nature 620:181
Coulis, G., Jaime, D., Guerrero-Juarez, C., Kastenschmidt, J.M., Farahat, P.K., Nguyen, Q., Pervolarakis, N., McLinden, K., Thurlow, L., Movadedi, S., Hughes, B.S., Duarte, J., Sorn, A., Montoya, E., Mozaffar, I., Dragan, M., Othy, S., Joshi, T., Han, C.P., Kimonis, V., MacLean, A.A., Nie, Q., Wallace, L.M, Harper, S.Q., Mosaffar, T., Hogarth, M.W., Bhattacharya, J., Jaiswal, J.K., Golann, D.R., Su, Q., Kessenbrock, K., Stec, M., Spencer, J.J., Zamudio, J.R. and Villalta, S.A.  Single-cell and spatial transcriptomics identify a macrophage population associated with skeletal muscle fibrosis.  (2023)  Science Advances 9:eadd9984
Trinh, A. Huang, Y., Shao, H., Ram, A., Morival, J., Wang, J., Chung E.J. and Downing, T.L.  Targeting the ADPKD methylome using nanoparticle-mediated combination therapy.  (2023) APL Bioengineering 7: 026111
Greilach, S.A., McIntyre, L.L., Nguyen, Q.H., Silva, J., Kessenbrock, K., Lane, T.E., and Walsh, C.M. Presentation of Human Neural Stem Cell Antigens Drives Regulatory T Cell Induction. (2023) J Immunol. 2023 Jun 1;210(11):1677-1686.
Stabell, A.R., Lee, G.E., Jia, Y., Wong, K.N., Wang, S., Ling, J., Nguyen, S.D., Sen, G.L., Nie, Q., and Atwood, S.X. Single-cell transcriptomics of human-skin-equivalent organoids. (2023) Cell Rep. 2023 May 30;42(5):112511.
Morales-Cruz, A., Aguirre-Liguori, J., Massonnet, M., Minio, A., Zaccheo, M., Cochetel, N., Walker, A., Riaz, S., Zhou, Y., Cantu, D., and Gaut, B.S. Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate. (2023) Commun Biol. 2023 May 30;6(1):580.
Reese, F., Williams, B., Balderrama-Gutierrez, G., Wyman, D., Çelik M. H., Rebboah, E., Rezaie, N., Trout, D., Razavi-Mohseni, M., Jiang, Y., Borsari, B., Morabito, S., Liang, H. Y., McGill, C. J., Rahmanian, S., Skar, J., Jiang, S., Zeng, W., Carvalho, K., Weimer, A.K., Dionne, L. A., McShane, A., Bedi, K., Elhajjayjy, S. I., Upchurch, S., Jou, J., Youngworth, I., Gabdank I., Sud, P., Jolanki, O., Strattan, S., Kagda, M. S., Snyder, M. P., Hitz, B. C., Moore, J. E., Weng, Z., Bennett, D., Reinholdt, L., Ljungman, M. Beer, M. A., Gerstein, M. B., Pachter, L., Guigó, R., Wold, B. J., and Mortazavi, A. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv 2023 May 16:2023.05.15.540865
Doratt, B. M., Sureshcandra, S., True, H., Rincon, M., Marshall, N., and Messaoudi, I. Mild/Asymptomatic Maternal SARS-CoV-2 Infection Leads to Immune Paralysis in Fetal Circulation and Immune Dysregulation in Fetal-Placental Tissues. 2023 May 11:2023.05.10.540233.
Batarseh, T.N., Batarseh, S.N., Rodríguez-Verdugo, A., and Gaut, B.S. Phenotypic and Genotypic Adaptation of Escherichia coli to Thermal Stress is Contingent on Genetic Background. (2023) Mol Biol Evol. 2023 May 2;40(5):msad108.
Sureshchandra, S., Doratt, B.M., True, H., Mendoza, N., Rincon, M., Marshall., N.E., Messaoudi, I. Multimodal profiling of term human decidua demonstrates immune adaptations with pregravid obesity. (2023) Cell Rep. 2023 Jul 25; 42(7): 112769.
Miyoshi, E., Morabito, S., Henningfield, C. M., Rahimzadeh N., Shabestari, S. K., Das, S., Michael, N., Reese, F., Shi, Z., Cao, Z., Scarfone, V., Arreola, M. A., Lu, J., Wright, S., Silva, J., Leavy, K., Lott, I. T., Doran, E., Young, W. H., Shahin, S., Perez-Rosendahl, M., Head, E., Green, K. N., and Swarup, V. Spatial and single-nucleus transcriptomic analysis of genetic and sporadic forms of Alzheimer's Disease. bioRxiv 2023 Jul 26:2023.07.24.550282.
Sato, S., Hishida, T., Kinouchi, K., Hatanaka, F., Li, Y., Nguyen, Q., Chen, Y., Wang, P.H., Kessenbrock, K., Li, W., Izpisua Belmonte, J.C. and Sassone-Corsi, P. The circadian clock CRY1 regulates pluripotent stem cell identity and somatic cell reprogramming.  (2023) Cell Reports 42: 112590
Das, B.K., Kannan, A., Velasco, G.J., Junika, M.D., Lambrecht, N.,  Nguyen, Q., Zhao, H.,  Wu, J. and Gao L.  Single-cell dissection of Merkel cell carcinoma heterogeneity unveils transcriptomic plasticity and therapeutic vulnerabilities.  (2023) Cell Reports Medicine 4: 101101
Dragan, M., Chen, Z., Li, Y.m, Le, J., Sun, P., Haensel, D., Sureshchandra, S., Pham, A., Lu, E., Pham, K.T., Verlande, A., Vu, R., Gutierrez, G., Li, W., Jang, C., Masri, S. and Dai, X.  Ovo1/2 loss-induced epidermal defects elicit skin immune activation and alter global metabolism.  (2023) EMBO Reports 24:e56214
Chen, J.K., Wiedemann, J., Nguyen, L., Lin, Z., Tahir, M.,  Hui, C-C.,  Plikus, M.V. and Andersen, B.  IRX5 promotes DNA damage repair and activation of hair follicle stem cells.  (2023)  Cell Reports  18: 1227-1243
Segaliny, A.I., Jayaraman, J., Chen, X., Chong, J., Luxon, R., Fung, A., Fu, Q., Jiang, X., Rivera, R., Ma, X., Ren, Ci., Zimak, J., Hedde, P.N., Shang, Y., Wu, G., and Zhao, W. A high throughput bispecific antibody discovery pipeline. (2023) Commun Biol. 2023 Apr 7;6(1):380.
DeRogatis, J.M., Neubert, E.N., Viramontes, K.M., Henriquez, M.L., Nicholas, D.A. and Tinoco, R.  Cell-intrinsic CD38 expression sustains exhausted CD8+ T  cells by regulating their survival and metabolism during chronic viral infection.  (2023)  Journal of Virology epub April 11
Gupta, M., Wang, J., Garfio, C. M., Vandewalle, A., and Spitale, R. C. Cycloaddition enabled mutational profiling of 5-vinyluridine in RNA. Chem Commun (Camb). 2023 Mar 14;59(22):3257-3260.
Stabell, A. R., Lee, G. E., Jia, Y., Wong, K. N., Wang, S., Ling, J., Nguyen, S. D., Sen, G. L. Nie, Q., and Atwood, S. X. Single-cell transcriptomics of human-skin-equivalent organoids. Cell Rep. 2023 May 30;42(5):112511.
Nee, K., Ma, D., Nguyen, Q.H., Pein, M., Pervolarakis, N., Insua-Rodriguez, J., Gong, Y., Hernandez, G., Alshetaiwi, H., Williams, J., Rauf, M., Dave K.R., Boyapati, K., Hasnain, A., Calderon, C., Markaryan, A., Edwards,R., Lin, E., Parajuli, R., Zhou, P., Nie, Q., Shalabi, S., LaBarge, M.A. and Kessenbrock, K.  Preneoplastic stromal cells promote BRCA1-mediated breast tumorigenesis.  (2023) Nature Genetics epub March 13
Dolinko, A.H., Chwa, M., Schneider, K., Singh, M.K., Atilano, S., Wu, J. and Kenney, M.C.  Hypoxia-induced transcripional differences in African and Asian versus European diabetic cybrids.  (2023)  Scientific Reports 13:3818
Workman, M.J., Lim, R.G., Wu, J., Frank, A., Ornelas, L., Panther, L., Galvez, E., Perez, D., Meepe, I., Lei, S., Valencia, V., Gomez, E., Liu, C., Moran, R., Pinedo, L., Tsitkov, S., Ho, R., Kaye, J.A., the Answer ALS Consortium, Thompson, T., Rothstein, J.D., Finkbeiner, S., Fraenkel, E., Sareen, D., Thompson, L.M. and Svendsen, C.N.  Large-scale differentiation of iPSC-derived motor neurons from ALS and control subjects. (2023) Neuron 111:1-14
Urban, L.A., Li, J., Gundogdu, G., Trinh, A., Shao, H., Nguyen, T., Mauney, J.R. and Downing, T.L.  DNA methylation dynamics during esophageal epithelial regeneration following repair with accellular silk fibroin grafts in rat.  (2023)  Advanced Biology 2000160
Manjunath, L., Oh, S., Ortega, P., Bouin, A., Bournique, E., Sanchez, A., Martensen, P.M., Auerbach, A.A., Becker, J.T., Seldin, M., Harris, R.S., Semler, B.L., and Buisson, R. APOBEC3B drives PKR-mediated translation shutdown and protects stress granules in response to viral infection. (2023) Nat Commun. 2023; 14: 820
Raus, A.M., Fuller, T.D., Nelson, N.e., Valientes, D.A., Bayat, A. and Ivy, A.S.  Early-life exercise primes the murine neural epigenome to facilitate gene expression and hippocampal memory consolidation.  (2023)  Communications Biology 6:18
Yang, J.C., Jacobs, J.P, Hwang, M., Sabui, S., Liang, F.,  Said, H.M. and Skupsky, J.  Biotin deficiency induces intestinal dysbiosis associated with inflammatory bowel disease-like phenotype.  (2023)  Nutrients epub January 4
Ren, M. and Lotfipour, S.  Antibotic knockdown of gut bacteria sex-dependently enhances intravenous fentanyl self-administration in adult Sprague Dawley rats.  (2023) International Journal of Molecular Sciences 24: 409
Reyes-Ortiz, A.M., Abud, E.M., Burns, M.S., Wu, J., Hernandez, S.J., McClure, N., Wang, K.Q., Schulz, ClJ., Miramontes, R., Lau, Al, Neethu, M., Miyoski, E., Van Vactor, D., Reidling, J.C., Blurton-Jones, M., Swarup, V., Poon, W.W., Lim, R.G. and Thompson, L.M.  Single-nuclei transcriptome analysis of Huntington disease iPSC and mouse astrocytes implicates maturation and functional deficits.  (2023)  iScience 26:105732
Chadarevian, J.P., Lombroso, S.I., Peet, G.C., Hasselmann, J., Tu, Cl, Marzan, D.E., Capochi, J., Purnell, FS. Nemec, K.M., Lahian, A., Escobar, A., England, W., Chaluvadi, S., O’Brien, C.A., Yaqoob, F., Aisenberg, W.H., Pantiagua, M.P., Bennett, M.L.m, Davtyan, D., Spitale, R.C., Blurton-Jones, M. and Bennett, F.C.  Engineering an inhibitor-resistant human CSF1R variant for microglia replacement.  (2023)  Journal of Experimental Medicine  220(3): e20220857
Rothman, J. A., Saghir, A., Chung, Seung-Ah., Boyajian, N., Dinh, T., Kim, J., Oval, J., Sharavana, V., York, C., Zimmer-Faust, A. G., Langlois, K., Steele, J. A., Griffith, J. F., and Whiteson, K. L. Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020-21 reveals widespread transcription of antibiotic resistance genes. Water Res. 2023 Feb 1:229:119421.
Sureshchandra, S., Doratt, B.M., Mendza, N., Varlamov, O., Rincon, M., Marshall, N.E., and Messaoudi, I. Maternal obesity blunts antimicrobial responses in fetal monocytes. (2023) eLife. 2023; 12: e81320.
Thone, M.N., Chung, J.Y., Ingato, D., Lugin, M.L., and Kwon, Y.J. Cell-free, Dendritic Cell-mimicking Extracellular Blebs for Molecularly Controlled Vaccination. (2023) Adv Ther (Weinh). 2023 Jan;6(1):2200125.
Hernandez, S.J., Lim, R.G., Onur, T., Dane, M.A., Smith, R., Wang, K., Jean, G. E-H., Devlin, K., Miramontes, R., Wu, J., Casale, M., Kilburn, D., Heiser, L.M., Korkola, J.E., Van Vactor, D., Botas, J, Thompson-Peer, K.L. and  Thompson, L.M.  An altered extracellular matrix-integrin interface contributes to Huntington’s disease-associated CNS dysfunction in glial and vascular cells.  (2022)  Human Molecular Genetics epub Dec 22
Hjelm, B.E., Ramiro, C., Rollins, B.L., Omidsalar, A.A., Gerke, D.S., Das, S.C., Sequiera, A., Morgan, L., Schatzberg, A.F., Barchas, J.D. Lee, F.S., Myers, R.M., Watson, S.J., Akil, H., Bunney, W.E. and Vawter, M.P.  Large common mitochondrial DNA deletions are associated with a mitochondrial SNP T14798C near the 3′ breakpoints.  (2022) Complex Psychiatry epub November 14
Raus, A.M., Nelson, N.E., Fuller, T.D. and Ivy, A.S.  “SIT” with Emx1-NuTRAP Mice:  Simultaneous INTACT and TRAP for paired transcriptomic and epigenetic sequencing.  (2022)  Current Protocols 2: e570
Sami, J.D., Spitale, R.C. and Cleary, M.D.  mRNAs encoding neurodevelopmental regulators have equal N6-methyladenosine stoichiometry in Drosophila neuroblasts and neurons.  (2022)  Neural Development 17:9
Florio, E., Serra, M., Lewis, R.G., Kramár, E., Freidberg, M., Wood, M., Morelli, M., and Borrelli, E. D2R signaling in striatal spiny neurons modulates L-DOPA induced dyskinesia. (2022) iScience. 2022 Oct 21; 25(10): 105263.
Durairaj, G., Demir, O., Lim B., Baronio, R., Tifrea, D., Hall, L.V., DeForest, J.C., Lauinger, L., Jebril Fallatah, M.M., Yu, C., Bae, H., Lin, D-W., Kim J.K., Salehi, F., Jang, C., Qiao, F., Lathrop, R.H., Huang, L., Edwards, R., Rychnovsky, S., Amaro, R.E. and Kaiser, P.  Discovery of compounds that reactivate p53 mutants in vitro and in vivo.  (2022) Cell Chemical Biology 29: 1381-1395
Wu, S.C., Kim, A., Gu, Y., Martinez, D.I., Zocchi, L., Chen, ClC., Lopez, J., Salcido, K., Singh, S., Wu. J., Nael, A. and Benavente, C.  UHRF1 overexpression promotes osteosarcoma metastasis through altered exosome production and AMPK/SEMA3E suppression.  (2022) Oncogenesis epub September 22
Batarseh, T.N., Morales-Cruz, A., Ingel, B., Roger, M.C. and Gaut, B.S.  Using genomes and evolutionary analyses to screen for host-specificity and positive selection in the plant pathogen Xylella fastidiosa.  (2022) Applied and Environmental Microbiology epub August 22
Merleev, A.A., Le, S.T., Alexanian, C., Toussi, A., Xie, Y., Marusine, AlI., Watkins, S.M., Patel, F., Billi, A.C., Wiedemann, J., Izumiya,  Yl., Kumar, A., Uppala, R., Kahlenberg, J.M, Liu, F-t., Adamopoulos, I.E., Wang, E.A.,
Duan, J., Grando, C., Liu, S., Chernyavsky, A., Chen, J.K.,  Andersen, B. and  Grando, S.A.  The M3 muscarinic acetylcholine receptor promotes epidermal differentiation.  (2022)  epub July 21
Nourse, J.L., Leung, V.M., Abuwarda, H., Evans, E.L., Izquierdo-Ortiz, E., Ly, A.T., Truong, N., Smith, S., Bhavsar, H., Beertaccini, G., Monuki, E.S., Panicker, M.M. and Pathak, M.M.  Piezo1 regulates cholesterol biosynthesis to influence neural stem cell fate during brain development.  Journal of General Physiology 154(10):e202213084
Vu, R., Jin, S., Sun, P., Haensel, D., Nguyen, Q.H., Dragan, M., Kessenbrock, K., Nie, Q. and Dai, X.  Wound healing in aged skin exhibits systems-level alterations in cellular composition and cell-cell communication  (2022)  Cell Reports 40:111155
Shiu, J., Zhang, L., Lentsch, G., Flesher, J.L., Jin, S., Polleys, C., Jo, S.J., Missoni, C., Mobasher, P., Kwan, J., Ruis-Diaz, F., Tromberg, B.J., Georgakoudi, I., Nie, Q., Balu, M. and Ganesan, A.K.  Multimodal analysis of vitiligo skin identify tissue characteristics of stable disease.  (2022)  JCI Insight 7(13):e154585
Guerrero-Juarez C.F., Lee, G.H., Liu, Y., Wang, S., Karikomi, M., Sha, Yl, Chow, R.Y., Nguyen, T.T.L, Iglesias, V.S., Aasi, S., Drummond, M.L., Qie, Q., Sarin, K. and Atwood, S.X.  Single-cell analysis of human basal cell carcinoma reveals novel regulators of tumor growth and the tumor microenvironment.  (2022)  Science Advances 8:7981
Han, Y., Villarreal-Ponce, A., Gutierrez Jr., G., Nguyen, A., Sun, P., Wu, T., Sui, B., Berx, G., Brabletz, T., Kessenbrock, K, Zeng, Y.A., Watanabe, K. and Dai, X.  Coordinate control of basal epithelial cell fate and stem cell maintenance by core EMT transcription factor Zeb1. (2022) Cell Reports 38:110240
Oh, S. and Buisson, R.  A digital PCR-based protocol to detect and quantify RNA editing events at hotspots.  (2022)  Star Protocols 3:101148
Claes, C., England, W.E., Danhash, E.P., Shabestari, S.K., Jairaman, A., Chadarevian, J.P., Hasselmann, J., Tsai, A.P., Coburn, M.A., Sanchez, J., Lim, T.E., Hidalgo, J.L.S., Tu, C., Cahalan, M.D., Lamb, B.T., Landreth, G.E., Spitale, R.C. and Blurton-Jones, M.  The P522R protective variant of PLCG2 promotes the expression of antigen presentation genes by human microglia in an Alzheimer’s disease mouse model.  (2022) Alzheimer’s & Dementia  1-14
Chen, G.T., Tifrea, D.F., Murad, R., Habowski, A.N., Lyou, Y., Duong, M.R., Hosohama, L., Mortazavi, A., Edwards, R.A. and Waterman, M.L.  Disruption of beta-catenin-dependent Wnt signaling in colon cancer cells remodels the microenvironment to promote tumor invasion.  (2022)  Molecular Cancer Research 20:468-484
Listopad, S., Magnan, C., Asghar, A., Stolz, A., Tayek, J.A., Liu, Z-X., Morgan, T.R. and Norden-Krichmar, T.  Differentiating between liver diseases by applying multiclass machine learning approaches to transcriptomics of liver tissue or blood based samples.  (2022)  JHEP Reports epub August 17
Chun, S.K., Fortin, B.M., Fellows, R.C., Habowski, A.N., Verlande, A., Song, W.A., Mahieu, A.L., Lefebvre, A.E.Y.T., Sterrenberg, J.N., Velex, L.M.,  Digman, M.A., Edwards, R.A., Pannunzio, N.R., Seldink, M.M., Waterman, M.L. and Masri, S.  Disruption of the circadian clock drives Apc loss of heterozygosity to accelerate colorectal cancer.  (2022)  Science Advances 8: eabo2389
Liu, Y., Guerrero-Juarez, C.F., Xiao, F., Shettigar, N.U., Ramos, R., Kuan, C-H., Lin, Y-C., Martinez Lomeli, L., Park, J.M., Oh, J.W., Liu, R., Lin, S-J., Tartaglia, M., Yang, R-B., Yu, Z., Nie, Q., Li, J. and Plikus, M.V.  Hedgehog signaling reprograms hair follicle niche fibroblasts to a hyper-activated state.  (2022)  Developmental Cell 57.: 1758-1775
Leigh, S.C., Catabay, C. and German, D.P.  Sustained changes in digestive physiology and microbiome across sequential generations of zebrafish fed different diets.  (2022)  Comparative Biochemistry and Physiology, Part A.  273: 111285
Zhou, J.J., Pham, P.D., Han, H., Wang, W. and Cho, K.W.Y.  Foxh1 engages in chromatin regulaton revealed by protein interactome analyses.  (2022)  Development, Growth & Differentiation epub July 18
Petrus, P., Cervantes, M., Samad, M., Sato, T., Chao, A., Sato, S., Koronowski, K.B., Park, G., Alam, Y., Mejhert, N., Seldin, M.M, Monroy Kuhn, J.S., Dyar, K.A., Jutter, D., Baldi, P., Kaiser, P., Jang, C. and Sassone-Corsi, P.  Tryptophan metabolism is a physiological integrator regulating circadiun rhythms.  (2022)  Molecular Metabolism 101556
Cian, M.B., Mettlach, J.A., Zahn, A.E., Giordano, N.P., Minor, K.E., McClelland, M. and Dalebroux, Z.D.  Cardiolipin biosynthesis genes are not required for Salmonella enterica serovar Typhimurium pathogenesis in C57BL/6J mice.  (2022) Microbiology Spectrum 10(3): 02617-21
Viramontes, K.M., Newbert, E.N., DeRogatis, J.M. and Tinoco, R.  PD-1 immune checkpoint blockage and PSGL-1 inhibition syntergize to reinvigortate exhausted T cells.  (2022) Frontiers in Immunology 13: 869768
Wang, E., Sheehan, L, Ramirez, C., Densi, A., Rizvi, S., Ekka, R., Sutterlin, C. and Tan, M.  A reverse genetic approach for studying sRNAs in Chlamydia trachomatis.  (2022)  American Society for Microbiology mBio epub June 21
Guerrero-Juarez, C.F., Lee, G.H., Liu, Y., Wang, S., Karikomi, M., Sha, Y., Chow, R.Y., Nguyen, T.T.L., Iglesias, V.S., Aasi, S., Drummond, M.L., Nie, Q., Sarin, K. and Atwood S.X.  Single-cell analysis of human basal cell carcinoma reveals novel regulators of tumor growth and the tumor microenvironment.  (2022)  Science Advances 8: eabm7981
Kumar P, Brazel D, DeRogatis J, Valerin JBG, Whiteson K, Chow WA, Tinoco R, Moyers JT. The cure from within? a review of the microbiome and diet in melanoma. (2022) Cancer metastasis reviews 41(2):261-280. PMC9042647
Barbour, K.M., Weihe, C., Allison, S.D. and Martiny, J.B.H. Bacterial community response to environmental change varies with depth in the surface soil.  (2022) Soil Biology & Biochemistry 172: 108761
Shi, Z., Das, S., Morabito, S., Miyoshi, E. and Swarup, V.  Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue. (2022) Star Protocols 3:101491
Shabestari, S.K., Morabito, S., Danhash, E.P., McQuade, A., Ramierez Sanchez, J., Miyoshi, E., Chaderevian, J.P., Claes, C., Coburn, M.A., Hassselmann, J., Hidalgo, J., Tran, K.N., Martini, A.C., Rothermich, W.C., Pascual, J., Head, E., Hume, D.A., Pridans, C., Davtyan, H., Swarup, V. and Blurton-Jones, M.  Absence of microglia promotes diverse pathologies and early lethality in Alzheimer’s disease mice.  (2022)  Cell Reports 39: 110961
DeRogatis JM, Viramontes KM, Neubert EN, Henriquez ML, Guerrero-Juarez CF, Tinoco R. Targeting the PSGL-1 Immune Checkpoint Promotes Immunity to PD-1-Resistant Melanoma. (2022) Cancer immunology research 10(5):612-625. PMC9064985
Oliver, A., El Alaoui, K., Haunschild, C., Avelar-Barragan, J., Mendez Luwque, L.F., Whiteson, K. and Fleischman, A.G.  Fecal microbial community composition in myeloproliferative neoplasm patients is associated with an inflammatory state.  (2022)  Microbiology Spectrum epub April 22
Jahid, S., Ortega J.A., Vuong, L.M., Acquistapace, S.M., Hachey, S.J., Flesher, J.L., La Serra, M.A., Brindani, N., La Sala, G., Manigrasso, J., Arencibia, J.M., Bertozzi, S.M., Summa, M., Bertorelli, R., Armirotti, A., Jin, R., Liu, Z., Chen, C-F., Edwards, R., Hughes, C.W., De Vivo, M. and Ganesan, A.K.  Structure-based design of CDC42 effector interaction inhibitors for the treatment of cancer. (2022) Cell Reports 39:110641
Jansen, C., Paraiso, K.D., Zhou, J.J., Blitz, I.L., Fish, J.B., Charney, R.M., Cho J.S., Yasuoka, Y., Sudou, N., Bright, A.R., Wlizia, M., Veenstra, G.J.C., Taira, M., Zorn, A.M., Mortazavi, A. and Cho, K.W.Y.  Uncovering the mesendoderm gene regulatory network through multi-omic data integration.  (2022) Cell Reports  38(7): 110364
Macdonald, S.J., Cloud-Richardson, K.M. Sims-West, D.J. and Long, A.D.  Powerful, efficeint QTL mapping oin Drosophila melanogaster using bulked phenotyping and pooled sequencing.  (2022)  Genetics 200(3), iyab238
DeRogatis, J.M., Viramontes, K.M, Neubert, E.N., Henriquez, M.L., Guerrero-Juarez, C.F. and Tinoco, R.  Targeting the PSGL-1 immune checkpoint promotes immunity to PD-1 resistant melanoma.  (2022)  Cancer Immunology Research epub March 18
Long, P.N., Cook, V.J., Majumder, A., Barbour, A.G. and Long, A.D.  The utility of a closed breeding colong of Peromyscus leucopus for dissecting complex traits.  (2022)  Genetics  epub February 10
Gutierrez, G., Sun, P., Han, Y. and Dai, X.  Defining mammary basal cell transcriptional states using single cell sequencing.  (2022)  Scientific Reports  12:4893
Claes, C., England, W.E., Danhash, E.P., Shabestari, S.K., Jairaman, A., Chadarevian, J.P., Hasselmann, J., Tsai, A.P., Coburn, M.A., Sanchez, J., Lim, T.E., Hidalgo, J-L.S., Tu, C., Cahalan, M.D., Lamb, B.T., Landreth, G.E., Spitale, R.C., Blurton-Jones, M. and Davtyan, H.  The P522R protective variant of PLCG2 promotes the expression of antigen presentation genes by human microglia in an Alzheimer’s disease mouse model.  (2022) Alzheimer’s and Dementia  2022:1-14
Simakov, O., Bredeson, J., Berkoff, K., Marietaz, F., Mitros, T., Schultz, D.T., O’Connell, B.L., Dear, P., Martinez, D.E., Steele, R.E., Green R.E., David C.N. and Rokhsar, D.S.  Deeply conserved synteny and the evolutin of metazoan chromosomes (2022) Science Advances 8:eabi5884
Herrera, M.J., Heras, J. and German, D.P.  Comparative transcriptomics reveal tissue level specialization towards diet in prickleback fishes.  (2022)  Journal of Comparative Physiology B epub January 25
Viramontes KM, Neubert EN, DeRogatis JM, Tinoco R. PD-1 Immune Checkpoint Blockade and PSGL-1 Inhibition Synergize to Reinvigorate Exhausted T Cells. (2022) Frontiers in immunology 13:869768. PMC9237324
Vu, T., Vallmitjana, A., Gu, J., La, K., Xu, Q., Flores, J., Zimak, J., Shiul, J., Hosohama, L, Wu, J., Douglas, C., Waterman, M.L., Ganesan, A., Hedde, P.N., Gratton, E. and Zhao, W.  Spatial transcriptomics using combinatorial fluorescence spectraland lifetime encoding, imaging and analysis.  (2022)  Nature Communications 13: 169
Han, H., Nakaoka, J.J., Hofmann, L, Zhou, J.J., Yu, C., Zeng, L.,  Nan, J., Seo, G., Vargas, R.E., Yang, B., Qi, R., Bardwell, L., Fishman, D.A., Cho, K.W.Y., Huang, L., Luo, R., Warrior, R. and Wang, W.  The Hippo pathways kinases LATS1 and 2 attenuate cellular responses to heavy metals through phosphorylating MTF1.  (2022)  Nature Cell Biology 24(1): 74-87
Lombardo, J.A., Aliaghaei, M., Nguyen, Q.H., Kessenbrock, K. and Haun, J.B.  Microfluidic platform accelerates tissue processing into single cells for molecular analysis and primary culture models.  (2021)  Nature Communications 12:2858
Ma, D., Hernandez, G.A.,  Lefebvre, A.E.Y.T., Alshetaiwi, H., Blake, K., Dave, K.R., Rauf, M., Williams, J.W., Davis, R.T., Evans, K.T., Longworth, A., Masoud, M.Y.G., Lee, R., Edwards, R.A., Digman, M.A., Kessenbrock, K. and Lawson, D.A.  Patient-derived xenograft culture-transplant system for investigation of human breast cancer metastasis.  (2021)  Communications Biology 4:1268
Lewis, S.A., Doratt, B., Sureshchandra, S., Pan, T., Gonzales, S.W., Shen, W., Grant, K.A., and Messauodi, I.  Profiling of extracellular vesicle-bound miRNA to identify candidate biomarkers of chronic alcohol drinking in non-human primates.  (2021)  Alcoholism Clinical & Experimental Research  epub December 15
Hernandez-Davies, J., Dollinger, E., Pone, E., Felgner, J., Strohmeier, S., Jan, S., Albin, T., Jain, A., Nakajima, R., Jasinaskas, A., Krammer, F., Esser-Kahn, A., Felgner, P., Nie, Q., Davies, H.  Magnitude and breadth of antibody cross-reactivity induced by recombinant influenza hemagglutinin trimer vaccine is enhanced by combination adjuvants.  (2021)  Research Square  epub December 13
Dahlstrom, K.M. and Newman, D.K.  Soil bacteria protect fungi from phenazines by acting as toxin sponges.  (2021)  Current Biology 32:1-14
The NeuroLINCS Consortium, Li, J., Lim, R.G., Kaye, J.A., Dardov, V., Coyne, A.N., Wu, J., Milani, P., Cheng, A., Thompson, T.G., Ornelas, L, Frank, A., Adam, M., Banuelos, M.G., Casale, M., Cox, V., Escalante-Chong, R., Daigle, J.G., Gomez, E., Hayes, L., Holewenski, R., Lei, S., Lenail, A., Lima, L., Mandefro, B., Matlock, A., Panther, L., Patel-Murray, N.L., Pham, J., Ramamoorthy, D., Sacha, K., Shelley, B., Stocksdale, J., Trost, H., Wilheim, M., Venkatraman, V., Wassie, B.T., Wyman, S., Yang, S., NYGC ALS Consortium, Van Eyk, J.E., Lloyd T.E., Finkeiner, S., Fraenkel, E., Rothstein, J.D., Sareen, D., Svendsen, C.N., and Thompson, L.M.  An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients.  (2021)  iScience 103221
Greco, C.M., Koronowski, K.B., Smith, J.G., Shi, J., Kunderfranco, P., Carreiro, R., Chen, S., Samad, M., Welz, P-S., Zinna, V.M, Mortimer, T., Chun, S.K., Shimaji, K., Sato, T., Petrus, P., Kumar, A., Vaca-Dempere, M., Deryagian, O., Van, C., Kuhn, J.M.M, Lutter, D., Seldin, M.M., Masri, S., Li, W., Baldi, P., Dyer, K.A., Munoz-Canoves, P., Benitah, S.A. and Sassone-Corsi, P.  Integration of feeding behavior by the liver circadian clock reveals network dependency of metabolic rhythms.  (2021)  Science Advances 7:eabi7828
Wang, Y., Liu, X., Shehabet, M., Chim, N. and Chaput, J.C.  Transliteration of synthetic genetic enzymes.  (2021)  Nucleic Acids Research epub October 11
Borrego, S.L., Fahrmann, J., Hou, J., Lin, D-W., Tromberg, B.J. Fiehn, O. and Kasier, P.  Lipid remodeling in response to methionine stress in MDA-MBA-468 triple-negative breast cancer cells.  (2021)  Journal of Lipid Research 62:100056
Kashgari, G., Venkatesh, S., Refuerzo, S., Pham, B., Bayat, A., Herndon Klein, R., Ramos, R., Ta, A.P., Plikus, M.V., Wang, P.H. and Andersen, B.  GRHL3 activates FSCN1 to relax cell-cell adhesions between migrating keratinocytes during wound reepithelialization.  (2021)  Journal of Clinical Investigation Insight  epub September 8
Jayaswal, V., Ndo, C., Ma, H-C., Clifton, B.D., Pombi, M., Cabrera, A.C., Mouline, K., Diabate, A., Dabire, R., Ayala, D. and Ranz, J.M.  Intraspecific transcriptome variation and sex-biased expression in Anopheles arabiensis.  (2021)  Genome Biology & Evolution 13(9)
Oh, S., Bournique, E., Bowen, D., Jalili, P., Sanchez, A., Ward, I., Dannanberg, A., Munjunath, L., Tran, G.P., Semler, B.L., Maciejowski, J., Seldin, M. and Buisson, Remi.  Genotoxic stress and viral infection induce transient expression of APOBEC3A and pro-inflammatory genes through two distinct pathways.  (2021) Nature Communications epub August 13
Sun, P., Vu, R., Dragan, M., Haensel, D., Gutierrez, G., Nguyen, Q., Greenberg, E., Chen, Z., Wu, J., Atwood, S., Pearlman, E., Shi, Y., Han, W., Kessenbrock, K., and Dai, X.  OVOL1 regulates psoriasis-like skin inflammation and epidermal hyperplasia.  (2021)  Journal of Investigative Dermatology  141(6): 1542-1552
Claes, C., Danhash, E.P., Hasselmann, J., Chaderevian, J.P., Shabestari, S.K., England, W.E., Lim, T.E., Hidalgo, J.L.S., Spitale, R.C., Davtyan, H. and Blurton-Jones, M.  Plaque-associated human microglia accumulate lipid droplets in a chimeric model of Alzheimer’s disease.  (2021)  Molecular Neurodegeneration 16:50
Westerman TL, McClelland M, Elfenbein JR. YeiE Regulates Motility and Gut Colonization in Salmonella enterica Serotype Typhimurium.(2021)  mBio.  12(3):e0368020
Rahmatpanah, R., De Robles, G., Lilly, M., Keane, T., Kuman, V., Mercola, D., Randhawa, P. and McClelland, M.  RNA expression differences in prostate tumors and tumor-adjacent stroma between Black and White Americans.  (2021)  Oncotarget epub June 22
Rebboah, E., Reese, F., Williams, K., Baldarama-Guiterrez, G., McGill, C., Trout, D., Rodriquez, I., Liang, H., Wold, B. and Mortazavi, A. Mapping and modeling the genomic basis of differential RNA isoform expression at single cell resolution using LR-Split-Seq (2021) Genome Biology 22:286
Brami-Cherrier, K., Lewis, R.G., Cervantes, M., Liu, Y., Tognini, P., Baldi, P., Sassone-Corsi, P. and Borrelli, E.  Cocaine-mediated circadian reprogramming in the striatum through dopamine D2R and PPARy activation.  (2020)  Nature Communication 11:4448
Nguyen BD, Cuenca V M, Hartl J, Gül E, Bauer R, Meile S, Rüthi J, Margot C, Heeb L, Besser F, Escriva PP, Fetz C, Furter M, Laganenka L, Keller P, Fuchs L, Christen M, Porwollik S, McClelland M, Vorholt JA, Sauer U, Sunagawa S, Christen B, Hardt WD. Import of Aspartate and Malate by DcuABC Drives H2/Fumarate Respiration to Promote Initial Salmonella Gut-Lumen Colonization in Mice. (2020)  Cell Host Microbe.  Jun 10;27(6):922-936.e6
Sureshchandra, S., Mendoza, N., Jankeel, A., Wilson, R.M., Marshall, N.E. and Messaoudi, I.  Phenotypic and epigenetic adaptations of cord blood CD4+ T cells to maternal obesity.  (2021) Frontiers in Immunology 12:617592
Edson JA, Chu W, Porwollik S, Tran K, Iribe N, McClelland M, Kwon YJ. Eradication of Intracellular Salmonella Typhimurium by Polyplexes of Acid-Transforming Chitosan and Fragment DNA. Macromol Biosci. (2021) Apr 18;:e2000408
Esteves NC, Porwollik S, McClelland M, Scharf BE. The multi-drug efflux system AcrABZ-TolC is essential for infection of Salmonella (2021) Typhimurium by the flagellum-dependent bacteriophage Chi. J Virol.  epub Mar 17
Hachey, S.J., Movsesyan, S., Nguyen, Q.H., Blurton-Sojo, G., Tankazyan, A., Hoang,T., Zhao,D., Wang, S., Hatch, M.M., Celaya, E., Gomez, S., Chen, G.T., Davis, R.T., Nee, K., Prvolarakis, N., Lawson,D.A., Kessenbrock, K., Lee, A.P., Lowengrub, J., Waterman, M.L. and Hughes, C.W.  An in vitro vascularized micro-tumor model of human colorectal cancer recapitulates in vivo responses to standard-of-care therapy.  (2021)  Lab on a Chip epub Feb 19
Alldredge J, Randall L, De Robles G, Agrawal A, Mercola D, Liu M, Randhawa P, Edwards R, McClelland M, Rahmatpanah F.  (2020) Transcriptome Analysis of Ovarian and Uterine Clear Cell Malignancies. Front Oncol.  10:598579
Ruiz-Vega, R., Chen, C.-F., Razzak, E., Vasudeva, P., Krasieve, T.B., Shiu, J., Caldwell, M.G., Yan, H., Lowengrub, J., Ganesan, A.K., and Lander A.D.  Dynamics of nevus development implicate cell cooperation in the growth arrest of transformed melanocytes.  (2020) eLife 9:e61026
Wang, S., Drummond, M.L., Guerrero-Juarez, C.F., Tarapore, E., MacLean, A.L., Stabell, A.R., Wu, S.C., Gutierrez, G., That, B.T., Benavente, C.A., Nie, Q. and Atwood, S.X.  Single cell transcriptomics of human epidermis identifies basal stem cell transition states.  (2020)  Nature Communications 11:4239
Song, Y., Guerrero-Juarez, C.F., Chen, Z., Tang, Yl., Ma, X., Lu, C., Bi, X., Deng,M., Bu, L., Tian, Y., Liu, R., Zhao, R., Xu, J., Sheng, X., Du., S., Liu, Y., Zhu, Y., Shan, S., Chen, H., Zhao, Y., Zhou, G., Shuai, J., Ren, F., Xue, L., Ying, Z., Dai, X., Lengner, C.J., Andersen, B., Plikus, M.V., Nie, Q. and Yu, Z.  The Msi1-mTor pathway drives the pathogenesis of mammary and extramammory Paget’s disease.  (2020) Cell Research 30: 854-872
Li Y, Salazar JK, He Y, Desai P, Porwollik S, Chu W, Paola PS, Tortorello ML, Juarez O, Feng H, McClelland M, Zhang W. Mechanisms of Salmonella Attachment and Survival on In-Shell Black Peppercorns, Almonds, and Hazelnuts  (2020) Front Microbiol. 11:582202.
Greenberg, E.N., Marshall, M.E., Jin, S., Venkatesh, S., Dragan, M., Tsoi, L.C., Gudjonsson, J.E., Nie, Q., Takahashi, J.S. and Andersen, B.  Circadian control of interferon-sensitive gene expression in murine skin.  (2020)  Proceedings of the National Academy of Science 1117I11):5761-5771
Phillips, M.A., Kutch, I.C., Long, A.D. and Burke, M.K.  Increased time sampling in an evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change. (2020)  Molecular Ecology 2020:001:1-15
Jayeola V, McClelland M, Porwollik S, Chu W, Farber J, Kathariou S. Identification of Novel Genes Mediating Survival of Salmonella on Low-Moisture Foods via Transposon Sequencing Analysis.  (2020) Front Microbiol. 11:726
Batarsch, T.N., Hug, S.M., Batarsch, S.N. and Gaut, B.S.  Genetic mutations that drive evolutionary resecue to lethal temperature in Escherichia coli.  (2020)  Genome Biology & Evolution epub Aug 12
Habowski, A.N., Flesher,  J.L., Bates, J.M, Tsai, C-F., Martin, K., Zhao, R., Ganesan, A.K., Edwards, R.A., Shi, T., Wiley, H.S., Shi, Yl, Hertel, K.J. and Waterman M.L.  Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt.  (2020) Communications Biology. epub Aug 20
Arias, D.B., Gomez Pinto, K.A., Cooper, K.K. and Summers, M.L.  Transcriptomic analysis of cyanobacterial alkane overproduction reveals stress-related genes and inhibitors of lipid droplet formation.  (2020) Microbial Genomics 6(10): epub Sept 17
Greco, C.M., Garetto, G., Montelllier, E., Yu, L, Chen, S., Baldi, P., Sassone-Corsi, P. and Lucci, J.  A non-pharmacological therapeutic approach in the gut triggers distal metabolic rewiring capable of ameliorating diet-induced dysfunctions encompassed by metabolic syndrome.  (2020)  Scientific Reports 10: 12919
Alshetaiwi, H., Pervolarakis, N., McIntyre, L.L., Ma, D., Nguyen, Q., Rath, J.A., Nee, K., Hernandez, G., Evans, K., Torosian, L., Silva, A., Walsh, C. and Kessenbrock, K.  Defining the emergence of myeloid-derived suppressor cells in breast cancer using single-cell transcriptomics.  (2020)  Science Immunology 21: 5(44)eaay6017
Davis, R.T., Blake, K., Ma, D., Ishak Gabra, M.B., Hernandez, G.A., Phung, A.T., Yang, Y., Maurer, D., Lefebvre, A.E.Y.T., Alshetaiwi, H., Xiao, Z., Liu, J., Locasale, J.W., Digman, M.A., Mjolsness, E., Kong, M., Werb, Z and Lawson, D.A.  Transcriptional diversity and biogenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing.  (2020) Nature Cell Biology 22: 310-320
Jalili, P., Bowen, D., Langenbucher, A., Park, S., Aguirre, K., Corcoran, R.B., Fleischman, A.G., Lawrence, M.S., Zou, L., and Buisson, R.  (2020)  Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots.  (2020) Nature Communications 11: 2971
Zocchi, L. Mehta, A., Wu, S.C., Wu, J., Gu, Y., Wang, J., Suh, S., Spitale, R.C. and Benavente, C.A.  Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression.  (2020)  Oncogenesis 9:25
Nikoomanzar, A., Vallejo, D., Yik, E. and Chaput, J.C.  Programmed allelic mutagenesis of a DNA polymerase with single amino acid resolution.  (2020) ACS Synthetic Biology Jun 12 epub
Haensel, D., Jin, S., Sun, P., Cinco, R., Dragan, M., Nguyen, Q., Cang, Z., Gong, Y., Vu, R., MacLean, A.L., Kessenbrock, K., Gratton, E., Nie, Q. and Dai, X.  Defining epidermal basal cell states during skin homostasis and wound healing using single-cell transcriptomics.  (2020)  Cell Reports 30:  3932-3947
Chakraborty S, Liu L, Fitzsimmons L, Porwollik S, Kim JS, Desai P, McClelland M, Vazquez-Torres A. Glycolytic reprograming in Salmonella counters NOX2-mediated dissipation of ΔpH. (2020) Nature Communications.  11(1):1783
Fitzsimmons LF, Liu L, Kant S, Kim JS, Till JK, Jones-Carson J, Porwollik S, McClelland M, Vazquez-Torres A. SpoT Induces Intracellular Salmonella Virulence Programs in the Phagosome.  (2020) mBio. Feb 25;11(1)
Nainar, S., Cuthbert, B.J., Lim, N.M., England, W.E., Ke, K., Sophal, K., Quechol, R., Mobley, D.L., Goulding, C.W. and Spitale, R.C.  An optimized chemical-genetic method for cell-specific metabolic labeling of RNA.  (2020) Nature Methods Feb 3 epub
Wang, X., Hennig,T., Whisnant, A.W., Erhard, F., Prusty, B.K., Friedel, CC., Forouzmand, E., Hu, W., Erber,L, Chen, Y., Sandri-Goldin, R.M., Dolken, L., and Shi, Y.  Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27.  (2020) Nature Communications 11(1): 293
Crapser, J.D., Ochaba, J., Soni, N., Reidling, J.C. Thompson, L.M. and Green K.N.  Microglial depletion prevents extracellular matrix changes and striatal volume reduction in a model of Huntington’s disease.  (2020) Brain 143(1) : 266-288.
Heras, J., Chakraborty, M., Emerson, J.J. and German D.P.  Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish.  (2020)  Proceeding of Biological Science  Feb 26:287(1921)
Paraiso, K.D., Blitz, I.L., Coley, M., Cheung, J., Sudou, N., Taira, M. and Cho, K.W.Y.  Endodermal maternal transcription factors establish super-enhancers during zygotic genome activation.  (2019) Cell Reports 27(10):  2962-2977.
Gupta SK, Sharma P, McMillan EA, Jackson CR, Hiott LM, Woodley T, Humayoun SB, Barrett JB, Frye JG, McClelland M. Genomic comparison of diverse Salmonella serovars isolated from swine. (2019) PLoS One. 14(11):e0224518.
Khilyas IV, Tursunov KA, Shirshikova TV, Kamaletdinova LK, Matrosova LE, Desai PT, McClelland M, Bogomolnaya LM. Genome Sequence of Pigmented Siderophore-Producing Strain Serratia marcescens SM6. (2019) Microbiol Resour Announc. May 2;8(18)
Barter, T.T., Greenspan, Z.S., Phillips, M.A., Mueller, J.D., Rose, M.R. and Ranz, J.M.  Drosophila transcriptomics with and without ageing.  (2019)  Biogerontology 20:699-710
McMillan EA, Gupta SK, Williams LE, Jové T, Hiott LM, Woodley TA, Barrett JB, Jackson CR, Wasilenko JL, Simmons M, Tillman GE, McClelland M, Frye JG. Antimicrobial Resistance Genes, Cassettes, and Plasmids Present in Salmonella enterica Associated With United States Food Animals. (2019) Front Microbiol. 10:832
Cho, J.S., Blitz, I.L. and Cho, K.W.Y.  DNase-seq to study chromatin accessibility in early Xenopus tropicalis embryos.  (2019)  Cold Spring Harbor Protocols 4:  epub Apr 1
Reinink P, Buter J, Mishra VK, Ishikawa E, Cheng TY, Willemsen PTJ, Porwollik S, Brennan PJ, Heinz E, Mayfield JA, Dougan G, van Els CA, Cerundolo V, Napolitani G, Yamasaki S, Minnaard AJ, McClelland M, Moody DB, Van Rhijn I. Discovery of Salmonella trehalose phospholipids reveals functional convergence with mycobacteria. (2019) J Exp Med. 216(4):757-771
Li, C., Nguyen, V., Clark, K.N., Zahed, T., Sharkes, S., Filipp, F.V. and Boiko, A.D.  Down-regulation of FZD3 receptor suppresses growth and metastasis of human melanoma independently of canonical WNT signaling.  (2019)  Proceedings of the National Academy of Sciences 116(10):  4548-4557.
Reynolds, D.J. and Hertel, K.J.  Ultra-deep sequencing reveals pre-mRNA splicing as a sequence driven high-fidelity process.  (2019) PLOS ONE epub Oct 3
Allen, B.D., Apodaca, L.A., Syage, A.R., Markarian, M., Baddour, A.A.D., Minasyan, H., Alikhani, L, Lu, C., West, B.L., Giedzinski, E., Baulch, J.E. and Acharya, M.M.  Attenuation of neuroinflammation reverses Adriamycin-induced cognitive impairments.  (2019)  Acta Neuropathologica Communications 7: 186
Gaucher, J., Kinouchi, K., Ceglia, N., Montellier, E., Peleg, S., Magdalen Greco, C., Schmidt, A., Forne, I., Masri, S., Baldi, P., Imhof, A. and Sassone-Corsi, P.  Distinct metabolic adaptation of liver circadian pathways to acute and chronic patterns of alcohol intake.  (2019) Proceedings of the National Academy of Sciences 116(5): 25250-25259
Chen, Y-H., Su, C-C., Deng, W., Lock, L.F., Donovan, P.J., Kayala, M.A., Baldi, P., Lee, H-C., Chen, Y. and Wang, P.H.  Mitochondrial Akt signaling modulated reprogramming of somatic cells. (2019) Scientific Reports 9: 9919
Haensel, D., Sun, P., MacLean, A.L., Ma, X., Zhou, Y., Stemmler, M.P., Brabletz, S., Berx, C., Plikus, M.V., Nie, Q., Brabletz, T. and Dai, X.  An Ovol2-Zeb1 transcriptional circuit regulates epithelial directional migration and proliferation.  (2019)  EMBO Reports 20: e46273
Chakraborty, M., Emerson, J.J., Macdonald, S.J. and Long, A.D.  Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits.  (2019) Nature Communications 10(1): 4872
Zhou, Yl, Minio, A., Massonnet, M., Solares, E., Lv, Y., Beridze, T., Cantu, D., and Gaut, B.S.  The population genetics of structural variants in grapevine domestication.  (2019) Nature Plants 5: 965-979
Roessler, K., Muyle, A., Diez, C.M., Gaut, G.R.J., Bousios, A., Stitzer, M.C., Seymour, D.K., Dowbley, J.F., Liu, Q., and Gaut, B.S.  The genome-wide dynamics of purging during selfing in maize.  (2019) Nature Plants 5: 980-990
Seymour, D.K. and Gaut, B.S.  Phylogenetic shifts in gene body methylation correlate with gene expression and reflect trait conservation. (2019) Molecular Biology and Evolution 37(1): 31-43
Long, A.D., Baldwin-Brown, J., Tao, Y., Cook, V.J., Balderrama-Guiterrez, G., Corbett-Detig, R., Mortazavi, A. and Barbour, A.G.  The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections.  (2019) Science Advances 5: eaaw6441
Kedaigle, A.J., Reidling, J.C., Lim, R.G., Adam, M., Wu, J., Wassie, B., Stocksdale, J.T., Casale, M.S., Fraenkel, E., and Thompson, L.T.  Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington’s disease mice.  (2019)  Human Molecular Genetics epub 7 Nov
Hasselmann, J., Coburn, M.A., England, W., Figueroa Velez, D.X., Shabestari, S.K., Tu, C.H., McQuade, A., Kolahourzan, M., Echeverria, K., Claes, C., Nakayama, T., Azevedo, R., Coufal, N.G., Han, C.Z., Cummings, B.J., Davtyan, H., Glass, C.K., Healy, L.M., Gandhi, S.P., Spitale, R.C., and Blurton-Jones, M.  Development of a chimeric model to study and manipulate human microglia in vivo. (2019) Neuron 103: 1-18.
Wong, W.Y., Simakov, O., Bridge, D.M., Cartwright, P., Bellantuono, A.J., Kuhn, A., Holstein, T.W., David, C.N., Steele, R.E. and Martinez, D.E. Expansion of a single transposable element family is associated with genome-size increase and radiation in the genus Hydra. (2019)  Proc. Natl. Acad. Sci. U.S.A. epub 28 Oct
Hinckley WE, Keymanesh K,Cordova JA, Brusslan JA. The HAC1 histone acetyltransferase promotes leaf senescence and regulates the expression of ERF022.  (2019) Plant Direct. 3: 1–10.
Flesher, J. L., Paterson‐Coleman, E. K., Vasudeva, P. , Ruiz‐Vega, R. , Marshall, M. , Pearlman, E. , MacGregor, G. R., Neumann, J. and Ganesan, A. K. Delineating the Role of MITF Isoforms in Pigmentation and Tissue Homeostasis. (2019) Pigment Cell Melanoma Res. epub 28 Sept
Koronowski, K.B., Kinouchi, K., Welz, P-S., Smith, J.G., Zinna, V.M., Shi, J., Samad, M., Chen, S., Magnan, C.N., Kinchen, J.M., Li, W., Baldi, P., Benitah, S.A. and Sassone-Corsi, P.  Defining the independence of the liver circadian clock.  (2019)  Cell 177: 1448-1462
Nikoomanzar, A., Vallejo, D. and Chaput, J.C.  Elucidating the determinants of polymerase specificity by microfluidic-based deep mutational scanning.  (2019)  ACS Synthetic Biology epub May 3
Li, X., Zhao, Q., Wei, W., Lin, Q., Magnan, C., Emami, M.R., Wearick-Silva, L.E., Viola, T.W., Marshall, P.R., Yin, J., Madugalle,  S.U., Wang, Z., Nainar, S., Borberg Vagbo, C., Leighton, J.J., Zajaczkowshi, E.L, Ke, K., Grassi-Oliviera, R., Bjoras, M., Baldi, P.F., Spitale, R.C. and Bredy, T.W.  The DNA modification N6-methyl-2′-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction.  (2019) Nature Neuroscience 22: 534-544
Barr, T., Lewis, S.A., Sureshchandra, S., Doratt, B., Grant, K.A. and Messaoudi, I.  Chronic ethanol consumption alters lamina propria leukocyte response to stimulation in a region-dependent manner.  (2019)  FASEB epub 21 Mar
Hjelm, B.E., Rollins, B., Morgan, L., Sequeira, A., Mamdani, F., Pereira, F., Damas, J., Webb, M.G., Weber, M.D., Schatzberg, A.F., Barchas, J.D., Lee, F.S., Akil, H., Watson, S.J., Myers, R.M., Chao, E.C., Kimonis, V., Thompson, P.M., Bunney, W.E. and Vawter, M.P.  Splice-break:  exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA delection breakpoints and analyses of psychiatric disorders.  (2019)  Nucleic Acids Research epub 14 Mar
Kedaigle, A.J., Fraenkel, E., Atwal, R.S., Wu, M., Gusella, J.F., MacDonald, M.E., Kaye, J.A., Finkbeiner, S., Mattis, V.B., Tom, C.M., Svendsen, C., King, A.R., Chen, Y., Stocksdale, J.T., Lim, R.G., Casale, M., Wang, P.H., Thompson, L.M., Akimov, S.S., Ratovitski, T., Arbez, N. and Ross, C.A.  Bioenergetic deficits in Huntington’s disease iPSC-derived neural cells and rescue with glycolytic metabolites. (2019) Human Molecular Genetics epub 15 Feb
Harari, N., Sakheneny, L., Khalifa-Malka, L., Busch, a., Hertel, K.J., Hebrok, M. and Landsman, L.  Pancreatic pericytes orginate from the embryonic pancreatic mesenchyme.  (2019)  Developmental Biology epub 13 Feb
Guerrero-Juarez, C.F., Dehia, P.H., Jin, S., Ruiz-Vega, R., Ma, D., Liu, Yl, Yamaga, K., Shestova, O., Gay, D.L., Yang, Z., Kessenbrock, K., Nie, Q., Pear, W.S., Cotsarelis, G. and Plikus, M.V.  Single-cell analysis reveals fibroblast heterogeneity and myeloid-derived adipocyte progenitors in murine skin wounds.  (2019)  Nature Communications 10(1): 650-667.
Ellis MJ, Tsai CN, Johnson JW, French S, Elhenawy W, Porwollik S, Andrews-Polymenis H, McClelland M, Magolan J, Coombes BK, Brown ED. A macrophage-based screen identifies antibacterial compounds selective for intracellular Salmonella Typhimurium. (2019) Nature Communications. 10(1):197
Sharma, P.P., MacLean, A.L., Meinecke, L., Clouthier, D.E., Nie, Q. and Schilling, T.F.  Transcriptomics reveals complex kinetics of dorsal-ventral patterning gene expression in the mandibular arch (2018) Genesis epub 18 December
Kim, S.W., Brown, D.J. and Jester, J.V.  Transcriptome analysis after PPARg activation in human meibomian gland epithelial cells (hMGEC).  (2019) The Ocular Surface epub 8 Feb
Kinouchi, K., Magnan, C., Ceglia, N., Liu,  Yl, Cervantes, M., Pastore, N., Huyng, T., Ballabio, A., Baldi, P., Masri, S. and Sassone-Corsi, P.  Fasting imparts a switch to alternative daily pathways in liver and muscle.  (2018)  Cell Reports 25: 3299-3314
Yale, A.R., Nourse, J.L., Lee, K.R., Ahmed, S.N., Arulmoli, J., Jiang, A.Y.L., McDonnell, L.P., Botten, G.A., Lee, A.P., Monuki, E.S., Demetriou, M. and Flanagan, L.A.  Cell surface N-glycans influence electrophysiological properties and fate potential of neural stem cells. (2018)  Stem Cell Reports 11: 869-882
Zecena, H., Tveit, D., Wang, Z., Farhat, A., Panchal, P., Liu, J., Singh, S.J., Sanghera, A., Bainwal,A., Teo, S.Y., Meyskens, F.L. Jr., Liu-Smith, F. and Filipp, F.V.  Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma.  (2018) BMC Systems Biology 12: 33
Mahmoud, R., Singh, P., Weiss, L, Lakatos, A., Oakes, M., Hossain, W., Butler, M.G. and Kimonis, V.  Newborn screening for Prader-Willi syndrome is feasible:  Early diagnosis for better outcomes.  (2018)  American Journal of Medical Genetics  epub 17 December
Wang, Y., Ngor, A.K., Nikoomanzar, A. and Chaput J.C.  Evolution of a general RNA-cleaving FANA enzyme.  (2018) Nov 9(1): 5067-5077
Fitzsimmons L, Liu L, Porwollik S, Chakraborty S, Desai P, Tapscott T, Henard C, McClelland M, Vazquez-Torres A. Zinc-dependent substrate-level phosphorylation powers Salmonella growth under nitrosative stress of the innate host response. (2018) PLoS Pathogy 14(10):e1007388.
Duong, V.T., Unhelkar, M.H., Kelly, J.E., Kim, S.H., Butts, C.T. and Martin, R.W.  Protein Structure networks provide insight into the active site flexibility in esterase/lipases from the carnivorous plant Drosera capensis.  (2018)  Integrative Biology epub 5 December
McQuade, A., Coburn, M., Tu, C.H., Hasselmann, J., Davtyan, H. and Blurton-Jones, M.  Development and validation of a simplified method to generate human microglia from pluripotent stem cells. (2018)  Molecular Neurodegeneration 13(1): 67-80
Meinecke, L., Sharma, P.P., Du, H., Zhang, L., Nie, Q. and Schilling T.  Modeling craniofacial development reveals spatiotemporal constraints on robust patterning of the mandibular arch.  (2018)  PLOS Computational Biology  epub 27 November
Zhang, X., Baars, O. and Morel, F.M.M.  Genetic, structural, and functional diversity of low and high-affinity siderophores in strains of nitrogen fixing Azotobacter chroococcum.  (2018)  The Royal Society of Chemistry epub 16 November
Solares, E.A., Chakraborty, M., Miller, D.E., Kalsow, S., Hall, K., Perera, A.G., Emerson, J.J. and Hawley, R.S.  Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long read sequencing.  (2018)  Oct 3:  8(10):  3143-3154
Rahmatpanah, F., Agrawal, S., Jaiswal, N., Ngyuen, H.M., McClelland, M and Agrawal, A.  Airway epithelial cells prime plasmacytoid dendritic cells to respond to pathogens via secretion of growth factors.  (2018) Mucosal Immunology epub 02 October
Elmore, M.R.P., Hohsfield, L.A., Kramar, E.A., Soreq, L., Lee, R.J., Pham, S.T., Najafi, A.R., Spangenberg, E.E., Wood, M.A., West, B.L. and Green, K.N.  Replacement of microglia in the aged brain reverses cognitive, synaptic, and neuronal deficits in mice.  (2018) Aging Cell epub 02 October
Kwapis, J.L., Alaghband, Yl, Kramar, E.A., Lopex, A.J., Ciernia, A.V., White, A.O., Shu, G., Rhee, D., Michael, C.M., Montellier, E., Liu, Y., Magnan, C.N., Chen, S., Sassone-Corsi, P., Baldi, P., Matheos, D.P. and Wood, M.A.  Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory.  (2018)  Nature Communications 9(1): 3323-3337
Zhong, D., Lo, E., Want, X., Yewhalaw, D., Zhou, G., Ateli, H.E., Githeko, A., Hemming-Schroeder, E., Lee, M.-C., Afrane, Y. and Yan, G.  Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa.  (2018) Malaria Journal 17: 185
Zecena, H., Tveit, D., Wang, Z., Farhat, A., Panchal, P., Liu, J., Sing, S.J., Sangher, A., Bainiwal, A., Teo, S.Y., Meyskens, F.L., Liu-Smith, F. and Filipp, F.V.  Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma.  (2018) BMC Systems Biology 12: 33
Dhar, S.S., Zhao, D., Lin, T., Gu, B., Pai, K., Wu, S.J., Alam, H., Lv, J., Yun, K., Gopalakrishnan, V., Flores, E.R., Northcott, P.A., Rajaram, V., Li, W., Shilatifard, A., Sillitoe, R.V., Chen, K and Lee, M.G.  MLL4 is required to maintain broad H3K4me3 peaks and super-enhancers at tumor suppressor genes.  (2018) Molecular Cell 70: 1-17
Nguyen, Q.H., Pervolarakis, N., Blake, K., Ma, D., Davis, R.T., James, N., Phung, A.T., Wiley, E., Kumar, R., Jabart, E., Driver, I., Rock, J., Goga, A., Khan, S.A., Lawson, D.A., Werb, Z. and Kessenbrock, K.  Profiling human breast epithelial cells using single cell RNA sequencing identifies cell diversity.  (2018) Nature Communications 9(1): 2028
Martinez-Steele, L., Lowe, C.G., Okihiro, M.S. and Berlemont, R.  Draft genome sequences of nine new Carnobacterium maltaromaticum strains isolated from diseased sharks.  (2018)  Genome Announcements, 6(18): e00354-18
Zocchi, L., Wu, S.C., Wu, J., Hayama, K.L. and Benavente, C.A.  The cyclin-dependent kinase inhibitor flavopiridol (alvocidib) inhibits metastasis of human osteosarcoma cells.  Oncotarget 9(34): 23505-23518
Najafi, A.R., Crapser, J., Jiang, S., Ng, W., Mortazavi, A., West, B.L. and Green, K.N.  A limited capacity for microglial repopulation in the adult brain.  (2018)  GLIA 66: 2385-2396
Rahmatpanah, R., Agrawal, S.,  Scarfone, V., Kapadia, S., Mercola, D. and Agrawal, A.  Transcriptional profiling of age-associated gene expression changes in human circulatory CD1c myeloid dendritic cell subset.  (2018) Journal of Gerontology A Biol Sci Med Sci epub Apr 28
Porwollik, S., Genovese, K., Chu, W., Loneragea, G.H., Edrington, T. and McClelland, M.  Neutral barcoding of genomes reveals the dynamics of Salmonella colonization in cattle and their peripheral lymph nodes. (2018)  Veterinary Medicine epub May 15
Yamamoto, C.M., Oakes, M.L., Murakami, T., Muto, M.G., Berkowitz, R.S. and Ng, S-W.  Comparison of benign peritoneal fluid- and ovarian cancer ascites-derived extracelluar vesicle RNA biomarkers.  (2018) Journal of Ovarian Research 11:20-29
Sierra, R.A., Hoverter, N.P., Ramirez, R.N., Vuong, L.M., Mortazavi, A., Merrill, B.J., Waterman, M.L. and Donovan, P.J.  TCF7L1 suppresses primitive streak gene expression to support human embryonic stem cell pluripotency.  (2018) Development January 18 Epub
Zhu, Y., Wang, X., Forouzmand, E., Jeong, J., Qiao, F., Sowd, G.A., Engelman, A.N., Xie, X., Hertel, K.J. and Shi, Y.  Molecular mechanisms for CFlm-mediated regulation of mRNA alternative polyadenylation.  (2018) Molecular Cell 69: 62-74
Chakraborty, M., VanKuren, N.W., Zhao, R., Zhang, X., Kalsow, S. and Emerson, J.J.  Hidden genetic variation shapes the structure of functional elements in Drosophila.  (2018) Nature Genetics 50: 20-25
Baldwin-Brown, J.G., Weeks, S.C. and Long, A.D.  A new standard for crustacean genomes:  the highly contiguous, annotated genome assembly of the clam shrimp Eulimnadia texana reveals HOX gene order and identifies the sex chromosome.  (2018) Genome Biology & Evolution 10(1): 143-156
Hu, D., Wang, Y., Haensel, D., Lee, B., Dai, X. and Nie Q.  Multiscale modeling of layer formation in epidermis.  (2018)  PLOS Computational Biology Feb 26 epub
Nguyen, H.X., Hooshmand, M.J., Saiwai, H., Maddox, J., Salehi, A., Lakatos, A., Nishi, R.A., Salazar, D., Uchida, N. and Anderson, A.J.  Systemic neutrophil depletion modulates the migration and fate of transplanted human neural stem cells to rescue functional repair. (2017) The Journal of Neuroscience 37(38): 926909287
Hernandez, M.X., Jiang, S., Cole, T.A., Chu, S-H., Fonseca, M.I., Fang, M.J., Hohsfield, L.A., Torres, M.D., Green, K.N., Wetsel, R.A., Mortazavi, A., and Tenner, A.J.  Prevention of C5aR1 signaling delays microglial inflammatory polarization, favors clearance pathways and suppresses cognitive loss (2017) Molecular Neurodegeneration 12: 66-85
Chakraborty, M., VanKuren, N.W., Zhao, R, Zhang, X., Kalsow, S., Emerson, J.J. Hidden genetic variation shapes the structure of functional elements in Drosophila.  (2017) Nature Genetics December 18 Epub
Elbir, H., Sitlani, P., Bergstrom, S. and Barbour, A.G.  Chromosome and megaplasmid sequences of Borrelia anserina (Sakharoff 1891), the agent of avian spirochetosis and type species of the genus. (2017) Genome Announcement 5(11): e00018-17
Moser, B.A., Steinhardt, R.C. and Esser-Kahn, A.P.  Surface coating of nanoparticles reduces background inflammatory activity while increasing particle uptake and delivery.  (2017) ACS Biomaterial Science Engineering 3(2);  206-213
Zhou, Y., Massonnet, M., Sanjak, J.S., Cantu, D. and Gaut, B.S.  Evolutionary genomics of grape (Vitus vinifera ssp. vinifera) domestication. (2017)  Proceedings of the National Academy of Sciences 114(44):  11715-11720
Herndon Klein, R., Hu, W., Kashgari, G., Lin, Z., Nguyen, T., Doan, M. and Andersen, B.  Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation.  (2017)  Journal of Biological Chemistry 292(46):  18937-18950
Gonzalez-Gonzalez, A., Hug, S.M., Rodriguez-Verdugo, A., Patel, J.S. and Gaut, B.S.  Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects on Escherichia coli gene expression.  (2017)  Molecular Biological Evolution 34(11):  2839-2855
Macias-Munoz, A., McCulloch, K.J. and Briscoe, A.D. Copy number variation and expression analysis reveals a non-orthologous pinta gene family member involved in butterfly vision. (2017) Genome Biology and Evolution November 9 Epub
Tognini, P., Murakami, M., Liu, Y., Eckel-Mahan, K.L., Newman, J.C., Verdin, E., Baldi, P. and Sassone-Corsi, P.  Distinct circadian signatures in liver and gut clocks revealed by ketogenic diet. (2017) Cell Metabolism 26: 523-538
Orozco-Solis, R., Montellier, E., Aguilar-Arnal, L., Sato, S., Vawter, M.P., Bunney, B.G., Bunney, W.E. and Sassone-Corsi, P.  A circadian genomic signature common to ketamine and sleep deprivation in the anterior cingulate cortex.  (2017) Biological Psychiatry 82:351-360
Wang, H., van Spyk, E., Liu, Q., Geyfman, M., Salmans, M.L., Kuman, V., Ihler, A., Li, N., Takahashi, J.S. and Andersen, B.  Time-restricted feeding shifts the skin circadian clock and alters UVB-induced DNA damage.  (2017) Cell Reports 20: 1061-1072
Ruiz, R., Jahid, S., Harris, M., Marzese, D.M., Espitia, F., Vasudeva, P., Chen, C-F., de Feraudy, S., Wu, J., Gillen, D.L., Krasieva, T.B., Tromberg, B.J., Pavan, W.J., Hoon, D.S. and Ganesan, A.K. The RhoJ-BAD signaling network:  An Achilles’ heel for BRAF mutant melanomas.  (2017) PLOS Genetics July 28 Epub
Abdelsayed, M.M., Ho, B.T., Vu, M.K.M., Polanco, J., Spitale, R.C. and Luptak, A.  Multiplex aptamer discovery through Apta-Seq and its application to ATP aptamers derived from Human-Genomic SELEX.  (2017) ACS June 19 Epub
 Rogers, R.L., Shao, L. and Thornton, K.R. Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba.  (2017) PLOS Genetics May 22 Epub
Herndon Klein, R., Lin, Z., Hopkin, A. S., Gordon, W., Tsoi, L.C., Liang, Y., Gudjonsson, J.E. and Andersen, B.  (2017)  GRHL3 binding and enhancers rearrange as epidermal keratinocytes transistion between functional states.  (2017) PLOS Genetics April 26 Epub
Chen, C-F., Ruiz-Vega, R., Vasudeva, P., Espitia, F., Krasiava, T.B., de Ferauly. S., Tromberg, B.J., Huang, S., Garner, C.P., Wu, J., Hoon, D.S. and Ganesan, A.K. ATR mutations promote the growth of melanoma tumors by modulating the immune microenvironment.  (2017)  Cell Reports 18: 2331-2342
Charney, R.M., Forouzmand, E., Cho, J.S., Cheung, J., Paraiso, K.D., Yasuoka, Y., Shuji, T., Taira, M., Blitz, I.L., Xie, X. and Cho, K.W.Y.  Foxh1 occupies cis-regulatory modules prior to dynamic transcription factor interactions controlling the mesendoderm gene program.  (2017)  Developmental Cell 40: 595-607
Hwang, H.S., Parfitt, G.J., Brown, D.J. and Jester, J.V.  Meibocyte differentiation and renewal:  Insights into novel mechanisms of meibomian gland dysfunction (MGD).  (2017)  Experimental Eye Research 163: 37-45
Lim, R., Salazar, L.I, Stocksdale, J.T., Lau, AlI., Reidling, J.C., Winokur, S.T., Casale, M.S., Thompson, L.M. and HD IPSC Consortium. Developmental alterations in Huntington’s disease neural cells and pharmacological rescue in cells and mice.  (2017)  Nature Neuroscience 20(5): 648-660
de Moraes, M.H., Desai, P., Porwolilk, S., Canals, R., Perez, D.R., Chu, W., McClelland, M. and Teplitski, M.  Salmonella persistence in tomatoes requires a distinct set of metabolic functions identified by transposon insertion sequencing.  (2017) Applied and Environmental Microbiology 83(5): e03028-16
 Singh-Taylor, A., Molet, J., Jiang, S., Korosi, A., Bolton, J.L., Noam, Y., Simeone, K., Cope, J., Chen, Y., Mortazavi, A. and Baram, T.Z.  NRSF-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilience.  (2017) Molecular Psychiatry Jan 11 Epub
Unhelkar, M.H., Duong, V.T., Enendu, K.N., Kelly J.E., Tahir, S., Butts, C.T. and Martin, R.W.  Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis (2017) Biochem Biophysis Acta 1861(3): 636-643
Clifton, B.D., Librado, P., Yeh, S-D., Solares, E.S., Real, D.A., Jayasekera, S.U., Zhang, W., Shi, M, Park, R.D., Magie, R.D., Ma, H-C., Xia, X-Q., Marco, A., Rozas, J. and Ranz, J.M. Rapid functional and sequence differentiation  of a tandemly repeated species-specific multigene family in Drosophila. (2016) Molecular Biology & Evolution 34(1): 51-65
Taylor, P.H., Cinquin, A. and Cinquin, O.  Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq. (2016) Genome Research 26: 1600-1611
Movassi, M., Orabb, T.L., Busch, A., Yao, O., Reynolds, D.J. and Shi, Y.  Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns.  (2016)  RNA BIOLOGY 13(7): 645-655
Butts, C., Bierma, J.C. and Martin, R.W.  Novel proteases from the genome of the carnivorous plant Drosera capensis:  structure prediction and comparative analysis. (2016)  Proteins. 84: 1517-1533.
Magnan, C., Yu, J., Chang, I., Jahn, E., Kanomata, Y., Wu, J., Zeller, M., Oakes, M., Baldi, P. and Sandmeyer, S.  Sequence assembly of Yarrowia lipolytica strain W29/CLIB89 shows transposable element diversity. (2016) PLOS one Sept 7, 2016
Zeng, W., Jian, S., Kong, X., El-Ali, N., Ball, A.R.Jr., Ma, C.I-H., Hashimoto, N., Yokomori, K. and Mortazavi, A.  Single nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity. (2016) Nucleic Acids Research 44(21): e158-173
Chakraborty, M., Baldwin-Brown, J.G., Long, A.D. and Emerson, J.J.  Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage.  (2016)  Nucleic Acids Research Jul 25 Epub
Butts, C.T., Zhang, X., Kelly, J.E., Roskamp, K.W., Unhelkar, M.H., Freites, J.A., Tahir, S. and Martin, R.  Sequence comparison, molecular modeling, and network analysis predict structural diversity in cysteine proteases from the Cape sundew, Drosera capensis. (2016) Computational and Structural Biotechnology Journal 14: 271-282.
Mkhikian, H., Mortales, C-L., Zhou, R.W., Khachikyan, K., Wu, G., Haslam, S.M., Kavarian, P., Dell, A. and Demetriou, M.  Golgi self-correction generates bioequivalent glycans to preserve cellular homeostasis.  (2016)  eLife 5: 14814
Herndon Klein, R., Stephens, D.N., Ho, H., Chen, J.K., Salmans, M.L., Wang, W., Yu, Z. and Andersen, B.  Cofactors of LIM domains associate with estrogen receptor alpha to regulate the expression of noncoding RNA H19 and corneal epithelial progenitor cell function. (2016) Journal of Biological Chemistry Apr 29 Epub
Masri, S., Papagiannakopoulos, T., Kinochi, K., Liu, Y., Cervantes, M., Baldi, P., Jacks, T. and Sassone-Corsi, P. Lung adenocarcinoma distally rewires hepatic circadian homeostasis. (2016) Cell 165: 896-909
Marsh, S.E., Abud, E.M., Lakatos, A., Karimzadeh, A., Yeung, S.T., Davtyan, H., Fote, G.M., Lau, L., Weinger, J.G., Lane, T.E., Inlay, M.A., Poon, W.W. and Blurton-Jones, M. The adaptive immune system restrains Alzheimer’s disease pathogenesis by modulating microglial function. (2016) Proc Natl Academy of Science Feb 16 Epub
Spangenberg, E.E., Lee, R.J., Najafi, A.R., Rice, R.A., Elmore, M.R.P., Blurton-Jones, M., West, B.L. and Green, K.N. Eliminating microglia in Alzheimer’s mice prevents neuronal loss without modulating amyloid-B pathology. (2016) Brain Feb 26 Epub
Schneider, K., Valdez, J., Nguyen, J., Vawter, M., Galke, B., Kurtz, T.W. and Chan, J.Y. Increased energy expenditure, UCP1 expression and resistance to diet-induced obesity in mice lacking nuclear factor-erythroid-2 related transcription factor-2 (Nrf2). (2016) Journal of Biological Chemistry  Feb 3 Epub
Elhadad, D., Desai, P., Grassl, G.A., McClelland, M., Rahav and Gal-Mor, O. Differences in host cell invassion and SPI-1 expression between Salmonella enterica serovar Paratyphi A and the non-Typhoidal serovar Typhimurium. (2016) Infection and Immunity Feb 8 Epub
Barbour, A.G., Multiple and diverse vsp and vlp sequences in Boreelia miaymotoi, a hard tick-borne zoontoic pathogen. PLos One (2016) 11(1):  e0146283
Paterson, E.K., Fielder, T.J., MacGregor, G.R., Ito, S., Wakamatsu, K., Gillen, D.L., Eby, V., Boissy, R.E. and Ganesan, A.K.  Tyrosinase depletion prevents the maturation of melansomes in the mouse hair follicle.  PLos One (2016) 10(11):  e0143702
Tom, J.K., Dotsey, E.Y., Wong, H.Y., Stutts, L. Moore, T., Davies, D.H., Felgner, P.L. and Esser-Kahn, A.P.  Modulation of innate immune responses via covalently linked TLR agaonists. (2016) ACS Oct 28 Epub
Begum, A.N., Guoynes, C., Cho, J., Hao, J., Lutfy, K. and Hong, Y. Rapid generation of sub-type, region-specific neurons and neural networks from human pluripotent stem cell-derived neurospheres. (2015) Stem Cell Research 15: 731-741
Mesak, F., Tatarenkov, A. and Avise, J.C.  Transcriptomics of diapause in an isogenic self-fertilizing vertebrate.  BMC Genomics (2015) 16: 989-1000
Agrawal, S., Ganguly, S., Hajian, P., Cao, J-N, Agrawal, A. PDGF upregulates CLEC-2 to induce T regulatory cells. Oncotarget (2015) 6(30): 28621-28632
Macias-Munoz, A., Smith, G., Monteiro, A. and Briscoe, A.  Transcriptome-wide differential gene expression in Bicyclus anynana butterflies:  Female vision-related genes are more plastic.  Molecular Biology and Evolution (2015) Sept 14 Epub
Lane, S., Di Lena, P., Tormanen, K., Baldi, P. and Liu, H.  Function and regulation of Cph2 in Candida albicans.  Eukaryotic Cell (2015)  Sept 4 Epub
Elhadad, D., Desai, P., Rahav, G., McClelland, M., and Gal-Mor, O.  Flagellin is required for host cell invasion and normal Salmonella pathogenicity island I expression by Salmonella enterica serovar paratyphi A.  Infection and Immunity (2015) 83(9): 3355-3368
Rahmatpanah, F.B., Jia, Z., Chen, X., Char, J.E., Men, B., Franke, A-C., Jones, F.E., McClelland, M., and Mercola. D. A class of genes in the HER2 regulon that is poised for transcription in breast cancer cell lines and expressed in human breast tumors. Oncotarget (2015) 6(2): 1286-1301
Salehi, F., Baronio, R., Idrogo-Lam, R., Vu, H., Hall, L.V., Kaiser, P. and Lathrop, R.H. CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generational sequencing. (2015) PLOS 10(2): e0116877
Hoverter, N.P., Zeller, M.D., McQuade, M.M., Garibaldi, A., Busch, A., Selwan, E.M., Hertel, K.J., Baldi, P. and Waterman, M. The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition.  Nucleic Acids Research (2014) 42(9): 13615-13632
Chiu, W.T., Le, R.C., Blitz, I.L., Fish, M.B., Li, Y., Biesinger, J., Xie, X. and Cho, K.W. Genome-wide view of TGFB/Foxh1 regulation of the early mesendoderm program. Development (2014) Oct 30 Epub
Gordon, M.W., Zeller, M.D., Klein, R.H., Swindell, W.R., Ho, H., Espetia, F., Gudionsson, J.E., Baldi, P.F. and Andersen, B.  A GRHL3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia.  J. Clin. Invest (2014) Oct 27 Epub
Rogers, R.L., Shao, L., Sanjak, J.S., Andolfatto, P. and Thornton, K.R.  Revised annotations, sex-biased expression and lineage-specific genes in the Drosophila melanogaster group.  G3 (Bethesda) (2014) Oct 1 Epub
Rogers, R.L., Cridland, J.M., Shao, L., Hu, T.T., Andolfatto, P. and Thornton, K.R.  Landscape of standing variation for tandem duplications inDrosophila yakuba and Drosophila simulans.  Mol. Biol. Evol. (2014) 31(7): 1750-1766.
Smith, G., Macias-Munoz, A. and Briscoe, A.D. Genome sequence of a novel Iflavirus from mRNA sequencing of the butterfly Heliconius erato.  Genome Announcements (2014) 2(1):  e00398-14.
Diez, C.M., Meca, E., Tenaillon, M.I., and Gaut, B.S. Three groups of transposable elements with contrasting copy number dynamics and host responses in the Maize (Zea mays ssp. mays) genome.  PLOS Genetics (2014) 10(4):  e1004298.
Salmans, M.L., Zhengquan Y., Watanabe, K., Cam, E., Sun, P., Smyth, P., Dai, X. and Andersen, B.  The co-factor of LIM domains (CLIM/LDB/NLI) maintains basal mammary epithelial stem cells and promotes breast tumorigenesis.  PLOS Genetics (2014) 10: e1004520
Pate, K.T., Stringari, C., Sprowl-Tania, S., Wang,  K., TeSiaa, T., Hoverter, N.P., McQuade, M.M., Garner, C., Digman, M.A., Teitell, M.A., Edwards, R.A., Gratton, E., and Waterman, M.L.  Wnt signaling directs a metabolic program of glycolysis and angiogenesis in colon cancer. EMBO (2014) May 13 Epub
Allison, S.D., Lu, L., Kent, A.G., Martiny, A.C.  Extracellular enzyme production and cheating in Pseudomonas fluorescens depend on diffusion rates. Frontiers in Microbiology (2014) 5: 169.
Berlemont, R., Allison, S.D., Weihe, C., Lu, Y., Brodie, E.L., Martiny, J.B.H., Martiny, A.C. Cellulolytic potential under environmental changes in microbial communities from grassland litter.  Frontiers in Microbiology (2014) 5: 639.
Watanabe, K., Villarreal-Ponce, A., Sun, P., Salmans, M.L., Fallahi, M., Andersen, B. and Dai,X.  Mammary morphogenesis and regeneration require the inhibition of EMT at terminal end buds by Ovol2 transcription repressor.  Developmental Cell (2014) 29: 59-74.
Lee, B., Villarreal-Ponce, A., Fallahi, M., Ovadia, J., Sun, P., Yu, Q-C., Ito, S., Sinha, S., Nie, Q. and Dai, X.  Transcriptional mechanisms link epithelial plasticity to adhesion and differentiation of epidermal progenitor cells. Developmental Cell (2014) 29: 47-58.
Burke, M., King, E.G., Shahrestani, P., Rose, M.R. and Long, A.D.  Genome-wide association study of extreme longevity in Drosophila melanogaster. Genome Biology and Evolution (2014) 6(1): 1-11.
Salazar, L., Kashiwada, T., Krejci, P., Meyer, A.N., Casale, M., Hallowell, M., Wilcox, W.R., Donoghue, D.J. and Thompson, L.M.  Fibroblast growth factor receptor 3 interacts with and activates TGFB-activated kinase 1 tyrosine phosphorylation and NFkB signaling in multiple myeloma and bladder cancer. PLOS One (2014) 9: e86470
Barbour, A.G. and Campeau Miller, S. Genome sequence of Borrelia parkeri, an agent of enzootic relapsing fever in western North America. Genome Announc (2014) 2(1): e00018
Eckel-Mahan, K.L., Patel, V.R., de Mateo, S., Orozco-Solis, R., Ceglia, N.J., Sahar, B., Dilag-Penilla, S.A., Dyar, K.A., Baldi, P. and Sassone-Corsi, P. Reprogramming of the circadian clock by nutritional challenge.  Cell (2013) 155: 1464-1478
Aguilar-Arnal, L., Hakim, O., Patel, V.R., Baldi, P., Hager, G.L. and Sassone-Corsi, P. Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nature Structural and Molecular Biology (2013) 20: 1206-1213.
Stephens, D.N., Herndon-Klein, R., Salmons, M.L., Gordon, W., Ho, H. and Andersen, B. The Ets transcription factor EHF as a regulatory of cornea epithelial cell identity.  Journal of Biological Chemistry (2013) 288: 34304-34324
Briscoe, A.D., Macias-Munoz, A., Koszak, K.M., Walters, J.R., Yuan, F., Jamie, G.A., Martin, S.H., Dasmahapatra, K.K., Ferguson, L.C., Mallet, J., Jacquin-Joly, E. and Jiggins, C.D. Female behaviour drives expression and evolution of gustatory receptors in butterflies.  PLOS Genetics (2013) 9(7): e1003620
Takumo, S. and Gaut, B.  Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc. Natl. Acad. Sci. (2013) 110(5): 1797-1802
Liu, P., Chernyshov, A., Najdi, T., Fu, Y., Dickerson, J., Sandmeyer, S. and Jarboe, L.  Membrane stress caused by octanoic acid inSaccharomyces cerevisiae Appl. Microbiol Biotechnol. (2013) 97: 3239-3251
Pedram, A., Razandi, M., O’Mahony, F., Harvey, H., Harvey, B.J. and Levin, E.R. Estrogen reduces lipid content in the liver exclusively from membrane receptor signalling. Science Signalling (2013) 6(276): ra36
Gu, B., Watanabe, K., Sun, P., Fallahi, M. and Dai, X.  Chromatin effector Pygo2 mediates Wnt-Notch crosstalk to suppress luminal/alveolar potential of mammary stem and basal cells.  Cell Stem Cell (2013) 13:48-61
Vogel-Ciernia, A., Matheos, D.P., Barrett, R.M., Kramar, E.A., Azzawi, S., Chen, Y., Magnan, C.N., Zeller, M., Sylvain, A., Haettig, J., Jia, Y., Tran, A., Dang, R., Post, R.J., Chabrier, M., Babayan, A.H., Wu, J.I., Crabtree, G.R., Baldi, P., Baram, T.Z., Lynch, G., and Wood, M.A. The neuron-specific chromatin regulatory subunti BAF53b is necessary for synaptic plasticity and memory. Nature Neuroscience (2013) 16(5): 552-563
Lee, B., Geyfman, M., Andersen, B. and Dai, X.  Analysis of gene expression in skin using laser capture microdissection.  Methods Mol. Biol. (2013) 989:  109-117.
Hu, T.T., Eisen, M.B., Thornton, K.R. and Andolfatto, P.  A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.  Genome Research (2013) 23(1): 89-98
Gordon, W., Galitovskiy, V., Edwards, R., Andersen, B. and Grando, S.A.  The tobacco carcinogen nitrosamine induces a differential gene expression response in tumour susceptible A/J and resistant C3H mouse lungs.  European Journal of Cancer (2013) 49: 725-733.
Laquer, V.T., Hevezi, P.A., Albrecht, H., Chen, T.S., Zlotnik, A., and Kelly, K.M., Microarray analysis of port wine stains before and after pulsed dye laser treatment. Lasers in Surgery and Medicine (2013) 45: 67-75
Benoit, M.E., Hernandez, M.X., Dinh, M.L., Benavente, F., Vasquez, O. and Tenner, A.J.  C1q-induced LRP1B and GPR6 proteins expressed early in alzheimer disease mouse models, are essential for the C1q-mediated protection against amyloid-B neurotoxicity.  J. Biological Chemistry (2013) 288(1):  654-665.
Yang, J., Gu, P., Menges, S. and Klassen, H. Quantitative changes in gene transcription during induction of differentiation in porcine neural progenitor cells.  Molecular Vision (2012) 18:  1484-1504.
Benoit, M.E., Clarke, E.V., Morgado, P., Fraser, D.A. and Tenner, A.J.  Complement protein C1q directs macrophage polarization and limits inflammasome activity during the uptake of apoptotic cells.  J. Immunology (2012) 188(11): 5682-5693.
Hoverter, N.P., Ting, J.-H., Sundaresh, S., Baldi, P. and Waterman, M.L. A WNT/p21 circuit directed by the C-Clamp, a sequence-specific DNA binding domain in TCFs. Mol. and Cellular Biol.  (2012) 32(18): 3648-3862
Cribbs, D.H., Berchtold, N.C., Perreau, V., Coleman, P.D., Rogers, J., Tenner, A.J., and Cotman, C.W.  Extensive innate immune gene activation accompanies brain aging, increasing vulnerability to cognitive decline and neurodegeneration:  a microarray study.  J. of Neuroinflammation (2012) 9: 179-197.
The Heliconius Genome Consortium, Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.  Nature (2012) 487(7405):  94-98.
Geyfman, M., Kumar, V., Liu, Q., Ruiz, R., Gordon, W., Espitia, F., Cam, E., Millar, S.E., Smyth, P., Ihler, A., Takahashi, J.S. and Andersen, B., Brain and muscle Arnt-like protein-1 (BMAL1) controls circadian cell proliferation and susceptibility to UVB-induced DNA damage in the epidermis.  Proc. Natl. Acad. Sci. (2012) 109(29): 11758-11763.
Smith, M., Flodman, P.L., Gargus, J.J., Simon, M.T., Verrell, K., Haas, R., Reinger, G.E., Naviaux, R., Osann, K., Spence, M.A. and Wallace, D.C., Mitochondrial and ion channel gene alterations in autism.  Biochemica et Biophysica Acta (2012) Apr [Eub ahead of print]
Kayala, M.A. and Baldi, P., Cyber-T web server:  differential analysis of high-throughput data.  Nucleic Acids Research (2012) May 16 [Epub ahead of print]
Mackay, T., Richards, S., Stone, E.A., Brabadilla, A., et.al., The Drosophila melanogaster genetic reference panel.  Nature (2012) 482: 173-178
Garrigan, D., Kingan, S.B., Geneva, A.J., Andolfatto, P., Clark, A.G., Thornton, K.R. and Presgraves, D.C.  Genome sequencing reveals complex speciation in the Drosophila simulans clade.  Genome Research (2012) Apr 13 [Epub ahead of print]
Tenaillon, O., Rodriquez-Verdugo, A., Gaut, R.L., McDonald, P., Bennett, A.F., Long, A.D. and Gaut, B.S., The molecular diversity of adaptive convergence. Science (2012) 335(6067): 457-461
Muto, A., Calof, A., Lander, A., and Schilling, T.  Multifactorial origins of heart and gut defects in nipbl-deficient Zebrafish, a model of Cornelia de Lange Syndrome.  PLos Biol. (2011) 9(10): e1001181
Bhandari, A., Salmans, M., Gordon, W., and Anderson, B. Transcriptional regulation of epidermal barrier formation. Methods Mol. Biol. (2011) 763: 51-71.
Lee, C., Lee, C., Hu, T., Nguyen, J., Zhang, J., Martin, M., Vawter, M., Huang, E., and Chan, J.  Loss of nuclear factor E2-related factor 1 in the brain leads to dysregulation of proteasome gene expression and neurodegeneration.  Proc. Natl. Acad. Sci. (2011)  108(20): 8408-8413.
Jia, Z., Wang, Y., Sawyers, A., Yao, H., Rahmatpanah, F., Xia, X-Q., Xu, Q., Pio, R., Turan, T., Koziol, J., Goodison, S., Carpenter, P., Wang-Rodgriguez, J., Simoneau, A., Meyskens, F., Sutton, M., Lernhardt, W., Beach, T., Monforte, J., McClelland, M. and Mercola, D.,  Diagnosis of Prostate Cancer using Differentially Expressed Genes in Stroma.  Cancer Research (2011) 71(7): 2476-2487.
Im, S-S., Yousef, L., Biaschitz, C., Liu, J.Z., Edwards, R.A., Young, S.G., Raffatellu, M. and Osborne, T.F.  Linking lipid metabolism to the innate immune response in macrophages through sterol regulatory element binding protein 1-a.  Cell Metabolism (2011) May 4 13:  540-549.
Garner, C. Confounded by sequencing depth in association studies of rare alleles. Genet. EpidemIol. (2011) 35(4): 261-268
Benoit, M.E. and Tenner, J.J.  Complement protein C1q-mediated neuroprotection is correlated with regulation of neuronal gene and miRNA expression.  J. Neuroscience (2011) 31(9):  3459-3469
Katada, S. and Sassone-Corsi, P. The histone methyltransferase MLL1 permits the oscillation of circadian gene expression. Nature Struct. Mol. Biol. (2010) 11: 1414-21.
Grimaldi, B., Bellet, M. M., Katada, S., Astarita, G., Hirayama, J., Amin, R. H., Granneman, J. G., Piomelli, D., Leff, T. and Sassone-Corsi. P.  PER2 controls lipid metabolism by direct regulation of PPAR. Cell Metabolism (2010) 12: 508-20.
Daily KM, Rigor PM, Christley SE, Xie X, Baldi PF, Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies. BMC Bioinformatics (2010) 11: 514-26.
Wang Y, Xia XQ, Jia Z, Sawyers A, Yao H, Wang-Rodriquez J, Mercola D, McClelland M. In silico estimates of tissue components in surgical samples based on expression profiling data Cancer Res. (2010)  Aug 15;70(16):6448-55. Epub 2010 Jul 27.
Liu Q, Lin KK, Andersen B, Smyth P, Ihler A. Estimating replicate time shifts using Gaussian process regression Bioinformatics. (2010) Mar 15;26(6):770-6. Epub 2010 Feb 9.
Geyfman M, Andersen B.  Clock genes, hair growth and aging  Aging (Albany NY).  (2010) Mar 31;2(3):122-8.
Zhao F, Edwards R, Dizon D, Afrasiabi K, Mastroianni JR, Geyfman M, Ouellette AJ, Andersen B, Lipkin SM. Disruption of Paneth and goblet cell homeostasis and increased endoplasmic reticulum stress in Agr2-/- mice.   Dev Biol. (2010) Feb 15;338(2):270-9. Epub 2009 Dec 16.
Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X. Identifying gene regulatory networks in schizophrenia  Neuroimage. (2010) Jun 22.
Swamidass SJ, Azencott CA, Daily KM, Baldi PF. A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinformatics (2010) 26: 1348-56.
Sikandar SS, Pate KT, Dizon D, Edwards RA, Waterman ML, Lipkin SM, Anderson SA: NOTCH signaling is required for formation and self-renewal of tumor-initiating cells and for repression of secretory cell differentiation in colon cancer. Cancer Res (2010) 70, 1469-78.
Molina DM, Pal S, Kayala MA, Teng A, Kim PJ, Baldi PF, Felgner PL, Liang X. Identification of immunodominant antigens of Chlamydia trachomatis using proteome microarrays. Vaccine (2010) 28, 3014-24.
Mochon AB, Ye J, Kayala MA, Wingard JR, Clancy CJ, Nguyen MH, Felgner PL, Baldi PF, Liu H: Serological profiling of a Candida albicans protein microarray reveals permanent host-pathogen interplay and stage-specific responses during candidemia. PLoS Pathog  (2010) 6, e1000827.
Liu Q, Lin KK, Andersen B, Smyth PJ, Ihler AT. Estimating replicate time shifts using Gaussian process regression. Bioinformatics (2010) 26, 770-6.
Leng D, Burk CR, Nakajima-Sasaki R, Kayala MA, Atluri VL, Pablo J, Unal B, Ficht TA, Gotuzzo E, Saito M, Morrow WJ, Liang X, Baldi PF, Gilman RH, Vinetz JM, Tsolis RM, Felgner PL, Liang L. Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens. PLoS Negl Trop Dis (2010) 4, e673.
Kim YK, Kwon YJ. Separation and recovery of nucleic acids with improved biological activity by acid-degradable polyacrylamide gel electrophoresis. Electrophoresis (2010) 31, 1656-61.
Garner CP. A statistical method for scanning the genome for regions with rare disease alleles. Genet Epidemiol (2010) 34, 386-95.
Crompton PD, Kayala MA, Traore B, Kayentao K, Ongoiba A, Weiss GE, Molina DM, Burk CR, Waisberg M, Jasinskas A, Tan X, Doumbo S, Doumtabe D, Kone Y, Narum DL, Liang X, Doumbo OK, Miller LH, Doolan DL, Baldi PF, Felgner PL, Pierce SK: A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray. Proc Natl Acad Sci U S A (2010) 107, 6958-63.
Yu Z, Mannik J, Soto A, Lin KK., and Andersen B.  The epidermal differentiation-associated factor Grainyhead-like factor Get1/Grhl3 is also involved in urothelial differentiation. EMBO J. (2009) 28:1890-1903.
Lin KK, Kumar V, Geyfman M, Chudova D, Ihler AT, Smyth P, Paus R, Takahashi JS, and Andersen B.  Circadian clock genes contribute to the regulation of hair follicle cycling. PLOS Genetics. (2009) 5(7):e1000573.
Brandon MC, Ruiz-Pesini E, Mishmar D, Procaccio V, Lott MT, Nguyen KC, Spolim S, Patil U, Baldi P, Wallace DC. MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences. Hum Mutat. (2009) Jan;30(1):1-6.
Brandon MC, Wallace DC, Baldi P. Data structures and compression algorithms for genomic sequence data. Bioinformatics. (2009) Jul 15;25(14):1731-8. Epub 2009 May 15.
Chudova D, Ihler A, Lin KK, Andersen B, Smyth P. Bioinformatics. Bayesian detection of non-sinusoidal periodic patterns in circadian expression data. (2009) Dec 1;25(23):3114-20. Epub 2009 Sep 22
Kawauchi S, Calof AL, Santos R, Lopez-Burks ME, Young CM, Hoang MP, Chua A, Lao T, Lechner MS, Daniel JA, Nussenzweig A, Kitzes L, Yokomori K, Hallgrimsson B, Lander AD. Multiple organ system defects and transcriptional dysregulation in the Nipbl(+/-) mouse, a model of Cornelia de Lange Syndrome. PLoS Genet. (2009) Sep;5(9):e1000650. Epub 2009 Sep 18
Seo, Y-K., Chong, H.K., Infante, A.M., Im, S-S., Xie, X. and Osborne, T.F.  Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif.  Proc. Natl. Acad. Sci.  (2009) Aug 18 106(33):  13765-13769.
Tang Y, Simoneau AR, Liao WX, Yi G, Hope C, Liu F, Li S, Xie J, Holcombe RF, Jurnak FA, Mercola D, Hoang BH, Zi X. WIF1, a Wnt pathway inhibitor, regulates SKP2 and c-myc expression leading to G1 arrest and growth inhibition of human invasive urinary bladder cancer cells.Mol Cancer Ther. (2009) Feb;8(2):458-68. Epub 2009 Jan 27.
Vardar-Sengul S, Arora S, Baylas H, Mercola D. Expression profile of human gingival fibroblasts induced by interleukin-1beta reveals central role of nuclear factor-kappa B in stabilizing human gingival fibroblasts during inflammation. J Periodontol. (2009) May;80(5):833-49.
Jia Z, Wang Y, Ye K, Li Q, Tang S, Xu S, Mercola D. Association Study between Gene Expression and Multiple Relevant Phenotypes with Cluster Analysis.Lect Notes Comput Sci. (2009) 5483:1-12.
Yu Z, Bhandari A, Mannik J, Pham T, Xu X, and Andersen B.  Grainyhead-like factor Get1/Grhl3 regulates formation of the epidermal leading edge during eyelid closure. Developmental Biology (2008) 319:56-67.
Yusuf I, Kharas MG, Chen J, Peralta RQ, Maruniak A, Sareen P, Yang VW, Kaestner KH, Fruman DA. KLF4 is a FOXO target gene that suppresses B cell proliferation.  Int Immunol. (2008) May;20(5):671-81. Epub 2008 Mar 28.
Subramaniam V, Golik P, Murdock DG, Levy S, Kerstann KW, Coskun PE, Melkonian GA, Wallace DC. MITOCHIP assessment of differential gene expression in the skeletal muscle of Ant1 knockout mice: coordinate regulation of OXPHOS, antioxidant, and apoptotic genes. Biochim Biophys Acta. (2008) Jul-Aug;1777(7-8):666-75. Epub 2008 Mar 28.
Jia Z, Tang S, Mercola D, Xu S.Detection of Quantitative Trait Associated Genes Using Cluster Analysis. Lect Notes Comput Sci. (2008) Apr 1;4973:83-94.
Arora S, Wang Y, Jia Z, Vardar-Sengul S, Munawar A, Doctor KS, Birrer M, McClelland M, Adamson E, Mercola D. Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip.  Genome Biol. (2008) 9(11):R166. Epub 2008 Nov 25.
Biessmann H., Nguyen Q K, Le D, Walter M F. Microarray-based survey of a subset of putative olfactory genes in the mesquito Anopheles gambiae. Insect Mol Biol. (2005) Nov; 14(6): 575-589.
Samoszuk M, Tan J, Chorn G. Clonogenic growth of human breast cancer cells co-cultured in direct contact with serum-activated fibroblasts. Breast Cancer Res. (2005) 7(3): R274-83.
Marinotti O, Nguyen QK, Calvo E, James AA, Ribeiro JM. Microarray analysis of genes showing variable expression following a blood meal in Anopheles gambiae. Insect Mol Biol. (2005) Aug; 14(4): 365-73.
Samoszuk M, Tan J, Chorn G. Clonogenic growth of human breast cancer cells co-cultured in direct contact with serum-activated fibroblasts. Breast Cancer Res. (2005) 7(3): R274-83.
Furuta S, Jiang X, Gu B, Cheng E, Chen PL, Lee WH. Depletion of BRCA1 impairs differentiation but enhances proliferation of mammary epithelial cells. Proc Natl Acad Sci U S A. (2005) Jun 28; 102(26): 9176-81.
Shin Y, Kitayama A, Koide T, Peiffer DA, Mochii M, Liao A, Ueno N, Cho KW. Identification of neural genes using Xenopus DNA microarrays. Dev Dyn. 2005 Feb; 232(2):432-44. Erratum in: Dev Dyn. (2005) May; 233(1): 248.
Itoh T, Karlsberg K, Kijima I, Yuan YC, Smith D, Ye J, Chen S. Letrozole-, anastrozole-, and tamoxifen-responsive genes in MCF-7aro cells: a microarray approach. Mol Cancer Res. (2005) Apr; 3(4): 203-18.
Davies DH, Liang X, Hernandez JE, Randall A, Hirst S, Mu Y, Romero KM, Nguyen TT, Kalantari-Dehaghi M, Crotty S, Baldi P, Villarreal LP, Felgner PL. Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc Natl Acad Sci U S A. (2005) Jan 18; 102(3): 547-52.
Davies DH, Liang X, Hernandez JE, Randall A, Hirst S, Mu Y, Romero KM, Nguyen TT, Kalantari-Dehaghi M, Crotty S, Baldi P, Villarreal LP, Felgner PL. Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc Natl Acad Sci U S A. (2005) Jan 18; 102(3): 547-52.
Li L, Roden J, Shapiro BE, Wold BJ, Bhatia S, Forman SJ, Bhatia R. Reproducibility, fidelity, and discriminant validity of mRNA amplification for microarray analysis from primary hematopoietic cells. J Mol Diagn. (2005) Feb; 7(1): 48-56.
Wang A, Crowley DE. Global gene expression responses to cadmium toxicity in Escherichia coli. J Bacteriol. (2005) May; 187(9): 3259-66.
Guan Y, Nothnagel EA. Binding of arabinogalactan proteins by Yariv phenylglycoside triggers wound-like responses in Arabidopsis cell cultures. Plant Physiol. (2004) Jul; 135(3): 1346-66.
Connolly PH, Caiozzo VJ, Zaldivar F, Nemet D, Larson J, Hung SP, Heck JD, Hatfield GW, Cooper DM. Effects of exercise on gene expression in human peripheral blood mononuclear cells. J Appl Physiol. (2004) Oct; 97(4):1461-9.
Jonathan A. Deane, Matthew J. Trifilo, Claudine M. Yballe, Sangdun Choi, Thomas E. Lane, and David A. Fruman. Enhanced T Cell Proliferation in Mice Lacking the p85 Subunit of Phosphoinositide 3-Kinase. J Immunol (2004) 172: 6615-6625.
Lin KK, Chudova D, Hatfield GW, Smyth P, Andersen B. Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate variance. Proc Natl Acad Sci U S A. (2004) Nov 9; 101(45): 15955-60. Epub 2004 Nov 1.
Wang R, Tischner R, Gutierrez RA, Hoffman M, Xing X, Chen M, Coruzzi G, Crawford NM. Genomic analysis of the nitrate response using a nitrate reductase-null mutant of Arabidopsis. Plant Physiol. (2004) Sep; 136(1): 2512-22.
Wong R, Tran V, Morhenn V, Hung SP, Andersen B, Ito E, Wesley Hatfield G, Benson NR. Use of RT-PCR and DNA microarrays to characterize RNA recovered by non-invasive tape harvesting of normal and inflamed skin. J Invest Dermatol. (2004) Jul; 123(1): 159-67.
Ja-Ryong Koo, MD, Kai Hui Liang, MD, Nosratola D Vaziri, MD. Microarray Analysis of Altered Gene Expression in Kidneys of Adult Spontaneously Hypertensive Rats. The Journal of Applied Research (2004) 4(1): 111-126.
Colangelo EP, Guerinot ML. The essential basic helix-loop-helix protein FIT1 is required for the iron deficiency response. Plant Cell. (2004) Dec; 16(12): 3400-12.
Glaser J, Gonzalez R, Perreau VM, Cotman CW, Keirstead HS. Neutralization of the chemokine CXCL10 enhances tissue sparing and angiogenesis following spinal cord injury. J Neurosci Res. (2004) Sep 1; 77(5): 701-8.
Paintlia AS, Paintlia MK, Singh AK, Stanislaus R, Gilg AG, Barbosa E, Singh I. Regulation of gene expression associated with acute experimental autoimmune encephalomyelitis by Lovastatin. J Neurosci Res. (2004) Jul 1; 77(1): 63-81.
Leonhardt N, Kwak JM, Robert N, Waner D, Leonhardt G, Schroeder JI. Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant. Plant Cell. (2004) Mar; 16(3): 596-615.
Sharman EH, Sharman KG, Ge YW, Lahiri DK, Bondy SC. Age-related changes in murine CNS mRNA gene expression are modulated by dietary melatonin. J Pineal Res. (2004) Apr; 36(3): 165-70.
Klevecz RR, Bolen J, Forrest G, Murray DB. A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc Natl Acad Sci U S A. (2004) Feb 3; 101(5): 1200-5. Epub 2004 Jan 20.
Winokur ST, Chen YW, Masny PS, Martin JH, Ehmsen JT, Tapscott SJ, van der Maarel SM, Hayashi Y, Flanigan KM. Expression profiling of FSHD muscle supports a defect in specific stages of myogenic differentiation. Hum Mol Genet. (2003) Nov 15; 12(22): 2895-907.
Dewing P, Shi T, Horvath S, Vilain E. Sexually dimorphic gene expression in mouse brain precedes gonadal differentiation. Brain Res Mol Brain Res. (2003) Oct 21; 118(1-2): 82-90.
Li T, Chen YH, Liu TJ, Jia J, Hampson S, Shan YX, Kibler D, Wang PH. Using DNA microarray to identify Sp1 as a transcriptional regulatory element of insulin-like growth factor 1 in cardiac muscle cells. Circ Res. (2003) Dec 12; 93(12): 1202-9.
Sok JC, Kuriakose MA, Mahajan VB, Pearlman AN, DeLacure MD, Chen FA.Tissue-specific gene expression of head and neck squamous cell carcinoma in vivo by complementary DNA microarray analysis. Arch Otolaryngol Head Neck Surg.(2003) Jul; 129(7): 760-70.
Jean S. Wong, Xiaoqin Ye, Christy R. Muhlenkamp, and Sarjeet S. Gill. Effect of a peroxisome proliferator on 3b-hydroxysteroid dehydrogenase. Biochem and Biophys Rsrch Comm (2002) Mar. 11; 293: 549–553.
Wong JS, Gill SS. Gene expression changes induced in mouse liver by di(2-ethylhexyl) phthalate. Toxicol Appl Pharmacol. 2002 Dec 15; 185(3): 180-96.
Yang WC, Devi-Rao GV, Ghazal P, Wagner EK, Triezenberg SJ. General and specific alterations in programming of global viral gene expression during infection by VP16 activation-deficient mutants of herpes simplex virus type 1. J Virol. (2002) Dec; 76(24): 12758-74.
Mahajan VB, Wei C, McDonnell PJ 3rd. Microarray analysis of corneal fibroblast gene expression after interleukin-1 treatment. Invest Ophthalmol Vis Sci. (2002) Jul; 43(7): 2143-51.
Mak PA, Laffitte BA, Desrumaux C, Joseph SB, Curtiss LK, Mangelsdorf DJ, Tontonoz P, Edwards PA. Regulated expression of the apolipoprotein E/C-I/C-IV/C-II gene cluster in murine and human macrophages. A critical role for nuclear liver X receptors alpha and beta. J Biol Chem. (2002) Aug 30; 277(35): 31900-8.
Tong L, Shen H, Perreau VM, Balazs R, Cotman CW. Effects of exercise on gene-expression profile in the rat hippocampus. Neurobiol Dis. (2001) Dec; 8(6): 1046-56.
Hampson S, Baldi P, Kibler D, Sandmeyer SB. Analysis of yeast’s ORF upstream regions by parallel processing, microarrays, and computational methods. Proc Int Conf Intell Syst Mol Biol. (2000) 8:190-201.