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Riley, L. A., Zhang, X., Douglas, C. M., Mijares, J. M., Hammers, D. W., Wolff, C. A., Wood, N. B., Olafson, H. R., Du, P., Labeit, S., Previs, M. J., Wang, E. T., & Esser, K. A. (2022). The skeletal muscle circadian clock regulates titin splicing through RBM20. eLife, 11, e76478. https://doi.org/10.7554/eLife.76478

Raj, R., Dahlen, D., Duyck, K., & Yu, C. R. (2022). Maximal Dependence Capturing as a Principle of Sensory Processing. Frontiers in Computational Neuroscience, 16, 857653. https://doi.org/10.3389/fncom.2022.857653

Mighell, T. L., Nishida, A., O’Connell, B. L., Miller, C. V., Grindstaff, S., Thornton, C. A., Adey, A. C., Doherty, D., & O’Roak, B. J. (2022). Cas12a-Capture: A Novel, Low-Cost, and Scalable Method for Targeted Sequencing. The CRISPR Journal, 5(4), 548–557. https://doi.org/10.1089/crispr.2021.0140

Co, M., Barnard, R. A., Jahncke, J. N., Grindstaff, S., Fedorov, L. M., Adey, A. C., Wright, K. M., & O’Roak, B. J. (2022). Shared and Distinct Functional Effects of Patient-Specific Tbr1 Mutations on Cortical Development. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience, 42(37), 7166–7181. https://doi.org/10.1523/JNEUROSCI.0409-22.2022

Sun, B. B., Kurki, M. I., Foley, C. N., Mechakra, A., Chen, C.-Y., Marshall, E., Wilk, J. B., Biogen Biobank Team, Chahine, M., Chevalier, P., Christé, G., FinnGen, Palotie, A., Daly, M. J., & Runz, H. (2022). Genetic associations of protein-coding variants in human disease. Nature, 603(7899), 95–102. https://doi.org/10.1038/s41586-022-04394-w

Hunter, S., Sigauke, R. F., Stanley, J. T., Allen, M. A., & Dowell, R. D. (2022). Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries. BMC Genomics, 23(1), 187. https://doi.org/10.1186/s12864-022-08352-8

Varco-Merth, B. D., Brantley, W., Marenco, A., Duell, D. D., Fachko, D. N., Richardson, B., Busman-Sahay, K., Shao, D., Flores, W., Engelman, K., Fukazawa, Y., Wong, S. W., Skalsky, R. L., Smedley, J., Axthelm, M. K., Lifson, J. D., Estes, J. D., Edlefsen, P. T., Picker, L. J., … Okoye, A. A. (2022). Rapamycin limits CD4+ T cell proliferation in simian immunodeficiency virus-infected rhesus macaques on antiretroviral therapy. The Journal of Clinical Investigation, 132(10), e156063. https://doi.org/10.1172/JCI156063

Dannebaum, R., Suwalski, P., Asgharian, H., Du Zhipei, G., Lin, H., Weiner, J., Holtgrewe, M., Thibeault, C., Müller, M., Wang, X., Karadeniz, Z., Saccomanno, J., Doehn, J.-M., Hübner, R.-H., Hinzmann, B., Blüher, A., Siemann, S., Telman, D., Suttorp, N., … Heidecker, B. (2022). Highly multiplexed immune repertoire sequencing links multiple lymphocyte classes with severity of response to COVID-19. EClinicalMedicine, 48, 101438. https://doi.org/10.1016/j.eclinm.2022.101438

Burns, A. M., Farinelli-Scharly, M., Hugues-Ascery, S., Sanchez-Mut, J. V., Santoni, G., & Gräff, J. (2022). The HDAC inhibitor CI-994 acts as a molecular memory aid by facilitating synaptic and intracellular communication after learning. Proceedings of the National Academy of Sciences of the United States of America, 119(22), e2116797119. https://doi.org/10.1073/pnas.2116797119

DuTell, V., Gibaldi, A., Focarelli, G., Olshausen, B. A., & Banks, M. S. (2022). High-fidelity eye, head, body, and world tracking with a wearable device. Behavior Research Methods. https://doi.org/10.3758/s13428-022-01888-3

Joseph, M., Wu, Y., Dannebaum, R., Rubelt, F., Zlatareva, I., Lorenc, A., Du, Z. G., Davies, D., Kyle-Cezar, F., Das, A., Gee, S., Seow, J., Graham, C., Telman, D., Bermejo, C., Lin, H., Asgharian, H., Laing, A. G., Del Molino Del Barrio, I., … Hayday, A. C. (2022). Global patterns of antigen receptor repertoire disruption across adaptive immune compartments in COVID-19. Proceedings of the National Academy of Sciences of the United States of America, 119(34), e2201541119. https://doi.org/10.1073/pnas.2201541119

Pan, L., Tormey, D., Bobon, N., & Baumann, P. (2022). Rap1 prevents fusions between long telomeres in fission yeast. The EMBO Journal, 41(20), e110458. https://doi.org/10.15252/embj.2021110458

Lavinder, T. R., Fachko, D. N., Stanton, J., Varco-Merth, B., Smedley, J., Okoye, A. A., & Skalsky, R. L. (2022). Effects of Early Antiretroviral Therapy on the Composition and Diversity of the Fecal Microbiome of SIV-infected Rhesus Macaques (Macaca mulatta). Comparative Medicine, 72(5), 287–297. https://doi.org/10.30802/AALAS-CM-22-000020

Chen, Y. A., Kankel, M. W., Hana, S., Lau, S. K., Zavodszky, M. I., McKissick, O., Mastrangelo, N., Dion, J., Wang, B., Ferretti, D., Koske, D., Lehman, S., Koszka, K., McLaughlin, H., Liu, M., Marshall, E., Fabian, A. J., Cullen, P., Marsh, G., … Lo, S.-C. (2023). In vivo genome editing using novel AAV-PHP variants rescues motor function deficits and extends survival in a SOD1-ALS mouse model. Gene Therapy, 30(5), 443–454. https://doi.org/10.1038/s41434-022-00375-w

Nichols, R. V., O’Connell, B. L., Mulqueen, R. M., Thomas, J., Woodfin, A. R., Acharya, S., Mandel, G., Pokholok, D., Steemers, F. J., & Adey, A. C. (2022). High-throughput robust single-cell DNA methylation profiling with sciMETv2. Nature Communications, 13(1), 7627. https://doi.org/10.1038/s41467-022-35374-3

Gotting, K., May, D. S., Sosa-Calvo, J., Khadempour, L., Francoeur, C. B., Berasategui, A., Thairu, M. W., Sandstrom, S., Carlson, C. M., Chevrette, M. G., Pupo, M. T., Bugni, T. S., Schultz, T. R., Johnston, J. S., Gerardo, N. M., & Currie, C. R. (2022). Genomic diversification of the specialized parasite of the fungus-growing ant symbiosis. Proceedings of the National Academy of Sciences of the United States of America, 119(51), e2213096119. https://doi.org/10.1073/pnas.2213096119

Araya, P., Kinning, K. T., Coughlan, C., Smith, K. P., Granrath, R. E., Enriquez-Estrada, B. A., Worek, K., Sullivan, K. D., Rachubinski, A. L., Wolter-Warmerdam, K., Hickey, F., Galbraith, M. D., Potter, H., & Espinosa, J. M. (2022). IGF1 deficiency integrates stunted growth and neurodegeneration in Down syndrome. Cell Reports, 41(13), 111883. https://doi.org/10.1016/j.celrep.2022.111883

Al-Muhanna, F. A., Dowdell, A. K., Al Eleq, A. H., Albaker, W. I., Brooks, A. W., Al-Sultan, A. I., Al-Rubaish, A. M., Alkharsah, K. R., Sulaiman, R. M., Al-Quorain, A. A., Cyrus, C., Alali, R. A., Vatte, C., Robinson, F. L., Zhou, X., Snyder, M. P., Almuhanna, A. F., Keating, B. J., Piening, B. D., & Al-Ali, A. K. (2022). Gut microbiota analyses of Saudi populations for type 2 diabetes-related phenotypes reveals significant association. BMC Microbiology, 22(1), 301. https://doi.org/10.1186/s12866-022-02714-8

Bolouri, H., Ries, R. E., Wiedeman, A. E., Hylkema, T., Scheiding, S., Gersuk, V. H., O’Brien, K., Nguyen, Q.-A., Smith, J. L., Alice Long, S., & Meshinchi, S. (2022). Inflammatory bone marrow signaling in pediatric acute myeloid leukemia distinguishes patients with poor outcomes. Nature Communications, 13(1), 7186. https://doi.org/10.1038/s41467-022-34965-4

Sanchez, M. R., Biondi, T. C., Kunde, Y. A., Eng, W., Nalley, J. O., Ganuza, E., Hovde, B. T., Corcoran, A. A., & Starkenburg, S. R. (2022). The Genome Sequence of an Algal Strain of Nannochloropsis QH25. Microbiology Resource Announcements, e0092122. https://doi.org/10.1128/mra.00921-22

Ors, A., Chitsazan, A. D., Doe, A. R., Mulqueen, R. M., Ak, C., Wen, Y., Haverlack, S., Handu, M., Naldiga, S., Saldivar, J. C., & Mohammed, H. (2022). Estrogen regulates divergent transcriptional and epigenetic cell states in breast cancer. Nucleic Acids Research, gkac908. https://doi.org/10.1093/nar/gkac908

Garrison, Z., Chang, M., Hornick, N., Yu, W. Y., Cheng, J. B., & Kulkarni, R. P. (2022). A Novel Potential Role for Monocytes Revealed by Single Cell Analysis of Immunotherapy Induced Immune Related Adverse Events. Cancers, 14(21), 5407. https://doi.org/10.3390/cancers14215407

David, J. K., Maden, S. K., Wood, M. A., Thompson, R. F., & Nellore, A. (2022). Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads. Genome Biology, 23(1), 240. https://doi.org/10.1186/s13059-022-02789-6

Sepe, J. J., Gardner, R. T., Blake, M. R., Brooks, D. M., Staffenson, M. A., Betts, C. B., Sivagnanam, S., Larson, W., Kumar, S., Bayles, R. G., Jin, H., Cohen, M. S., Coussens, L. M., & Habecker, B. A. (2022). Therapeutics That Promote Sympathetic Reinnervation Modulate the Inflammatory Response After Myocardial Infarction. JACC. Basic to Translational Science, 7(9), 915–930. https://doi.org/10.1016/j.jacbts.2022.04.009

Fankhauser, R., Chang, M., Garrison, Z., Berryman, R., Lucero, O. M., Fuiten, A., DePatie, N., Seifert, H., & Kulkarni, R. P. (2022). Single-Cell Identification of Melanoma Biomarkers in Circulating Tumor Cells. Cancers, 14(19), 4921. https://doi.org/10.3390/cancers14194921

Brown, S. Z., McCarthy, G. A., Carroll, J. R., Di Niro, R., Pelz, C., Jain, A., Sutton, T. L., Holly, H. D., Nevler, A., Schultz, C. W., McCoy, M. D., Cozzitorto, J. A., Jiang, W., Yeo, C. J., Dixon, D. A., Sears, R. C., & Brody, J. R. (2022). The RNA-Binding Protein HuR Posttranscriptionally Regulates the Protumorigenic Activator YAP1 in Pancreatic Ductal Adenocarcinoma. Molecular and Cellular Biology, 42(7), e00018-22. https://doi.org/10.1128/mcb.00018-22

Hill, J. H., Massaquoi, M. S., Sweeney, E. G., Wall, E. S., Jahl, P., Bell, R., Kallio, K., Derrick, D., Murtaugh, L. C., Parthasarathy, R., Remington, S. J., Round, J. L., & Guillemin, K. (2022). BefA, a microbiota-secreted membrane disrupter, disseminates to the pancreas and increases β cell mass. Cell Metabolism, S1550-4131(22)00391-6. https://doi.org/10.1016/j.cmet.2022.09.001

Gross, S. M., Dane, M. A., Smith, R. L., Devlin, K. L., McLean, I. C., Derrick, D. S., Mills, C. E., Subramanian, K., London, A. B., Torre, D., Evangelista, J. E., Clarke, D. J. B., Xie, Z., Erdem, C., Lyons, N., Natoli, T., Pessa, S., Lu, X., Mullahoo, J., … Heiser, L. M. (2022). A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. Communications Biology, 5(1), 1066. https://doi.org/10.1038/s42003-022-03975-9

Haynes, D., Reiter, T., Velasco, R., Chang, M., Kulkarni, R., Kent, G., Strunck, J., Cassidy, P., & Greiling, T. M. (2022). Pityriasis rubra pilaris transcriptomics implicate Th17 signaling and correlate with response to ixekizumab, with distinct gene expression profiles in non-responders. The Journal of Investigative Dermatology, S0022-202X(22)01938-8. https://doi.org/10.1016/j.jid.2022.09.005

Le, Q., Hadland, B., Smith, J. L., Leonti, A., Huang, B. J., Ries, R., Hylkema, T. A., Castro, S., Tang, T. T., McKay, C. N., Perkins, L., Pardo, L., Sarthy, J., Beckman, A. K., Williams, R., Idemmili, R., Furlan, S., Ishida, T., Call, L., … Meshinchi, S. (2022). CBFA2T3-GLIS2 model of pediatric acute megakaryoblastic leukemia identifies FOLR1 as a CAR T cell target. The Journal of Clinical Investigation, 132(22), e157101. https://doi.org/10.1172/JCI157101

Loeb, K. R., Le, Q. H., Tang, T., Castro, S. K., Pardo, L., McKay, C. N., Perkins, L., Smith, J. L., Kirkey, D. C., Abrahams, C., Bedard, K., Molina, A., Eidenschink Brodersen, L., Loken, M. R., Tarlock, K., & Meshinchi, S. (2022). Targeting FOLR1 in high-risk CBF2AT3-GLIS2 Pediatric AML with STRO-002 FOLR1-Antibody-Drug Conjugate. Blood Advances, bloodadvances.2022008503. https://doi.org/10.1182/bloodadvances.2022008503

Denans, N., Tran, N. T. T., Swall, M. E., Diaz, D. C., Blanck, J., & Piotrowski, T. (2022). An anti-inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish. Nature Communications, 13(1), 5356. https://doi.org/10.1038/s41467-022-33015-3

Bailon-Zambrano, R., Sucharov, J., Mumme-Monheit, A., Murry, M., Stenzel, A., Pulvino, A. T., Mitchell, J. M., Colborn, K. L., & Nichols, J. (2022). Variable paralog expression underlies phenotype variation. ELife, 11, e79247. https://doi.org/10.7554/eLife.79247

Huang, B. J., Smith, J. L., Farrar, J. E., Wang, Y.-C., Umeda, M., Ries, R. E., Leonti, A. R., Crowgey, E., Furlan, S. N., Tarlock, K., Armendariz, M., Liu, Y., Shaw, T. I., Wei, L., Gerbing, R. B., Cooper, T. M., Gamis, A. S., Aplenc, R., Kolb, E. A., … Meshinchi, S. (2022). Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia. Nature Communications, 13(1), 5487. https://doi.org/10.1038/s41467-022-33244-6

Zimmerman, S. M., Fropf, R., Kulasekara, B. R., Griswold, M., Appelbe, O., Bahrami, A., Boykin, R., Buhr, D. L., Fuhrman, K., Hoang, M. L., Huynh, Q., Isgur, L., Klock, A., Kutchma, A., Lasley, A. E., Liang, Y., McKay-Fleisch, J., Nelson, J. S., Nguyen, K., … Beechem, J. M. (2022). Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling. Genome Research, 32(10), 1892–1905. https://doi.org/10.1101/gr.276206.121

Kieran Blair, S. R., Hull, J., Escalona, M., Finger, A., Joslin, S. E. K., Sahasrabudhe, R., Marimuthu, M. P. A., Nguyen, O., Chumchim, N., Morris, E. R., Velazquez, S., & Schreier, A. (2022). The reference genome of the Vernal Pool Tadpole Shrimp, Lepidurus packardi. The Journal of Heredity, 113(6), 706–711. https://doi.org/10.1093/jhered/esac051

Carratt, S. A., Kong, G. L., Curtiss, B. M., Schonrock, Z., Maloney, L., Maniaci, B. N., Blaylock, H. Z., Baris, A., Druker, B. J., Braun, T. P., & Maxson, J. E. (2022). Mutated SETBP1 activates transcription of Myc programs to accelerate CSF3R-driven myeloproliferative neoplasms. Blood, 140(6), 644–658. https://doi.org/10.1182/blood.2021014777

Tsui, D. C. C., Drusbosky, L. M., Wienke, S., Gao, D., Bubie, A., Barbacioru, C., & Camidge, D. R. (2022). Oncogene Overlap Analysis of Circulating Cell-free Tumor DNA to Explore the Appropriate Criteria for Defining MET Copy Number-Driven Lung Cancer. Clinical Lung Cancer, S1525-7304(22)00159-0. https://doi.org/10.1016/j.cllc.2022.07.002

Xu, Y., Twarog, M., Li, N., Banks, A., Schustak, J., Bao, Y., Huang, Q., & Medley, Q. G. (2022). Zinc transport from the endoplasmic reticulum to the cytoplasm via Zip7 is necessary for barrier dysfunction mediated by inflammatory signaling in RPE cells. PloS One, 17(7), e0271656. https://doi.org/10.1371/journal.pone.0271656

Yashar, W. M., Kong, G., VanCampen, J., Curtiss, B. M., Coleman, D. J., Carbone, L., Yardimci, G. G., Maxson, J. E., & Braun, T. P. (2022). GoPeaks: Histone modification peak calling for CUT&Tag. Genome Biology, 23(1), 144. https://doi.org/10.1186/s13059-022-02707-w

Sanders, C. K., Biondi, T. C., Eng, W., Kunde, Y. A., Hovde, B. T., & Dale, T. (2022). High-Quality Genome Assembly of Nannochloris desiccata 2437 and Its Associated Bacterial Community. Microbiology Resource Announcements, 11(7), e0071021. https://doi.org/10.1128/mra.00710-21

Gutierrez, J., Davis, B. A., Nevonen, K. A., Ward, S., Carbone, L., & Maslen, C. L. (2022). DNA Methylation Analysis of Turner Syndrome BAV. Frontiers in Genetics, 13, 872750. https://doi.org/10.3389/fgene.2022.872750

Claridge, S. E., & Hopkins, B. D. (2022). PI3King the Environment for Growth: PI3K Activation Drives Transcriptome Changes That Support Oncogenic Growth. Cancer Research, 82(12), 2216–2218. https://doi.org/10.1158/0008-5472.CAN-22-1466

Curtiss, B. M., VanCampen, J., Macaraeg, J., Kong, G. L., Taherinasab, A., Tsuchiya, M., Yashar, W. M., Tsang, Y. H., Horton, W., Coleman, D. J., Estabrook, J., Lusardi, T. A., Mills, G. B., Druker, B. J., Maxson, J. E., & Braun, T. P. (2022). PU.1 and MYC transcriptional network defines synergistic drug responses to KIT and LSD1 inhibition in acute myeloid leukemia. Leukemia, 36(7), 1781–1793. https://doi.org/10.1038/s41375-022-01594-1

Bruce, M., DeWees, D., Harmon, J., Cates, L., Khaing, Z. Z., & Hofstetter, C. P. (2022). Blood Flow Changes Associated with Spinal Cord Injury Assessed by Non-linear Doppler Contrast-Enhanced Ultrasound. Ultrasound in Medicine & Biology, 48(8), 1410–1419. https://doi.org/10.1016/j.ultrasmedbio.2022.03.004

Blair, T. C., Bambina, S., Kramer, G. F., Dowdell, A. K., Alice, A. F., Baird, J. R., Lund, A. W., Piening, B. D., Crittenden, M. R., & Gough, M. J. (2022). Fluorescent tracking identifies key migratory dendritic cells in the lymph node after radiotherapy. Life Science Alliance, 5(9), e202101337. https://doi.org/10.26508/lsa.202101337

James, C. A., Yu, K. K. Q., Mayer-Blackwell, K., Fiore-Gartland, A., Smith, M. T., Layton, E. D., Johnson, J. L., Hanekom, W. A., Scriba, T. J., & Seshadri, C. (2022). Durable Expansion of TCR-δ Meta-Clonotypes After BCG Revaccination in Humans. Frontiers in Immunology, 13, 834757. https://doi.org/10.3389/fimmu.2022.834757

Driskill, M., Pardee, K., Hummer, K. E., Zurn, J. D., Amundsen, K., Wiles, A., Wiedow, C., Patzak, J., Henning, J. A., & Bassil, N. V. (2022). Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers. PloS One, 17(4), e0257746. https://doi.org/10.1371/journal.pone.0257746

Willcox, A. C., Sung, K., Garrett, M. E., Galloway, J. G., Erasmus, J. H., Logue, J. K., Hawman, D. W., Chu, H. Y., Hasenkrug, K. J., Fuller, D. H., Matsen Iv, F. A., & Overbaugh, J. (2022). Detailed analysis of antibody responses to SARS-CoV-2 vaccination and infection in macaques. PLoS Pathogens, 18(4), e1010155. https://doi.org/10.1371/journal.ppat.1010155

Oladeinde, A., Abdo, Z., Zwirzitz, B., Woyda, R., Lakin, S. M., Press, M. O., Cox, N. A., Thomas, J. C., Looft, T., Rothrock, M. J., Zock, G., Plumblee Lawrence, J., Cudnik, D., Ritz, C., Aggrey, S. E., Liachko, I., Grove, J. R., & Wiersma, C. (2022). Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens. Applied and Environmental Microbiology, 88(9), e0251721. https://doi.org/10.1128/aem.02517-21

Uppala, J. K., Sathe, L., Chakraborty, A., Bhattacharjee, S., Pulvino, A. T., & Dey, M. (2022). The cap-proximal RNA secondary structure inhibits preinitiation complex formation on HAC1 mRNA. Journal of Biological Chemistry, 298(3). https://doi.org/10.1016/j.jbc.2022.101648

Claridge, S. E., & Hopkins, B. D. (2022). Circling back to PTEN: Fumarate inhibits canonical tumor suppressor. Molecular Cell, 82(7), 1244–1245. https://doi.org/10.1016/j.molcel.2022.03.013

Lee, K.-Y., Seah, C., Li, C., Chen, Y.-F., Chen, C.-Y., Wu, C.-I., Liao, P.-C., Shyu, Y.-C., Olafson, H. R., McKee, K. K., Wang, E. T., Yeh, C.-H., & Wang, C.-H. (2022). Mice lacking MBNL1 and MBNL2 exhibit sudden cardiac death and molecular signatures recapitulating myotonic dystrophy. Human Molecular Genetics, 31(18), 3144–3160. https://doi.org/10.1093/hmg/ddac108

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., Aganezov, S., Hoyt, S. J., Diekhans, M., Logsdon, G. A., Alonge, M., Antonarakis, S. E., Borchers, M., Bouffard, G. G., Brooks, S. Y., … Phillippy, A. M. (2022). The complete sequence of a human genome. Science, 376(6588), 44–53. https://doi.org/10.1126/science.abj6987

Brooks, K. E., Daughtry, B. L., Davis, B., Yan, M. Y., Fei, S. S., Shepherd, S., Carbone, L., & Chavez, S. L. (2022). Molecular contribution to embryonic aneuploidy and karyotypic complexity in initial cleavage divisions of mammalian development. Development (Cambridge, England), 149(7), dev198341. https://doi.org/10.1242/dev.198341

Baek, S., Tran, N. T. T., Diaz, D. C., Tsai, Y.-Y., Acedo, J. N., Lush, M. E., & Piotrowski, T. (2022). Single-cell transcriptome analysis reveals three sequential phases of gene expression during zebrafish sensory hair cell regeneration. Developmental Cell, 57(6), 799-819.e6. https://doi.org/10.1016/j.devcel.2022.03.001

Guan, X., Polesso, F., Wang, C., Sehrawat, A., Hawkins, R. M., Murray, S. E., Thomas, G. V., Caruso, B., Thompson, R. F., Wood, M. A., Hipfinger, C., Hammond, S. A., Graff, J. N., Xia, Z., & Moran, A. E. (2022). Androgen receptor activity in T cells limits checkpoint blockade efficacy. Nature. https://doi.org/10.1038/s41586-022-04522-6

Piening, B. D., Dowdell, A. K., Zhang, M., Loza, B.-L., Walls, D., Gao, H., Mohebnasab, M., Li, Y. R., Elftmann, E., Wei, E., Gandla, D., Lad, H., Chaib, H., Sweitzer, N. K., Deng, M., Pereira, A. C., Cadeiras, M., Shaked, A., Snyder, M. P., & Keating, B. J. (2022). Whole transcriptome profiling of prospective endomyocardial biopsies reveals prognostic and diagnostic signatures of cardiac allograft rejection. The Journal of Heart and Lung Transplantation: The Official Publication of the International Society for Heart Transplantation, 41(6), 840–848. https://doi.org/10.1016/j.healun.2022.01.1377

Ravisankar, S., Murphy, M. J., Redmayne-Titley, N., Davis, B., Luo, F., Takahashi, D., Hennebold, J. D., & Chavez, S. L. (2022). Long-term Hyperandrogenemia and/or Western-style Diet in Rhesus Macaque Females Impairs Preimplantation Embryogenesis. Endocrinology, 163(4), bqac019. https://doi.org/10.1210/endocr/bqac019

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Das, S., Saqib, M., Meng, R. C., Chittur, S. V., Guan, Z., Wan, F., & Sun, W. (2022). Hemochromatosis drives acute lethal intestinal responses to hyperyersiniabactin-producing Yersinia pseudotuberculosis. Proceedings of the National Academy of Sciences, 119(2). https://doi.org/10.1073/pnas.2110166119

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Kaeding, A. J., Barwe, S. P., Gopalakrishnapillai, A., Ries, R. E., Alonzo, T. A., Gerbing, R. B., Correnti, C., Loken, M. R., Broderson, L. E., Pardo, L., Le, Q. H., Tang, T., Leonti, A. R., Smith, J. L., Chou, C. K., Xu, M., Triche, T., Kornblau, S. M., Kolb, E. A., … Meshinchi, S. (2021). Mesothelin is a novel cell surface disease marker and potential therapeutic target in acute myeloid leukemia. Blood Advances, 5(9), 2350–2361. https://doi.org/10.1182/bloodadvances.2021004424

Tarlock, K., Lamble, A. J., Wang, Y.-C., Gerbing, R. B., Ries, R. E., Loken, M. R., Brodersen, L. E., Pardo, L., Leonti, A., Smith, J. L., Hylkema, T. A., Woods, W. G., Cooper, T. M., Kolb, E. A., Gamis, A. S., Aplenc, R., Alonzo, T. A., & Meshinchi, S. (2021). CEBPA-bZip mutations are associated with favorable prognosis in de novo AML: A report from the Children’s Oncology Group. Blood, 138(13), 1137–1147. https://doi.org/10.1182/blood.2020009652

Fuiten, A. M., Fankhauser, R. G., Smit, D. J., Stark, M. S., Enright, T. F., Wood, M. A., DePatie, N. A., Pivik, K., Sturm, R. A., Berry, E. G., & Kulkarni, R. P. (2021). Genetic Analysis of Multiple Primary Melanomas Arising within the Boundaries of Congenital Nevi Depigmentosa. Pigment Cell & Melanoma Research. https://doi.org/10.1111/pcmr.12979

Bubie, A., Zoulim, F., Testoni, B., Miles, B., Posner, M., Villanueva, A., & Losic, B. (2021). Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling. IScience, 24(4), 102368. https://doi.org/10.1016/j.isci.2021.102368

Brown, L. C., Halabi, S., Schonhoft, J. D., Yang, Q., Luo, J., Nanus, D. M., Giannakakou, P., Szmulewitz, R. Z., Danila, D. C., Barnett, E. S., Carbone, E. A., Zhao, J. L., Healy, P., Anand, M., Gill, A., Jendrisak, A., Berry, W. R., Gupta, S., Gregory, S. G., … Armstrong, A. J. (2021). Circulating tumor cell chromosomal instability and neuroendocrine phenotype by immunomorphology and poor outcomes in men with mCRPC treated with abiraterone or enzalutamide. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research. https://doi.org/10.1158/1078-0432.CCR-20-3471

Yu, K. K., Fischinger, S., Smith, M. T., Atyeo, C., Cizmeci, D., Wolf, C. R., Layton, E. D., Logue, J. K., Aguilar, M. S., Shuey, K., Loos, C., Yu, J., Franko, N., Choi, R. Y., Wald, A., Barouch, D. H., Koelle, D. M., Lauffenburger, D., Chu, H. Y., … Seshadri, C. (2021). Comorbid illnesses are associated with altered adaptive immune responses to SARS-CoV-2. JCI Insight, 6(6). https://doi.org/10.1172/jci.insight.146242

Liggett, L. A., Galbraith, M. D., Smith, K. P., Sullivan, K. D., Granrath, R. E., Enriquez-Estrada, B., Kinning, K. T., Shaw, J. R., Rachubinski, A. L., Espinosa, J. M., & DeGregori, J. (2021). Precocious clonal hematopoiesis in Down syndrome is accompanied by immune dysregulation. Blood Advances, 5(7), 1791–1796. https://doi.org/10.1182/bloodadvances.2020003858

Quigg, K. H., Berggren, K. N., McIntyre, M., Bates, K., Salmin, F., Casiraghi, J. L., DʼAmico, A., Astrea, G., Ricci, F., McKay, M. J., Baldwin, J. N., Burns, J., Campbell, C., Sansone, V. A., & Johnson, N. E. (2021). 12-Month progression of motor and functional outcomes in congenital myotonic dystrophy. Muscle & Nerve, 63(3), 384–391. https://doi.org/10.1002/mus.27147

Qiu, Q., Wu, Y., Ma, L., Xu, W., Hills, M., Ramalingam, V., & Yu, C. R. (2021). Acquisition of innate odor preference depends on spontaneous and experiential activities during critical period. ELife, 10, e60546. https://doi.org/10.7554/eLife.60546

Galbraith, M. D., Kinning, K. T., Sullivan, K. D., Baxter, R., Araya, P., Jordan, K. R., Russell, S., Smith, K. P., Granrath, R. E., Shaw, J. R., Dzieciatkowska, M., Ghosh, T., Monte, A. A., D’Alessandro, A., Hansen, K. C., Benett, T. D., Hsieh, E. W., & Espinosa, J. M. (2021). Seroconversion stages COVID19 into distinct pathophysiological states. ELife, 10. https://doi.org/10.7554/eLife.65508

Degnan, D. J., Bramer, L. M., White, A. M., Zhou, M., Bilbao, A., & McCue, L. A. (2021). PSpecteR: A User-Friendly and Interactive Application for Visualizing Top-Down and Bottom-Up Proteomics Data in R. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.0c00857

Yu, K. K., Fischinger, S., Smith, M. T., Atyeo, C., Cizmeci, D., Wolf, C. R., Layton, E. D., Logue, J. K., Aguilar, M. S., Shuey, K., Loos, C., Yu, J., Franko, N. M., Choi, R. Y., Wald, A., Barouch, D. H., Koelle, D. M., Lauffenburger, D., Chu, H. Y., … Seshadri, C. (2021). Comorbid illnesses are associated with altered adaptive immune responses to SARS-CoV-2. JCI Insight. https://doi.org/10.1172/jci.insight.146242

Kundu, P., Torres, E. R. S., Stagaman, K., Kasschau, K., Okhovat, M., Holden, S., Ward, S., Nevonen, K. A., Davis, B. A., Saito, T., Saido, T. C., Carbone, L., Sharpton, T. J., & Raber, J. (2021). Integrated analysis of behavioral, epigenetic, and gut microbiome analyses in AppNL-G-F, AppNL-F, and wild type mice. Scientific Reports, 11(1), 4678. https://doi.org/10.1038/s41598-021-83851-4

Donovan, D. A., Crandall, J. G., Truong, V. N., Vaaler, A. L., Bailey, T. B., Dinwiddie, D., Banks, O. G., McKnight, L. E., & McKnight, J. N. (2021). Basis of specificity for a conserved and promiscuous chromatin remodeling protein. ELife, 10. https://doi.org/10.7554/eLife.64061

Navarro Gonzalez, J., Zweig, A. S., Speir, M. L., Schmelter, D., Rosenbloom, K. R., Raney, B. J., Powell, C. C., Nassar, L. R., Maulding, N. D., Lee, C. M., Lee, B. T., Hinrichs, A. S., Fyfe, A. C., Fernandes, J. D., Diekhans, M., Clawson, H., Casper, J., Benet-Pagès, A., Barber, G. P., … Kent, W. J. (2021). The UCSC Genome Browser database: 2021 update. Nucleic Acids Research, 49(D1), D1046–D1057. https://doi.org/10.1093/nar/gkaa1070

2020

Adrion, J. R., Cole, C. B., Dukler, N., Galloway, J. G., Gladstein, A. L., Gower, G., Kyriazis, C. C., Ragsdale, A. P., Tsambos, G., Baumdicker, F., Carlson, J., Cartwright, R. A., Durvasula, A., Gronau, I., Kim, B. Y., McKenzie, P., Messer, P. W., Noskova, E., Ortega-Del Vecchyo, D., … Kern, A. D. (2020). A community-maintained standard library of population genetic models. ELife, 9, e54967. https://doi.org/10.7554/eLife.54967

Francoeur, C. B., Khadempour, L., Moreira-Soto, R. D., Gotting, K., Book, A. J., Pinto-Tomás, A. A., Keefover-Ring, K., & Currie, C. R. (2020). Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System. MBio, 11(5), e02146-20. https://doi.org/10.1128/mBio.02146-20

Schonhoft, J. D., Zhao, J. L., Jendrisak, A., Carbone, E. A., Barnett, E. S., Hullings, M. A., Gill, A., Sutton, R., Lee, J., Dago, A. E., Landers, M., Bakhoum, S. F., Wang, Y., Gonen, M., Dittamore, R., & Scher, H. I. (2020). Morphology-Predicted Large-Scale Transition Number in Circulating Tumor Cells Identifies a Chromosomal Instability Biomarker Associated with Poor Outcome in Castration-Resistant Prostate Cancer. Cancer Research, 80(22), 4892–4903. https://doi.org/10.1158/0008-5472.CAN-20-1216

Wood, M. A., Weeder, B. R., David, J. K., Nellore, A., & Thompson, R. F. (2020). Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival. Genome Medicine, 12(1), 33. https://doi.org/10.1186/s13073-020-00729-2

Smith, R., Liu, M., Liby, T., Bayani, N., Bucher, E., Chiotti, K., Derrick, D., Chauchereau, A., Heiser, L., Alumkal, J., Feiler, H., Carroll, P., & Korkola, J. E. (2020). Enzalutamide response in a panel of prostate cancer cell lines reveals a role for glucocorticoid receptor in enzalutamide resistant disease. Scientific Reports, 10(1), 21750. https://doi.org/10.1038/s41598-020-78798-x

Harrington, C. A., Fei, S. S., Minnier, J., Carbone, L., Searles, R., Davis, B. A., Ogle, K., Planck, S. R., Rosenbaum, J. T., & Choi, D. (2020). RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method. Scientific Reports, 10(1), 6271. https://doi.org/10.1038/s41598-020-62801-6

Khaing, Z. Z., Cates, L. N., Hyde, J., DeWees, D. M., Hammond, R., Bruce, M., & Hofstetter, C. P. (2020). Contrast-Enhanced Ultrasound for Assessment of Local Hemodynamic Changes Following a Rodent Contusion Spinal Cord Injury. Military Medicine, 185(Suppl 1), 470–475. https://doi.org/10.1093/milmed/usz296

Bubie, A., Gonzalez-Kozlova, E., Akers, N., Villanueva, A., & Losic, B. (2020). Tumor fitness, immune exhaustion and clinical outcomes: Impact of immune checkpoint inhibitors. Scientific Reports, 10(1), 5062. https://doi.org/10.1038/s41598-020-61992-2

Khaing, Z. Z., Cates, L. N., Dewees, D. M., Hyde, J. E., Gaing, A., Birjandian, Z., & Hofstetter, C. P. (2020). The effect of durotomy versus myelotomy on tissue sparing and functional outcome after spinal cord injury. Journal of Neurotrauma. https://doi.org/10.1089/neu.2020.7297

Okhovat, M., Nevonen, K. A., Davis, B. A., Michener, P., Ward, S., Milhaven, M., Harshman, L., Sohota, A., Fernandes, J. D., Salama, S. R., O’Neill, R. J., Ahituv, N., Veeramah, K. R., & Carbone, L. (2020). Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome. Proceedings of the National Academy of Sciences of the United States of America, 117(32), 19328–19338. https://doi.org/10.1073/pnas.2006038117

Burlingame, E. A., McDonnell, M., Schau, G. F., Thibault, G., Lanciault, C., Morgan, T., Johnson, B. E., Corless, C., Gray, J. W., & Chang, Y. H. (2020). SHIFT: Speedy histological-to-immunofluorescent translation of a tumor signature enabled by deep learning. Scientific Reports, 10(1), 17507. https://doi.org/10.1038/s41598-020-74500-3

Fernandes, J. D., Hinrichs, A. S., Clawson, H., Gonzalez, J. N., Lee, B. T., Nassar, L. R., Raney, B. J., Rosenbloom, K. R., Nerli, S., Rao, A. A., Schmelter, D., Fyfe, A., Maulding, N., Zweig, A. S., Lowe, T. M., Ares, M., Corbet-Detig, R., Kent, W. J., Haussler, D., & Haeussler, M. (2020). The UCSC SARS-CoV-2 Genome Browser. Nature Genetics, 52(10), 991–998. https://doi.org/10.1038/s41588-020-0700-8

Kurhanewicz, N. A., Dinwiddie, D., Bush, Z. D., & Libuda, D. E. (2020). Elevated Temperatures Cause Transposon-Associated DNA Damage in C. elegans Spermatocytes. Current Biology: CB, 30(24), 5007-5017.e4. https://doi.org/10.1016/j.cub.2020.09.050

Wells, D. K., van Buuren, M. M., Dang, K. K., Hubbard-Lucey, V. M., Sheehan, K. C. F., Campbell, K. M., Lamb, A., Ward, J. P., Sidney, J., Blazquez, A. B., Rech, A. J., Zaretsky, J. M., Comin-Anduix, B., Ng, A. H. C., Chour, W., Yu, T. V., Rizvi, H., Chen, J. M., Manning, P., … Defranoux, N. A. (2020). Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction. Cell. https://doi.org/10.1016/j.cell.2020.09.015

Hoff, F. W., van Dijk, A. D., Qiu, Y. H., Ruvolo, P. P., Gerbing, R. B., Leonti, A. R., Jenkins, G. N., Gamis, A. S., Aplenc, R., Kolb, E. A., Alonzo, T., Meshinchi, S., De Bont, E., Bruggeman, S. W., Kornblau, S. M., & Horton, T. M. (2020). Heat Shock Factor 1 (HSF1-pSer326) Predicts Response to Bortezomib-Containing Chemotherapy in Pediatric AML: A COG Study. Blood. https://doi.org/10.1182/blood.2020005208

Fernandes, J. D., Hinrichs, A. S., Clawson, H., Gonzalez, J. N., Lee, B. T., Nassar, L. R., Raney, B. J., Rosenbloom, K. R., Nerli, S., Rao, A. A., Schmelter, D., Fyfe, A., Maulding, N., Zweig, A. S., Lowe, T. M., Ares, M., Corbet-Detig, R., Kent, W. J., Haussler, D., & Haeussler, M. (2020). The UCSC SARS-CoV-2 Genome Browser. Nature Genetics. https://doi.org/10.1038/s41588-020-0700-8

Aoi, Y., Smith, E. R., Shah, A. P., Rendleman, E. J., Marshall, S. A., Woodfin, A. R., Chen, F. X., Shiekhattar, R., & Shilatifard, A. (2020). NELF Regulates a Promoter-Proximal Step Distinct from RNA Pol II Pause-Release. Molecular Cell, 78(2), 261-274.e5. https://doi.org/10.1016/j.molcel.2020.02.014

Chang, Y. H., Chin, K., Thibault, G., Eng, J., Burlingame, E., & Gray, J. W. (2020). RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging. Communications Biology, 3(1), 111. https://doi.org/10.1038/s42003-020-0828-1

Fei, S., Harrington, C., Minnier, J., Carbone, L., Searles, R., Davis, B., Ogle, K., Planck, S., Rosenbaum, J. T., & Choi, D. (2020). RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method. (2020). Sci Rep 10, 6271. https://doi.org/10.1038/s41598-020-62801-6

Harris, C. J., Davis, B. A., Zweig, J. A., Nevonen, K. A., Quinn, J. F., Carbone, L., & Gray, N. E. (2020). Age-Associated DNA Methylation Patterns Are Shared Between the Hippocampus and Peripheral Blood Cells. Frontiers in Genetics, 11, 111. https://doi.org/10.3389/fgene.2020.00111

Jorstad, N. L., Wilken, M. S., Todd, L., Finkbeiner, C., Nakamura, P., Radulovich, N., Hooper, M. J., Chitsazan, A., Wilkerson, B. A., Rieke, F., & Reh, T. A. (2020). STAT Signaling Modifies Ascl1 Chromatin Binding and Limits Neural Regeneration from Muller Glia in Adult Mouse Retina. Cell Reports, 30(7), 2195-2208.e5. https://doi.org/10.1016/j.celrep.2020.01.075

Lee, C. M., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., Gonzalez, J. N., Hinrichs, A. S., Lee, B. T., Nassar, L. R., Powell, C. C., Raney, B. J., Rosenbloom, K. R., Schmelter, D., Speir, M. L., Zweig, A. S., Haussler, D., Haeussler, M., Kuhn, R. M., & Kent, W. J. (2020). UCSC Genome Browser enters 20th year. Nucleic Acids Research, 48(D1), D756–D761. https://doi.org/10.1093/nar/gkz1012

Nguyen, A., David, J. K., Maden, S. K., Wood, M. A., Weeder, B. R., Nellore, A., & Thompson, R. F. (2020). Human Leukocyte Antigen Susceptibility Map for Severe Acute Respiratory Syndrome Coronavirus 2. Journal of Virology, 94(13). https://doi.org/10.1128/JVI.00510-20

Okhovat, M., Nevonen, K. A., Davis, B. A., Michener, P., Ward, S., Milhaven, M., Harshman, L., Sohota, A., Fernandes, J. D., Salama, S. R., O’Neill, R. J., Ahituv, N., Veeramah, K. R., & Carbone, L. (2020). Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.2006038117

Pollard, K., Banerjee, J., Doan, X., Wang, J., Guo, X., Allaway, R., Langmead, S., Slobogean, B., Meyer, C. F., Loeb, D. M., Morris, C. D., Belzberg, A. J., Blakeley, J. O., Rodriguez, F. J., Guinney, J., Gosline, S. J. C., & Pratilas, C. A. (2020). A clinically and genomically annotated nerve sheath tumor biospecimen repository. Scientific Data, 7(1), 184. https://doi.org/10.1038/s41597-020-0508-5

Smith, J. L., Ries, R. E., Hylkema, T., Alonzo, T. A., Gerbing, R. B., Santaguida, M. T., Eidenschink Brodersen, L., Pardo, L., Cummings, C. L., Loeb, K. R., Le, Q., Imren, S., Leonti, A. R., Gamis, A. S., Aplenc, R., Kolb, E. A., Farrar, J. E., Triche, T. J., Nguyen, C., … Meshinchi, S. (2020). Comprehensive Transcriptome Profiling of Cryptic CBFA2T3-GLIS2 Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 26(3), 726–737. https://doi.org/10.1158/1078-0432.CCR-19-1800

Smith, J. M., Lathara, M., Wright, H., Hill, B., Ganapati, N., Srinivasa, G., & Denny, C. T. (2020). Advancing clinical cohort selection with genomics analysis on a distributed platform. PloS One, 15(4), e0231826. https://doi.org/10.1371/journal.pone.0231826

Sridhar, A., Hoshino, A., Finkbeiner, C. R., Chitsazan, A., Dai, L., Haugan, A. K., Eschenbacher, K. M., Jackson, D. L., Trapnell, C., Bermingham-McDonogh, O., Glass, I., & Reh, T. A. (2020). Single-Cell Transcriptomic Comparison of Human Fetal Retina, hPSC-Derived Retinal Organoids, and Long-Term Retinal Cultures. Cell Reports, 30(5), 1644-1659.e4. https://doi.org/10.1016/j.celrep.2020.01.007

Tarlock, K., Alonzo, T., Wang, Y.-C., Gerbing, R. B., Ries, R. E., Hylkema, T., Smith, J. L., Maxson, J. E., & Meshinchi, S. (2020). Prognostic impact of CSF3R mutations in favorable risk childhood acute myeloid leukemia. Blood, 135(18), 1603–1606. https://doi.org/10.1182/blood.2019004179

Wagner, A. H., Walsh, B., Mayfield, G., Tamborero, D., Sonkin, D., Krysiak, K., Deu-Pons, J., Duren, R. P., Gao, J., McMurry, J., Patterson, S., Del Vecchio Fitz, C., Pitel, B. A., Sezerman, O. U., Ellrott, K., Warner, J. L., Rieke, D. T., Aittokallio, T., Cerami, E., … Variant Interpretation for Cancer Consortium. (2020). A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nature Genetics, 52(4), 448–457. https://doi.org/10.1038/s41588-020-0603-8

Wood, M. A., Nguyen, A., Struck, A. J., Ellrott, K., Nellore, A., & Thompson, R. F. (2020). Neoepiscope improves neoepitope prediction with multivariant phasing. Bioinformatics (Oxford, England), 36(3), 713–720. https://doi.org/10.1093/bioinformatics/btz653

Wood, M. A., Weeder, B. R., David, J. K., Nellore, A., & Thompson, R. F. (2020). Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival. Genome Medicine, 12(1), 33. https://doi.org/10.1186/s13073-020-00729-2

2019

Braun, T. P., Okhovat, M., Coblentz, C., Carratt, S. A., Foley, A., Schonrock, Z., Smith, B. M., Nevonen, K., Davis, B., Garcia, B., LaTocha, D., Weeder, B. R., Grzadkowski, M. R., Estabrook, J. C., Manning, H. G., Watanabe-Smith, K., Jeng, S., Smith, J. L., Leonti, A. R., … Maxson, J. E. (2019). Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia. Nature Communications, 10(1), 5455. https://doi.org/10.1038/s41467-019-13364-2

Brodsky, O. L., Shek, K. L., Dinwiddie, D., Bruner, S. G., Gill, A. S., Hoch, J. M., Palmer, M. I., & McGuire, K. L. (2019). Microbial Communities in Bioswale Soils and Their Relationships to Soil Properties, Plant Species, and Plant Physiology. Frontiers in Microbiology, 10, 2368. https://doi.org/10.3389/fmicb.2019.02368

Carbone, L., Davis, B. A., Fei, S. S., White, A., Nevonen, K. A., Takahashi, D., Vinson, A., True, C., Roberts, C. T., & Varlamov, O. (2019). Synergistic Effects of Hyperandrogenemia and Obesogenic Western-style Diet on Transcription and DNA Methylation in Visceral Adipose Tissue of Nonhuman Primates. Scientific Reports, 9(1), 19232. https://doi.org/10.1038/s41598-019-55291-8

Chen, Y., Fachko, D., Ivanov, N. S., Skinner, C. M., & Skalsky, R. L. (2019). Epstein-Barr virus microRNAs regulate B cell receptor signal transduction and lytic reactivation. PLoS Pathogens, 15(1), e1007535. https://doi.org/10.1371/journal.ppat.1007535

Coleman, D. J., Gao, L., King, C. J., Schwartzman, J., Urrutia, J., Sehrawat, A., Tayou, J., Balter, A., Burchard, J., Chiotti, K. E., Derrick, D. S., Sun, D., Xia, Z., Heiser, L. M., & Alumkal, J. J. (2019). BET bromodomain inhibition blocks the function of a critical AR-independent master regulator network in lethal prostate cancer. Oncogene, 38(28), 5658–5669. https://doi.org/10.1038/s41388-019-0815-5

Coleman, D. J., Gao, L., Schwartzman, J., Korkola, J. E., Sampson, D., Derrick, D. S., Urrutia, J., Balter, A., Burchard, J., King, C. J., Chiotti, K. E., Heiser, L. M., & Alumkal, J. J. (2019). Maintenance of MYC expression promotes de novo resistance to BET bromodomain inhibition in castration-resistant prostate cancer. Scientific Reports, 9(1), 3823. https://doi.org/10.1038/s41598-019-40518-5

Donovan, D. A., Crandall, J. G., Banks, O. G. B., Jensvold, Z. D., Truong, V., Dinwiddie, D., McKnight, L. E., & McKnight, J. N. (2019). Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning. Cell Reports, 29(8), 2520-2535.e4. https://doi.org/10.1016/j.celrep.2019.10.046

Wang, E. T., Treacy, D., Eichinger, K., Struck, A., Estabrook, J., Olafson, H., Wang, T. T., Bhatt, K., Westbrook, T., Sedehizadeh, S., Ward, A., Day, J., Brook, D., Berglund, J. A., Cooper, T., Housman, D., Thornton, C., & Burge, C. (2019). Transcriptome alterations in myotonic dystrophy skeletal muscle and heart. Human Molecular Genetics, 28(8), 1312–1321. https://doi.org/10.1093/hmg/ddy432

Dropulic, L. K., Oestreich, M. C., Pietz, H. L., Laing, K. J., Hunsberger, S., Lumbard, K., Garabedian, D., Turk, S. P., Chen, A., Hornung, R. L., Seshadri, C., Smith, M. T., Hosken, N. A., Phogat, S., Chang, L.-J., Koelle, D. M., Wang, K., & Cohen, J. I. (2019). A Randomized, Double-Blinded, Placebo-Controlled, Phase 1 Study of a Replication-Defective Herpes Simplex Virus (HSV) Type 2 Vaccine, HSV529, in Adults With or Without HSV Infection. The Journal of Infectious Diseases, 220(6), 990–1000. https://doi.org/10.1093/infdis/jiz225

Hoshino, A., Horvath, S., Sridhar, A., Chitsazan, A., & Reh, T. A. (2019). Synchrony and asynchrony between an epigenetic clock and developmental timing. Scientific Reports, 9(1), 3770. https://doi.org/10.1038/s41598-019-39919-3

Angelbello, A. J., Rzuczek, S. G., Mckee, K. K., Chen, J. L., Olafson, H., Cameron, M. D., Moss, W. N., Wang, E. T., & Disney, M. D. (2019). Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model. Proceedings of the National Academy of Sciences of the United States of America, 116(16), 7799–7804. https://doi.org/10.1073/pnas.1901484116

Braun, T. P., Okhovat, M., Coblentz, C., Carratt, S. A., Foley, A., Schonrock, Z., Curtiss, B. M., Nevonen, K., Davis, B., Garcia, B., LaTocha, D., Weeder, B. R., Grzadkowski, M. R., Estabrook, J. C., Manning, H. G., Watanabe-Smith, K., Jeng, S., Smith, J. L., Leonti, A. R., … Maxson, J. E. (2019). Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia. Nature Communications, 10(1), Article 1. https://doi.org/10.1038/s41467-019-13364-2

Lu, L. L., Smith, M. T., Yu, K. K. Q., Luedemann, C., Suscovich, T. J., Grace, P. S., Cain, A., Yu, W. H., McKitrick, T. R., Lauffenburger, D., Cummings, R. D., Mayanja-Kizza, H., Hawn, T. R., Boom, W. H., Stein, C. M., Fortune, S. M., Seshadri, C., & Alter, G. (2019). IFN-γ-independent immune markers of Mycobacterium tuberculosis exposure. Nature Medicine, 25(6), 977–987. https://doi.org/10.1038/s41591-019-0441-3

Lush, M. E., Diaz, D. C., Koenecke, N., Baek, S., Boldt, H., St Peter, M. K., Gaitan-Escudero, T., Romero-Carvajal, A., Busch-Nentwich, E. M., Perera, A. G., Hall, K. E., Peak, A., Haug, J. S., & Piotrowski, T. (2019). ScRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling. ELife, 8. https://doi.org/10.7554/eLife.44431

Okoye, A. A., DeGottardi, M. Q., Fukazawa, Y., Vaidya, M., Abana, C. O., Konfe, A. L., Fachko, D. N., Duell, D. M., Li, H., Lum, R., Gao, L., Park, B. S., Skalsky, R. L., Lewis, A. D., Axthelm, M. K., Lifson, J. D., Wong, S. W., & Picker, L. J. (2019). Role of IL-15 Signaling in the Pathogenesis of Simian Immunodeficiency Virus Infection in Rhesus Macaques. Journal of Immunology (Baltimore, Md.: 1950), 203(11), 2928–2943. https://doi.org/10.4049/jimmunol.1900792

Raboin, M. J., Letaw, J., Mitchell, A. D., Toffey, D., McKelvey, J., Roberts, C. T., Curran, J. E., & Vinson, A. (2019). Genetic Architecture of Human Obesity Traits in the Rhesus Macaque. Obesity (Silver Spring, Md.), 27(3), 479–488. https://doi.org/10.1002/oby.22392

Tettey, T. T., Gao, X., Shao, W., Li, H., Story, B. A., Chitsazan, A. D., Glaser, R. L., Goode, Z. H., Seidel, C. W., Conaway, R. C., Zeitlinger, J., Blanchette, M., & Conaway, J. W. (2019). A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing. Cell Reports, 27(13), 3770-3779.e7. https://doi.org/10.1016/j.celrep.2019.05.099

Tsujikawa, T., Thibault, G., Azimi, V., Sivagnanam, S., Banik, G., Means, C., Kawashima, R., Clayburgh, D. R., Gray, J. W., Coussens, L. M., & Chang, Y. H. (2019). Robust Cell Detection and Segmentation for Image Cytometry Reveal Th17 Cell Heterogeneity. Cytometry. Part A: The Journal of the International Society for Analytical Cytology, 95(4), 389–398. https://doi.org/10.1002/cyto.a.23726

Wilkerson, B. A., Chitsazan, A. D., VandenBosch, L. S., Wilken, M. S., Reh, T. A., & Bermingham-McDonogh, O. (2019). Open chromatin dynamics in prosensory cells of the embryonic mouse cochlea. Scientific Reports, 9(1), 9060. https://doi.org/10.1038/s41598-019-45515-2

Wood, M. A., Nellore, A., & Thompson, R. F. (2019). Tumor Mutation Burden-From Doubts to Concerns. JAMA Oncology. https://doi.org/10.1001/jamaoncol.2019.4138

Yu, K. K. Q., Wilburn, D. B., Hackney, J. A., Darrah, P. A., Foulds, K. E., James, C. A., Smith, M. T., Jing, L., Seder, R. A., Roederer, M., Koelle, D. M., Swanson, W. J., & Seshadri, C. (2019). Conservation of molecular and cellular phenotypes of invariant NKT cells between humans and non-human primates. Immunogenetics, 71(7), 465–478. https://doi.org/10.1007/s00251-019-01118-9

2018

2017

Morrison, J. A., McLennan, R., Wolfe, L. A., Gogol, M. M., Meier, S., McKinney, M. C., et al. (2017). Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions. eLife, 6, e28415. http://doi.org/10.7554/eLife.28415

Duyck, K., DuTell, V., Ma, L., Paulson, A., & Yu, C. R. (2017). Pronounced strain-specific chemosensory receptor gene expression in the mouse vomeronasal organ. BMC Genomics, 18(1), 965. http://doi.org/10.1186/s12864-017-4364-4

McLennan, R., Bailey, C. M., Schumacher, L. J., Teddy, J. M., Morrison, J. A., Kasemeier-Kulesa, J. C., et al. (2017). DAN (NBL1) promotes collective neural crest migration by restraining uncontrolled invasion. The Journal of Cell Biology, 216(10), 3339–3354. http://doi.org/10.1083/jcb.201612169

Mondo, S. J., Dannebaum, R. O., Kuo, R. C., Louie, K. B., Bewick, A. J., LaButti, K., et al. (2017). Widespread adenine N6-methylation of active genes in fungi. Nature Genetics, 49(6), 964–968. http://doi.org/10.1038/ng.3859

Gopalan, S., Gibbon, D., Seidel, C., Zhang, Y., Florens, L., Washburn, M., et al. (2017). Role of the ELL complex in transcriptional regulation in S. pombe. The FASEB Journal, 31(1 Supplement), 593.12–593.12. http://doi.org/10.1096/fj.1530-6860

Piunti, A., Hashizume, R., Morgan, M. A., Bartom, E. T., Horbinski, C. M., Marshall, S. A., et al. (2017). Therapeutic targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas. Nature Medicine, 23(4), 493–500. http://doi.org/10.1038/nm.4296

Davies, E. L., Lei, K., Seidel, C. W., Kroesen, A. E., McKinney, S. A., Guo, L., et al. (2017). Embryonic origin of adult stem cells required for tissue homeostasis and regeneration. eLife, 6, e21052. http://doi.org/10.7554/eLife.21052

Liang, K., Volk, A. G., Haug, J. S., Marshall, S. A., Woodfin, A. R., Bartom, E. T., et al. (2017). Therapeutic Targeting of MLL Degradation Pathways in MLL-Rearranged Leukemia. Cell, 168(1-2), 59–72.e13. http://doi.org/10.1016/j.cell.2016.12.011

Muerdter, F., Boryń, Ł. M., Woodfin, A. R., Neumayr, C., Rath, M., Zabidi, M. A., et al. (2017). Resolving systematic errors in widely-used enhancer activity assays in human cells enables genome-wide functional enhancer characterization. http://doi.org/10.1101/164590

Kozlovskaja-Gumbrienė, A., Yi, R., Alexander, R., elife, A. A. (2017). Proliferation-independent regulation of organ size by Fgf/Notch signaling. https://doi.org/10.7554/eLife.21049

2016

Xu, J., Xu, F., Letaw, J. H., Park, B. S., Searles, R. P., & Ferguson, B. M. (2016). Anti-Müllerian hormone is produced heterogeneously in primate preantral follicles and is a potential biomarker for follicle growth and oocyte maturation in vitro. Journal of Assisted Reproduction and Genetics, 33(12), 1665–1675. http://doi.org/10.1007/s10815-016-0804-3

Luttrell, S. M., Gotting, K., Ross, E., Alvarado, A. S., & Swalla, B. J. (2016). Head regeneration in hemichordates is not a strict recapitulation of development. Developmental Dynamics : an Official Publication of the American Association of Anatomists, 245(12), 1159–1175. http://doi.org/10.1002/dvdy.24457

Duncan, E. M., Chitsazan, A. D., Seidel, C. W., & Alvarado, A. S. (2016). Set1 and MLL1/2 Target Distinct Sets of Functionally Different Genomic Loci In Vivo. Cell Reports, 17(3), 930. http://doi.org/10.1016/j.celrep.2016.09.071

Bimber, B. N., Raboin, M. J., Letaw, J., Nevonen, K. A., Spindel, J. E., McCouch, S. R., et al. (2016). Whole-genome characterization in pedigreed non-human primates using genotyping-by-sequencing (GBS) and imputation. BMC Genomics, 17(1), 676. http://doi.org/10.1186/s12864-016-2966-x

Lei, K., Thi-Kim Vu, H., Mohan, R. D., McKinney, S. A., Seidel, C. W., Alexander, R., et al. (2016). Egf Signaling Directs Neoblast Repopulation by Regulating Asymmetric Cell Division in Planarians. Developmental Cell, 38(4), 413–429. http://doi.org/10.1016/j.devcel.2016.07.012

Gao, L., Coleman, D. J., King, C. J., Schwartzman, J., Wang, N., Esch, A., et al. (2016). Abstract 4700: BET bromodomain inhibition is a promising treatment strategy for distinct subsets of lethal castration-resistant prostate cancer. Cancer Research, 76(14 Supplement), 4700–4700. http://doi.org/10.1158/1538-7445.AM2016-4700

Rickels, R., Hu, D., Collings, C. K., Woodfin, A. R., Piunti, A., Mohan, M., et al. (2016). An Evolutionary Conserved Epigenetic Mark of Polycomb Response Elements Implemented by Trx/MLL/COMPASS. Molecular Cell, 63(2), 318–328. http://doi.org/10.1016/j.molcel.2016.06.018

Coleman, D. J., Van Hook, K., King, C. J., Schwartzman, J., Lisac, R., Urrutia, J., et al. (2016). Cellular androgen content influences enzalutamide agonism of F877L mutant androgen receptor. Oncotarget, 7(26), 40690–40703. http://doi.org/10.18632/oncotarget.9816

Braasch, I., Gehrke, A. R., Smith, J. J., Kawasaki, K., Manousaki, T., Pasquier, J., et al. (2016). The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics, 48(4), 427–437. http://doi.org/10.1038/ng.3526

Conley, M. N., Wong, C. P., Duyck, K. M., Hord, N., Ho, E., & Sharpton, T. J. (2016). Aging and serum MCP-1 are associated with gut microbiome composition in a murine model. PeerJ, 4, e1854. http://doi.org/10.7717/peerj.1854

2015

Lue, H.-W., Cole, B., Rao, S. A. M., Podalak, J., Gaest, A. V., King, C., et al. (2015). Src and STAT3 inhibitors synergize to promote tumor inhibition in renal cell carcinoma. Oncotarget, 6(42), 44675–44687. http://doi.org/10.18632/oncotarget.5971

Liang, K., Woodfin, A. R., Slaughter, B. D., Unruh, J. R., Box, A. C., Rickels, R. A., et al. (2015). Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis. Molecular Cell, 60(3), 435–445. http://doi.org/10.1016/j.molcel.2015.09.021

Tormey, D., Colbourne, J. K., Mockaitis, K., Choi, J.-H., Lopez, J., Burkhart, J., et al. (2015). Evolutionary divergence of core and post-translational circadian clock genes in the pitcher-plant mosquito, Wyeomyia smithii. BMC Genomics, 16(1), 754. http://doi.org/10.1186/s12864-015-1937-y

Woodward, J., King, C., Coleman, D., Lisac, R., Schwartzman, J., Wang, N., et al. (2015). Abstract 731: Integrative genomic analysis to identify emergent enzalutamide resistance mechanisms in castration-resistant prostate cancer. Cancer Research, 75(15 Supplement), 731–731. http://doi.org/10.1158/1538-7445.AM2015-731

Coleman, D., Van Hook, K., Lisac, R., King, C., Wang, N., Schwartzman, J., et al. (2015). Abstract 3592: Androgens interfere with enzalutamide agonism of mutant F876L androgen receptor. Cancer Research, 75(15 Supplement), 3592–3592. http://doi.org/10.1158/1538-7445.AM2015-3592

Robb, S. M. C., Gotting, K., Ross, E., & Sánchez Alvarado, A. (2015). SmedGD 2.0: The Schmidtea mediterranea genome database. Genesis (New York, N.Y. : 2000), 53(8), 535–546. http://doi.org/10.1002/dvg.22872

Chen, F. X., Woodfin, A. R., Gardini, A., Rickels, R. A., Marshall, S. A., Smith, E. R., et al. (2015). PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II. Cell, 162(5), 1003–1015. http://doi.org/10.1016/j.cell.2015.07.042

Kannan, R., Helston, R. M., Dannebaum, R. O., & Baumann, P. (2015). Diverse mechanisms for spliceosome-mediated 3′ end processing of telomerase RNA. Nature Communications, 6, 6104. http://doi.org/10.1038/ncomms7104

2014

Braasch, I., Guiguen, Y., Loker, R., Letaw, J. H., Ferrara, A., Bobe, J., & Postlethwait, J. H. (2014). Connectivity of vertebrate genomes: Paired-related homeobox (Prrx) genes in spotted gar, basal teleosts, and tetrapods. Comparative Biochemistry and Physiology. Toxicology & Pharmacology : CBP, 163, 24–36. http://doi.org/10.1016/j.cbpc.2014.01.005

Thornton, J. L., Westfield, G. H., Takahashi, Y.-H., Cook, M., Gao, X., Woodfin, A. R., et al. (2014). Context dependency of Set1/COMPASS-mediated histone H3 Lys4 trimethylation. Genes & Development, 28(2), 115–120. http://doi.org/10.1101/gad.232215.113