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Bioinformatics and Genomics Alumni Publications

2022

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. 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, S0301-5629(22)00094-1. https://doi.org/10.1016/j.ultrasmedbio.2022.03.004

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). Mutant-SETBP1 activates transcription of Myc programs to accelerate CSF3R-driven myeloproliferative neoplasms. Blood, blood.2021014777. https://doi.org/10.1182/blood.2021014777

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

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

Páez-Moscoso, D. J., Ho, D. V., Pan, L., Hildebrand, K., Jensen, K. L., Levy, M. J., Florens, L., & Baumann, P. (2022). A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function in telomerase biogenesis. Nature Communications, 13(1), 1067. https://doi.org/10.1038/s41467-022-28545-9

Galbraith, M. D., Kinning, K. T., Sullivan, K. D., Araya, P., Smith, K. P., Granrath, R. E., Shaw, J. R., Baxter, R., Jordan, K. R., Russell, S., Dzieciatkowska, M., Reisz, J. A., Gamboni, F., Cendali, F., Ghosh, T., Guo, K., Wilson, C. C., Santiago, M. L., Monte, A. A., … Espinosa, J. M. (2022). Specialized interferon action in COVID-19. Proceedings of the National Academy of Sciences of the United States of America, 119(11), e2116730119. https://doi.org/10.1073/pnas.2116730119

Claridge, S. E., Cavallo, J.-A., & Hopkins, B. D. (2022). Patient-Derived In Vitro and In Vivo Models of Cancer. Advances in Experimental Medicine and Biology, 1361, 215–233. https://doi.org/10.1007/978-3-030-91836-1_12

Johnson, B. E., Creason, A. L., Stommel, J. M., Keck, J. M., Parmar, S., Betts, C. B., Blucher, A., Boniface, C., Bucher, E., Burlingame, E., Camp, T., Chin, K., Eng, J., Estabrook, J., Feiler, H. S., Heskett, M. B., Hu, Z., Kolodzie, A., Kong, B. L., … Gray, J. W. (2022). An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Reports. Medicine, 3(2), 100525. https://doi.org/10.1016/j.xcrm.2022.100525

Kovalchick, L. V., Bates, K., Statland, J., Weihl, C., Kang, P. B., Lowes, L. P., Mozaffar, T., Straub, V., Wicklund, M., Heatwole, C., & Johnson, N. E. (2022). Patient reported quality of life in limb girdle muscular dystrophy. Neuromuscular Disorders: NMD, 32(1), 57–64. https://doi.org/10.1016/j.nmd.2021.11.002

Sanders, C. K., Hanschen, E. R., Biondi, T. C., Hovde, B. T., Kunde, Y. A., Eng, W. L., Kwon, T., & Dale, T. (2022). Phylogenetic analyses and reclassification of the oleaginous marine species Nannochloris sp. “desiccata” (trebouxiophyceae, chlorophyta), formerly Chlorella desiccata, supported by a high-quality genome assembly. Journal of Phycology. https://doi.org/10.1111/jpy.13242

Schapiro, D., Yapp, C., Sokolov, A., Reynolds, S. M., Chen, Y.-A., Sudar, D., Xie, Y., Muhlich, J., Arias-Camison, R., Arena, S., Taylor, A. J., Nikolov, M., Tyler, M., Lin, J.-R., Burlingame, E. A., Human Tumor Atlas Network, Chang, Y. H., Farhi, S. L., Thorsson, V., … Sorger, P. K. (2022). MITI minimum information guidelines for highly multiplexed tissue images. Nature Methods, 19(3), 262–267. https://doi.org/10.1038/s41592-022-01415-4

Garrett, M. E., Galloway, J. G., Wolf, C., Logue, J. K., Franko, N., Chu, H. Y., Matsen, F. A., & Overbaugh, J. M. (2022). Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection. ELife, 11, e73490. https://doi.org/10.7554/eLife.73490

Benet-Pagès, A., Rosenbloom, K. R., Nassar, L. R., Lee, C. M., Raney, B. J., Clawson, H., Schmelter, D., Casper, J., Gonzalez, J. N., Perez, G., Lee, B. T., Zweig, A. S., Kent, W. J., Haeussler, M., & Kuhn, R. M. (2022). Variant interpretation: UCSC Genome Browser Recommended Track Sets. Human Mutation. https://doi.org/10.1002/humu.24335

Umeda, M., Ma, J., Huang, B. J., Hagiwara, K., Westover, T., Abdelhamed, S., Barajas, J. M., Thomas, M. E., Walsh, M. P., Song, G., Tian, L., Liu, Y., Chen, X., Kolekar, P., Tran, Q., Foy, S. G., Maciaszek, J. L., Kleist, A. B., Leonti, A. R., … Klco, J. M. (2022). Integrated Genomic Analysis Identifies UBTF Tandem Duplications as a Recurrent Lesion in Pediatric Acute Myeloid Leukemia. Blood Cancer Discovery, 3(3), 194–207. https://doi.org/10.1158/2643-3230.BCD-21-0160

Danaher, P., Kim, Y., Nelson, B., Griswold, M., Yang, Z., Piazza, E., & Beechem, J. M. (2022). Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data. Nature Communications, 13(1), 385. https://doi.org/10.1038/s41467-022-28020-5

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

Baumdicker, F., Bisschop, G., Goldstein, D., Gower, G., Ragsdale, A. P., Tsambos, G., Zhu, S., Eldon, B., Ellerman, E. C., Galloway, J. G., Gladstein, A. L., Gorjanc, G., Guo, B., Jeffery, B., Kretzschumar, W. W., Lohse, K., Matschiner, M., Nelson, D., Pope, N. S., … Kelleher, J. (2022). Efficient ancestry and mutation simulation with msprime 1.0. Genetics, 220(3), iyab229. https://doi.org/10.1093/genetics/iyab229

2021

Peterson, T. C., Lechtenberg, K. J., Piening, B. D., Lucas, T. A., Wei, E., Chaib, H., Dowdell, A. K., Snyder, M., & Buckwalter, M. S. (2021). Obesity Drives Delayed Infarct Expansion, Inflammation, and Distinct Gene Networks in a Mouse Stroke Model. Translational Stroke Research, 12(2), 331–346. https://doi.org/10.1007/s12975-020-00826-9

Martin, P. J., Levine, D. M., Storer, B. E., Zheng, X., Jain, D., Heavner, B., Norris, B. M., Geraghty, D. E., Spellman, S. R., Sather, C. L., Wu, F., & Hansen, J. A. (2021). A Model of Minor Histocompatibility Antigens in Allogeneic Hematopoietic Cell Transplantation. Frontiers in Immunology, 12, 782152. https://doi.org/10.3389/fimmu.2021.782152

CSBC/PS-ON Image Analysis Working Group, Vizcarra, J. C., Burlingame, E. A., Hug, C. B., Goltsev, Y., White, B. S., Tyson, D. R., & Sokolov, A. (2021). A community-based approach to image analysis of cells, tissues and tumors. Computerized Medical Imaging and Graphics: The Official Journal of the Computerized Medical Imaging Society, 95, 102013. https://doi.org/10.1016/j.compmedimag.2021.102013

Bolouri, H., Ries, R., Pardo, L., Hylkema, T., Zhou, W., Smith, J. L., Leonti, A., Loken, M., Farrar, J. E., Triche, T. J., & Meshinchi, S. (2021). A B-cell developmental gene regulatory network is activated in infant AML. PloS One, 16(11), e0259197. https://doi.org/10.1371/journal.pone.0259197

Leung, K. L., Sanchita, S., Pham, C. T., Davis, B. A., Okhovat, M., Ding, X., Dumesic, P., Grogan, T. R., Williams, K. J., Morselli, M., Ma, F., Carbone, L., Li, X., Pellegrini, M., Dumesic, D. A., & Chazenbalk, G. D. (2020). Dynamic changes in chromatin accessibility, altered adipogenic gene expression, and total versus de novo fatty acid synthesis in subcutaneous adipose stem cells of normal-weight polycystic ovary syndrome (PCOS) women during adipogenesis: Evidence of cellular programming. Clinical Epigenetics, 12(1), 181. https://doi.org/10.1186/s13148-020-00970-x

Connerty, P., Moles, E., de Bock, C. E., Jayatilleke, N., Smith, J. L., Meshinchi, S., Mayoh, C., Kavallaris, M., & Lock, R. B. (2021). Development of siRNA-Loaded Lipid Nanoparticles Targeting Long Non-Coding RNA LINC01257 as a Novel and Safe Therapeutic Approach for t(8;21) Pediatric Acute Myeloid Leukemia. Pharmaceutics, 13(10), 1681. https://doi.org/10.3390/pharmaceutics13101681

Lee, B. T., Barber, G. P., Benet-Pagès, A., Casper, J., Clawson, H., Diekhans, M., Fischer, C., Gonzalez, J. N., Hinrichs, A. S., Lee, C. M., Muthuraman, P., Nassar, L. R., Nguy, B., Pereira, T., Perez, G., Raney, B. J., Rosenbloom, K. R., Schmelter, D., Speir, M. L., … Kent, W. J. (2021). The UCSC Genome Browser database: 2022 update. Nucleic Acids Research, gkab959. https://doi.org/10.1093/nar/gkab959

Itell, H. L., Weight, H., Fish, C. S., Logue, J. K., Franko, N., Wolf, C. R., McCulloch, D. J., Galloway, J., Matsen, F. A., Chu, H. Y., & Overbaugh, J. (2021). SARS-CoV-2 Antibody Binding and Neutralization in Dried Blood Spot Eluates and Paired Plasma. Microbiology Spectrum, e0129821. https://doi.org/10.1128/Spectrum.01298-21

He, Y., Sato, S., Tomomori-Sato, C., Chen, S., Goode, Z. H., Conaway, J. W., & Conaway, R. C. (2021). Elongin functions as a loading factor for Mediator at ATF6α-regulated ER stress response genes. Proceedings of the National Academy of Sciences of the United States of America, 118(39), e2108751118. https://doi.org/10.1073/pnas.2108751118

Huang, B. J., Smith, J. L., Wang, Y.-C., Taghizadeh, K., Leonti, A. R., Ries, R. E., Liu, Y., Kolekar, P., Tarlock, K., Gerbing, R., Crowgey, E., Furlan, S. N., Shaw, T. I., Hagiwara, K., Wei, L., Cooper, T. M., Gamis, A. S., Aplenc, R., Kolb, E. A., … Meshinchi, S. (2021). CBFB-MYH11 fusion transcripts distinguish acute myeloid leukemias with distinct molecular landscapes and outcomes. Blood Advances, 5(23), 4963–4968. https://doi.org/10.1182/bloodadvances.2021004965

Graff, J. N., Beer, T. M., Alumkal, J. J., Slottke, R. E., Redmond, W. L., Thomas, G. V., Thompson, R. F., Wood, M. A., Koguchi, Y., Chen, Y., Latour, E., Bergan, R. C., Drake, C. G., & Moran, A. E. (2020). A phase II single-arm study of pembrolizumab with enzalutamide in men with metastatic castration-resistant prostate cancer progressing on enzalutamide alone. Journal for Immunotherapy of Cancer, 8(2), e000642. https://doi.org/10.1136/jitc-2020-000642

Burlingame, E. A., Eng, J., Thibault, G., Chin, K., Gray, J. W., & Chang, Y. H. (2021). Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms. Cell Reports Methods, 1(4), 100053. https://doi.org/10.1016/j.crmeth.2021.100053

Gordon, N. S., Baxter, L. A., Goel, A., Arnold, R., Kaur, B., Liu, W., Pirrie, S. J., Hussain, S., Viney, R., Ford, D., Zarkar, A., Wood, M. A., Mitin, T., Thompson, R. F., James, N. D., Ward, D. G., & Bryan, R. T. (2022). Urine DNA for monitoring chemoradiotherapy response in muscle-invasive bladder cancer: A pilot study. BJU International, 129(1), 32–34. https://doi.org/10.1111/bju.15589

Benham-Pyle, B. W., Brewster, C. E., Kent, A. M., Mann, F. G., Chen, S., Scott, A. R., Box, A. C., & Sánchez Alvarado, A. (2021). Identification of rare, transient post-mitotic cell states that are induced by injury and required for whole-body regeneration in Schmidtea mediterranea. Nature Cell Biology. https://doi.org/10.1038/s41556-021-00734-6

Weeder, B. R., Wood, M. A., Li, E., Nellore, A., & Thompson, R. F. (2021). Pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification. Bioinformatics (Oxford, England), btab628. https://doi.org/10.1093/bioinformatics/btab628

Benham-Pyle, B. W., Brewster, C. E., Kent, A. M., Mann, F. G., Chen, S., Scott, A. R., Box, A. C., & Sánchez Alvarado, A. (2021). Identification of rare, transient post-mitotic cell states that are induced by injury and required for whole-body regeneration in Schmidtea mediterranea. Nature Cell Biology, 1–14. https://doi.org/10.1038/s41556-021-00734-6

Johnson, S. A., Seale, S. L., Gittelman, R. M., Rytlewski, J. A., Robins, H. S., & Fields, P. A. (2021). Impact of HLA type, age and chronic viral infection on peripheral T-cell receptor sharing between unrelated individuals. PLOS ONE, 16(8), e0249484. https://doi.org/10.1371/journal.pone.0249484

Mitchell, J. M., Sucharov, J., Pulvino, A. T., Brooks, E. P., Gillen, A. E., & Nichols, J. T. (2021). The alx3 gene shapes the zebrafish neurocranium by regulating frontonasal neural crest cell differentiation timing. Development (Cambridge, England), 148(7), dev197483. https://doi.org/10.1242/dev.197483

Schenning, K. J., Holden, S., Davis, B. A., Mulford, A., Nevonen, K. A., Quinn, J. F., Raber, J., Carbone, L., & Alkayed, N. J. (2021). Gene-Specific DNA Methylation Linked to Postoperative Cognitive Dysfunction in Apolipoprotein E3 and E4 Mice. Journal of Alzheimer’s Disease: JAD, 83(3), 1251–1268. https://doi.org/10.3233/JAD-210499

Sullivan, K. D., Galbraith, M. D., Kinning, K. T., Bartsch, K. W., Levinsky, N. C., Araya, P., Smith, K. P., Granrath, R. E., Shaw, J. R., Baxter, R. M., Jordan, K. R., Russell, S. A., Dzieciatkowska, M. E., Reisz, J. A., Gamboni, F., Cendali, F. I., Ghosh, T., Monte, A. A., Bennett, T. D., … Espinosa, J. M. (2021). The COVIDome Explorer researcher portal. Cell Reports, 36(7), 109527. https://doi.org/10.1016/j.celrep.2021.109527

Layton, E. D., Barman, S., Wilburn, D. B., Yu, K. K. Q., Smith, M. T., Altman, J. D., Scriba, T. J., Tahiri, N., Minnaard, A. J., Roederer, M., Seder, R. A., Darrah, P. A., & Seshadri, C. (2021). T Cells Specific for a Mycobacterial Glycolipid Expand after Intravenous Bacillus Calmette-Guérin Vaccination. Journal of Immunology (Baltimore, Md.: 1950), 206(6), 1240–1250. https://doi.org/10.4049/jimmunol.2001065

Turkarslan, S., Stopnisek, N., Thompson, A. W., Arens, C. E., Valenzuela, J. J., Wilson, J., Hunt, K. A., Hardwicke, J., de Lomana, A. L. G., Lim, S., Seah, Y. M., Fu, Y., Wu, L., Zhou, J., Hillesland, K. L., Stahl, D. A., & Baliga, N. S. (2021). Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions. The ISME Journal, 15(8), 2233–2247. https://doi.org/10.1038/s41396-021-00919-9

Wang, S. V., Kulldorff, M., Poor, S., Rice, D. S., Banks, A., Li, N., Lii, J., & Gagne, J. J. (2021). Screening Medications for Association with Progression to Wet Age-Related Macular Degeneration. Ophthalmology, 128(2), 248–255. https://doi.org/10.1016/j.ophtha.2020.08.004

Hunt, K. A., Forbes, J., Taub, F., Elliott, N., Hardwicke, J., Petersen, R., Stopnisek, N., Beck, D. A. C., & Stahl, D. A. (2021). An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates. Journal of Microbiological Methods, 188, 106294. https://doi.org/10.1016/j.mimet.2021.106294

Olson, B., Zhu, X., Norgard, M. A., Diba, P., Levasseur, P. R., Buenafe, A. C., Huisman, C., Burfeind, K. G., Michaelis, K. A., Kong, G., Braun, T., & Marks, D. L. (2021). Chronic cerebral lipocalin 2 exposure elicits hippocampal neuronal dysfunction and cognitive impairment. Brain, Behavior, and Immunity, 97, 102–118. https://doi.org/10.1016/j.bbi.2021.07.002

Dietz, M. S., Sutton, T. L., Walker, B. S., Gast, C. E., Zarour, L., Sengupta, S. K., Swain, J. R., Eng, J., Parappilly, M., Limbach, K., Sattler, A., Burlingame, E., Chin, Y., Gower, A., Mira, J. L. M., Sapre, A., Chiu, Y.-J., Clayburgh, D. R., Pommier, S. J., … Wong, M. H. (2021). Relevance of circulating hybrid cells as a non-invasive biomarker for myriad solid tumors. Scientific Reports, 11(1), 13630. https://doi.org/10.1038/s41598-021-93053-7

Zurn, J. D., Driskill, M., Jung, S., Main, D., Yin, M. H., Clark, M. C., Cheng, L., Ashrafi, H., Aryal, R., Clark, J. R., Worthington, M., Finn, C. E., Peace, C., Iezzoni, A., & Bassil, N. (2020). A Rosaceae Family-Level Approach To Identify Loci Influencing Soluble Solids Content in Blackberry for DNA-Informed Breeding. G3 (Bethesda, Md.), 10(10), 3729–3740. https://doi.org/10.1534/g3.120.401449

Lue, H.-W., Derrick, D. S., Rao, S., Van Gaest, A., Cheng, L., Podolak, J., Lawson, S., Xue, C., Garg, D., White, R., Ryan, C. W., Drake, J. M., Ritz, A., Heiser, L. M., & Thomas, G. V. (2021). Cabozantinib and dasatinib synergize to induce tumor regression in non-clear cell renal cell carcinoma. Cell Reports. Medicine, 2(5), 100267. https://doi.org/10.1016/j.xcrm.2021.100267

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, 183(3), 818-834.e13. https://doi.org/10.1016/j.cell.2020.09.015

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

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

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

Arnold, C. D., Nemčko, F., Woodfin, A. R., Wienerroither, S., Vlasova, A., Schleiffer, A., Pagani, M., Rath, M., & Stark, A. (2018). A high-throughput method to identify trans-activation domains within transcription factor sequences. The EMBO Journal, 37(16). https://doi.org/10.15252/embj.201798896

Burlingame, E. A., Margolin, A. A., Gray, J. W., & Chang, Y. H. (2018). SHIFT: Speedy histopathological-to-immunofluorescent translation of whole slide images using conditional generative adversarial networks. Proceedings of SPIE–the International Society for Optical Engineering, 10581. https://doi.org/10.1117/12.2293249

Gopalan, S., Gibbon, D. M., Banks, C. A., Zhang, Y., Florens, L. A., Washburn, M. P., Dabas, P., Sharma, N., Seidel, C. W., Conaway, R. C., & Conaway, J. W. (2018). Schizosaccharomyces pombe Pol II transcription elongation factor ELL functions as part of a rudimentary super elongation complex. Nucleic Acids Research, 46(19), 10095–10105. https://doi.org/10.1093/nar/gky713

Guo, J., Wilken, S., Jimenez, V., Choi, C. J., Ansong, C., Dannebaum, R., Sudek, L., Milner, D. S., Bachy, C., Reistetter, E. N., Elrod, V. A., Klimov, D., Purvine, S. O., Wei, C.-L., Kunde-Ramamoorthy, G., Richards, T. A., Goodenough, U., Smith, R. D., Callister, S. J., & Worden, A. Z. (2018). Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation. Nature Microbiology, 3(7), 781–790. https://doi.org/10.1038/s41564-018-0178-7

Haddad, J. F., Yang, Y., Takahashi, Y.-H., Joshi, M., Chaudhary, N., Woodfin, A. R., Benyoucef, A., Yeung, S., Brunzelle, J. S., Skiniotis, G., Brand, M., Shilatifard, A., & Couture, J.-F. (2018). Structural Analysis of the Ash2L/Dpy-30 Complex Reveals a Heterogeneity in H3K4 Methylation. Structure (London, England: 1993), 26(12), 1594-1603.e4. https://doi.org/10.1016/j.str.2018.08.004

Kasemeier-Kulesa, J. C., Schnell, S., Woolley, T., Spengler, J. A., Morrison, J. A., McKinney, M. C., Pushel, I., Wolfe, L. A., & Kulesa, P. M. (2018). Predicting neuroblastoma using developmental signals and a logic-based model. Biophysical Chemistry, 238, 30–38. https://doi.org/10.1016/j.bpc.2018.04.004

Khaing, Z. Z., Cates, L. N., DeWees, D. M., Hannah, A., Mourad, P., Bruce, M., & Hofstetter, C. P. (2018). Contrast-enhanced ultrasound to visualize hemodynamic changes after rodent spinal cord injury. Journal of Neurosurgery. Spine, 29(3), 306–313. https://doi.org/10.3171/2018.1.SPINE171202

Layton, E. D., Yu, K. K. Q., Smith, M. T., Scriba, T. J., De Rosa, S. C., & Seshadri, C. (2018). Validation of a CD1b tetramer assay for studies of human mycobacterial infection or vaccination. Journal of Immunological Methods, 458, 44–52. https://doi.org/10.1016/j.jim.2018.04.004

Liang, K., Smith, E. R., Aoi, Y., Stoltz, K. L., Katagi, H., Woodfin, A. R., Rendleman, E. J., Marshall, S. A., Murray, D. C., Wang, L., Ozark, P. A., Mishra, R. K., Hashizume, R., Schiltz, G. E., & Shilatifard, A. (2018). Targeting Processive Transcription Elongation via SEC Disruption for MYC-Induced Cancer Therapy. Cell, 175(3), 766-779.e17. https://doi.org/10.1016/j.cell.2018.09.027

Muerdter, F., Boryń, Ł. M., Woodfin, A. R., Neumayr, C., Rath, M., Zabidi, M. A., Pagani, M., Haberle, V., Kazmar, T., Catarino, R. R., Schernhuber, K., Arnold, C. D., & Stark, A. (2018). Resolving systematic errors in widely used enhancer activity assays in human cells. Nature Methods, 15(2), 141–149. https://doi.org/10.1038/nmeth.4534

Noort, S., Zimmermann, M., Reinhardt, D., Cuccuini, W., Pigazzi, M., Smith, J., Ries, R. E., Alonzo, T. A., Hirsch, B., Tomizawa, D., Locatelli, F., Gruber, T. A., Raimondi, S., Sonneveld, E., Cheuk, D. K., Dworzak, M., Stary, J., Abrahamsson, J., Arad-Cohen, N., … Zwaan, C. M. (2018). Prognostic impact of t(16;21)(p11;q22) and t(16;21)(q24;q22) in pediatric AML: A retrospective study by the I-BFM Study Group. Blood, 132(15), 1584–1592. https://doi.org/10.1182/blood-2018-05-849059

Páez-Moscoso, D. J., Pan, L., Sigauke, R. F., Schroeder, M. R., Tang, W., & Baumann, P. (2018). Pof8 is a La-related protein and a constitutive component of telomerase in fission yeast. Nature Communications, 9(1), 587. https://doi.org/10.1038/s41467-017-02284-8

Sehrawat, A., Gao, L., Wang, Y., Bankhead, A., McWeeney, S. K., King, C. J., Schwartzman, J., Urrutia, J., Bisson, W. H., Coleman, D. J., Joshi, S. K., Kim, D.-H., Sampson, D. A., Weinmann, S., Kallakury, B. V. S., Berry, D. L., Haque, R., Van Den Eeden, S. K., Sharma, S., … Alumkal, J. J. (2018). LSD1 activates a lethal prostate cancer gene network independently of its demethylase function. Proceedings of the National Academy of Sciences of the United States of America, 115(18), E4179–E4188. https://doi.org/10.1073/pnas.1719168115

Sluch, V. M., Banks, A., Li, H., Crowley, M. A., Davis, V., Xiang, C., Yang, J., Demirs, J. T., Vrouvlianis, J., Leehy, B., Hanks, S., Hyman, A. M., Aranda, J., Chang, B., Bigelow, C. E., & Rice, D. S. (2018). ADIPOR1 is essential for vision and its RPE expression is lost in the Mfrprd6 mouse. Scientific Reports, 8(1), 14339. https://doi.org/10.1038/s41598-018-32579-9

Tseng, C.-K., Wang, H.-F., Schroeder, M. R., & Baumann, P. (2018). The H/ACA complex disrupts triplex in hTR precursor to permit processing by RRP6 and PARN. Nature Communications, 9(1), 5430. https://doi.org/10.1038/s41467-018-07822-6

Wood, M. A., Paralkar, M., Paralkar, M. P., Nguyen, A., Struck, A. J., Ellrott, K., Margolin, A., Nellore, A., & Thompson, R. F. (2018). Population-level distribution and putative immunogenicity of cancer neoepitopes. BMC Cancer, 18(1), 414. https://doi.org/10.1186/s12885-018-4325-6

Wu, Y., Ma, L., Duyck, K., Long, C. C., Moran, A., Scheerer, H., Blanck, J., Peak, A., Box, A., Perera, A., & Yu, C. R. (2018). A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period. Neuron, 100(5), 1066-1082.e6. https://doi.org/10.1016/j.neuron.2018.09.051

2017

Azimi, V., Chang, Y. H., Thibault, G., Smith, J., Tsujikawa, T., Kukull, B., Jensen, B., Corless, C., Margolin, A., & Gray, J. W. (2017). BREAST CANCER HISTOPATHOLOGY IMAGE ANALYSIS PIPELINE FOR TUMOR PURITY ESTIMATION. Proceedings. IEEE International Symposium on Biomedical Imaging, 2017, 1137–1140. https://doi.org/10.1109/ISBI.2017.7950717

King, C. J., Woodward, J., Schwartzman, J., Coleman, D. J., Lisac, R., Wang, N. J., Van Hook, K., Gao, L., Urrutia, J., Dane, M. A., Heiser, L. M., & Alumkal, J. J. (2017). Integrative molecular network analysis identifies emergent enzalutamide resistance mechanisms in prostate cancer. Oncotarget, 8(67), 111084–111095. https://doi.org/10.18632/oncotarget.22560

Rudra, P., Shi, W. J., Vestal, B., Russell, P. H., Odell, A., Dowell, R. D., Radcliffe, R. A., Saba, L. M., & Kechris, K. (2017). Model based heritability scores for high-throughput sequencing data. BMC Bioinformatics, 18(1), 143. https://doi.org/10.1186/s12859-017-1539-6

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