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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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
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.
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-
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.
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.
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.
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.
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-
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.
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.
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-
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.
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-
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.
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/
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.
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/
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.
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-
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-
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-
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.
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.
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/
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.
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.