2023

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Stamp, J., DenAdel, A., Weinreich, D., & Crawford, L. (2023). Leveraging the Genetic Correlation between Traits Improves the Detection of Epistasis in Genome-wide Association Studies. G3 (Bethesda, Md.), jkad118. https://doi.org/10.1093/g3journal/jkad118

Degnan, D. J., Bramer, L. M., Flores, J. E., Paurus, V. L., Corilo, Y. E., & Clendinen, C. S. (2023). Evaluating Retention Index Score Assumptions to Refine GC-MS Metabolite Identification. Analytical Chemistry, 95(19), 7536–7544. https://doi.org/10.1021/acs.analchem.2c05783

Robinson, A., Babinski, M., Xu, Y., Kelliher, J., Longley, R., & Chain, P. (2023). A centralized resource for bacterial-fungal interactions research. Fungal Biology, 127(5), 1005–1009. https://doi.org/10.1016/j.funbio.2023.04.002

Hale, M. A., Bates, K., Provenzano, M., & Johnson, N. E. (2023). Dynamics and variability of transcriptomic dysregulation in congenital myotonic dystrophy during pediatric development. Human Molecular Genetics, 32(9), 1413–1428. https://doi.org/10.1093/hmg/ddac254

Flores, J. E., Bramer, L. M., Degnan, D. J., Paurus, V. L., Corilo, Y. E., & Clendinen, C. S. (2023). Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics. Journal of the American Society for Mass Spectrometry. https://doi.org/10.1021/jasms.3c00039

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), 37(21), 3723–3733. https://doi.org/10.1093/bioinformatics/btab628

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Prasse, T., Khaing, Z. Z., Cates, L. N., Dewees, D. M., Hyde, J. E., Bredow, J., & Hofstetter, C. P. (2023). A decrease in the neuroprotective effects of acute spinal cord decompression according to injury severity: Introducing the concept of a ceiling effect. Journal of Neurosurgery. Spine, 38(3), 299–306. https://doi.org/10.3171/2022.6.SPINE22383

Couvillion, S. P., Danczak, R. E., Naylor, D., Smith, M. L., Stratton, K. G., Paurus, V. L., Bloodsworth, K. J., Farris, Y., Schmidt, D. J., Richardson, R. E., Bramer, L. M., Fansler, S. J., Nakayasu, E. S., McDermott, J. E., Metz, T. O., Lipton, M. S., Jansson, J. K., & Hofmockel, K. S. (2023). Rapid remodeling of the soil lipidome in response to a drying-rewetting event. Microbiome, 11(1), 34. https://doi.org/10.1186/s40168-022-01427-4

Liao, Y.-C., Fulcher, J. M., Degnan, D. J., Williams, S. M., Bramer, L. M., Veličković, D., Zemaitis, K. J., Veličković, M., Sontag, R., Moore, R. J., Paša-Tolić, L., Zhu, Y., & Zhou, M. (2023). Spatially resolved top-down proteomics of tissue sections based on a microfluidic nanodroplet sample preparation platform. Molecular & Cellular Proteomics: MCP, 100491. https://doi.org/10.1016/j.mcpro.2022.100491

Bertrums, E. J. M., Smith, J. L., Harmon, L., Ries, R. E., Wang, Y.-C. J., Alonzo, T. A., Menssen, A. J., Chisholm, K. M., Leonti, A. R., Tarlock, K., Ostronoff, F., Pogosova-Agadjanyan, E. L., Kaspers, G. J. L., Hasle, H., Dworzak, M., Walter, C., Muhlegger, N., Morerio, C., Pardo, L., … Meshinchi, S. (2023). Comprehensive molecular and clinical characterization of NUP98 fusions in pediatric acute myeloid leukemia. Haematologica. https://doi.org/10.3324/haematol.2022.281653

Massaquoi, M. S., Kong, G. L., Chilin-Fuentes, D., Ngo, J. S., Horve, P. F., Melancon, E., Hamilton, M. K., Eisen, J. S., & Guillemin, K. (2023). Cell-type-specific responses to the microbiota across all tissues of the larval zebrafish. Cell Reports, 42(2), 112095. https://doi.org/10.1016/j.celrep.2023.112095

Farrar, J. E., Smith, J. L., Othus, M., Huang, B. J., Wang, Y.-C., Ries, R., Hylkema, T., Pogosova-Agadjanyan, E. L., Challa, S., Leonti, A., Shaw, T. I., Triche, T. J., Gamis, A. S., Aplenc, R., Kolb, E. A., Ma, X., Stirewalt, D. L., Alonzo, T. A., & Meshinchi, S. (2023). Long Noncoding RNA Expression Independently Predicts Outcome in Pediatric Acute Myeloid Leukemia. Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology, 41(16), 2949–2962. https://doi.org/10.1200/JCO.22.01114

Braun, T. P., Estabrook, J., Schonrock, Z., Curtiss, B. M., Darmusey, L., Macaraeg, J., Enright, T., Coblentz, C., Callahan, R., Yashar, W., Taherinasab, A., Mohammed, H., Coleman, D. J., Druker, B. J., Demir, E., Lusardi, T. A., & Maxson, J. E. (2023). Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors. Leukemia, 37(2), 478–487. https://doi.org/10.1038/s41375-022-01792-x

Hayat, A., Carter, E. P., King, H. W., Ors, A., Doe, A., Teijeiro, S. A., Charrot, S., Godinho, S., Cutillas, P., Mohammed, H., Grose, R. P., & Ficz, G. (2023). Low HER2 expression in normal breast epithelium enables dedifferentiation and malignant transformation via chromatin opening. Disease Models & Mechanisms, 16(2), dmm049894. https://doi.org/10.1242/dmm.049894

Le, Q. H., Tang, T., Leonti, A. R., Castro, S. K., McKay, C. N., Perkins, L., Pardo, L., Kirkey, D. C., Hylkema, T., Call, L., Manselle, M., Abrahams, C., Bedard, K., Molina, A., Eidenschink Brodersen, L., Loken, M. R., Tarlock, K., Meshinchi, S., & Loeb, K. R. (2023). Preclinical studies targeting CD74 with STRO-001 antibody-drug conjugate in acute leukemia. Blood Advances, bloodadvances.2022008303. https://doi.org/10.1182/bloodadvances.2022008303

Crowley, M. A., Garland, D. L., Sellner, H., Banks, A., Fan, L., Rejtar, T., Buchanan, N., Delgado, O., Xu, Y. Y., Jose, S., Adams, C. M., Mogi, M., Wang, K., Bigelow, C. E., Poor, S., Anderson, K., Jaffee, B. D., Prasanna, G., Grosskreutz, C., … Liao, S.-M. (2023). Complement factor B is critical for sub-RPE deposit accumulation in a model of Doyne honeycomb retinal dystrophy with features of age-related macular degeneration. Human Molecular Genetics, 32(2), 204–217. https://doi.org/10.1093/hmg/ddac187

Degnan, D. J., Stratton, K. G., Richardson, R., Claborne, D., Martin, E. A., Johnson, N. A., Leach, D., Webb-Robertson, B.-J. M., & Bramer, L. M. (2023). pmartR 2.0: A Quality Control, Visualization, and Statistics Pipeline for Multiple Omics Datatypes. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00610

van Lengerich, B., Zhan, L., Xia, D., Chan, D., Joy, D., Park, J. I., Tatarakis, D., Calvert, M., Hummel, S., Lianoglou, S., Pizzo, M. E., Prorok, R., Thomsen, E., Bartos, L. M., Beumers, P., Capell, A., Davis, S. S., de Weerd, L., Dugas, J. C., … Monroe, K. M. (2023). A TREM2-activating antibody with a blood-brain barrier transport vehicle enhances microglial metabolism in Alzheimer’s disease models. Nature Neuroscience, 26(3), 416–429. https://doi.org/10.1038/s41593-022-01240-0

Nassar, L. R., Barber, G. P., Benet-Pagès, A., Casper, J., Clawson, H., Diekhans, M., Fischer, C., Gonzalez, J. N., Hinrichs, A. S., Lee, B. T., Lee, C. M., Muthuraman, P., Nguy, B., Pereira, T., Nejad, P., Perez, G., Raney, B. J., Schmelter, D., Speir, M. L., … Kent, W. J. (2023). The UCSC Genome Browser database: 2023 update. Nucleic Acids Research, 51(D1), D1188–D1195. https://doi.org/10.1093/nar/gkac1072

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2022

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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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

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