2024
2023
2022
Riley, L. A., Zhang, X., Douglas, C. M., Mijares, J. M., Hammers, D. W., Wolff, C. A., Wood, N. B., Olafson, H. R., Du, P., Labeit, S., Previs, M. J., Wang, E. T., & Esser, K. A. (2022). The skeletal muscle circadian clock regulates titin splicing through RBM20. eLife, 11, e76478. https://doi.org/10.7554/eLife.76478
Raj, R., Dahlen, D., Duyck, K., & Yu, C. R. (2022). Maximal Dependence Capturing as a Principle of Sensory Processing. Frontiers in Computational Neuroscience, 16, 857653. https://doi.org/10.3389/fncom.2022.857653
Mighell, T. L., Nishida, A., O’Connell, B. L., Miller, C. V., Grindstaff, S., Thornton, C. A., Adey, A. C., Doherty, D., & O’Roak, B. J. (2022). Cas12a-Capture: A Novel, Low-Cost, and Scalable Method for Targeted Sequencing. The CRISPR Journal, 5(4), 548–557. https://doi.org/10.1089/crispr.2021.0140
Co, M., Barnard, R. A., Jahncke, J. N., Grindstaff, S., Fedorov, L. M., Adey, A. C., Wright, K. M., & O’Roak, B. J. (2022). Shared and Distinct Functional Effects of Patient-Specific Tbr1 Mutations on Cortical Development. The Journal of Neuroscience: The Official Journal of the Society for Neuroscience, 42(37), 7166–7181. https://doi.org/10.1523/JNEUROSCI.0409-22.2022
Sun, B. B., Kurki, M. I., Foley, C. N., Mechakra, A., Chen, C.-Y., Marshall, E., Wilk, J. B., Biogen Biobank Team, Chahine, M., Chevalier, P., Christé, G., FinnGen, Palotie, A., Daly, M. J., & Runz, H. (2022). Genetic associations of protein-coding variants in human disease. Nature, 603(7899), 95–102. https://doi.org/10.1038/s41586-022-04394-w
Hunter, S., Sigauke, R. F., Stanley, J. T., Allen, M. A., & Dowell, R. D. (2022). Protocol variations in run-on transcription dataset preparation produce detectable signatures in sequencing libraries. BMC Genomics, 23(1), 187. https://doi.org/10.1186/s12864-022-08352-8
Varco-Merth, B. D., Brantley, W., Marenco, A., Duell, D. D., Fachko, D. N., Richardson, B., Busman-Sahay, K., Shao, D., Flores, W., Engelman, K., Fukazawa, Y., Wong, S. W., Skalsky, R. L., Smedley, J., Axthelm, M. K., Lifson, J. D., Estes, J. D., Edlefsen, P. T., Picker, L. J., … Okoye, A. A. (2022). Rapamycin limits CD4+ T cell proliferation in simian immunodeficiency virus-infected rhesus macaques on antiretroviral therapy. The Journal of Clinical Investigation, 132(10), e156063. https://doi.org/10.1172/JCI156063
Dannebaum, R., Suwalski, P., Asgharian, H., Du Zhipei, G., Lin, H., Weiner, J., Holtgrewe, M., Thibeault, C., Müller, M., Wang, X., Karadeniz, Z., Saccomanno, J., Doehn, J.-M., Hübner, R.-H., Hinzmann, B., Blüher, A., Siemann, S., Telman, D., Suttorp, N., … Heidecker, B. (2022). Highly multiplexed immune repertoire sequencing links multiple lymphocyte classes with severity of response to COVID-19. EClinicalMedicine, 48, 101438. https://doi.org/10.1016/j.eclinm.2022.101438
Burns, A. M., Farinelli-Scharly, M., Hugues-Ascery, S., Sanchez-Mut, J. V., Santoni, G., & Gräff, J. (2022). The HDAC inhibitor CI-994 acts as a molecular memory aid by facilitating synaptic and intracellular communication after learning. Proceedings of the National Academy of Sciences of the United States of America, 119(22), e2116797119. https://doi.org/10.1073/pnas.2116797119
DuTell, V., Gibaldi, A., Focarelli, G., Olshausen, B. A., & Banks, M. S. (2022). High-fidelity eye, head, body, and world tracking with a wearable device. Behavior Research Methods. https://doi.org/10.3758/s13428-022-01888-3
Joseph, M., Wu, Y., Dannebaum, R., Rubelt, F., Zlatareva, I., Lorenc, A., Du, Z. G., Davies, D., Kyle-Cezar, F., Das, A., Gee, S., Seow, J., Graham, C., Telman, D., Bermejo, C., Lin, H., Asgharian, H., Laing, A. G., Del Molino Del Barrio, I., … Hayday, A. C. (2022). Global patterns of antigen receptor repertoire disruption across adaptive immune compartments in COVID-19. Proceedings of the National Academy of Sciences of the United States of America, 119(34), e2201541119. https://doi.org/10.1073/pnas.2201541119
Pan, L., Tormey, D., Bobon, N., & Baumann, P. (2022). Rap1 prevents fusions between long telomeres in fission yeast. The EMBO Journal, 41(20), e110458. https://doi.org/10.15252/embj.2021110458
Lavinder, T. R., Fachko, D. N., Stanton, J., Varco-Merth, B., Smedley, J., Okoye, A. A., & Skalsky, R. L. (2022). Effects of Early Antiretroviral Therapy on the Composition and Diversity of the Fecal Microbiome of SIV-infected Rhesus Macaques (Macaca mulatta). Comparative Medicine, 72(5), 287–297. https://doi.org/10.30802/AALAS-CM-22-000020
Chen, Y. A., Kankel, M. W., Hana, S., Lau, S. K., Zavodszky, M. I., McKissick, O., Mastrangelo, N., Dion, J., Wang, B., Ferretti, D., Koske, D., Lehman, S., Koszka, K., McLaughlin, H., Liu, M., Marshall, E., Fabian, A. J., Cullen, P., Marsh, G., … Lo, S.-C. (2023). In vivo genome editing using novel AAV-PHP variants rescues motor function deficits and extends survival in a SOD1-ALS mouse model. Gene Therapy, 30(5), 443–454. https://doi.org/10.1038/s41434-022-00375-w
Nichols, R. V., O’Connell, B. L., Mulqueen, R. M., Thomas, J., Woodfin, A. R., Acharya, S., Mandel, G., Pokholok, D., Steemers, F. J., & Adey, A. C. (2022). High-throughput robust single-cell DNA methylation profiling with sciMETv2. Nature Communications, 13(1), 7627. https://doi.org/10.1038/s41467-022-35374-3
Gotting, K., May, D. S., Sosa-Calvo, J., Khadempour, L., Francoeur, C. B., Berasategui, A., Thairu, M. W., Sandstrom, S., Carlson, C. M., Chevrette, M. G., Pupo, M. T., Bugni, T. S., Schultz, T. R., Johnston, J. S., Gerardo, N. M., & Currie, C. R. (2022). Genomic diversification of the specialized parasite of the fungus-growing ant symbiosis. Proceedings of the National Academy of Sciences of the United States of America, 119(51), e2213096119. https://doi.org/10.1073/pnas.2213096119
Araya, P., Kinning, K. T., Coughlan, C., Smith, K. P., Granrath, R. E., Enriquez-Estrada, B. A., Worek, K., Sullivan, K. D., Rachubinski, A. L., Wolter-Warmerdam, K., Hickey, F., Galbraith, M. D., Potter, H., & Espinosa, J. M. (2022). IGF1 deficiency integrates stunted growth and neurodegeneration in Down syndrome. Cell Reports, 41(13), 111883. https://doi.org/10.1016/j.celrep.2022.111883
Al-Muhanna, F. A., Dowdell, A. K., Al Eleq, A. H., Albaker, W. I., Brooks, A. W., Al-Sultan, A. I., Al-Rubaish, A. M., Alkharsah, K. R., Sulaiman, R. M., Al-Quorain, A. A., Cyrus, C., Alali, R. A., Vatte, C., Robinson, F. L., Zhou, X., Snyder, M. P., Almuhanna, A. F., Keating, B. J., Piening, B. D., & Al-Ali, A. K. (2022). Gut microbiota analyses of Saudi populations for type 2 diabetes-related phenotypes reveals significant association. BMC Microbiology, 22(1), 301. https://doi.org/10.1186/s12866-022-02714-8
Bolouri, H., Ries, R. E., Wiedeman, A. E., Hylkema, T., Scheiding, S., Gersuk, V. H., O’Brien, K., Nguyen, Q.-A., Smith, J. L., Alice Long, S., & Meshinchi, S. (2022). Inflammatory bone marrow signaling in pediatric acute myeloid leukemia distinguishes patients with poor outcomes. Nature Communications, 13(1), 7186. https://doi.org/10.1038/s41467-022-34965-4
Sanchez, M. R., Biondi, T. C., Kunde, Y. A., Eng, W., Nalley, J. O., Ganuza, E., Hovde, B. T., Corcoran, A. A., & Starkenburg, S. R. (2022). The Genome Sequence of an Algal Strain of Nannochloropsis QH25. Microbiology Resource Announcements, e0092122. https://doi.org/10.1128/mra.00921-22
Ors, A., Chitsazan, A. D., Doe, A. R., Mulqueen, R. M., Ak, C., Wen, Y., Haverlack, S., Handu, M., Naldiga, S., Saldivar, J. C., & Mohammed, H. (2022). Estrogen regulates divergent transcriptional and epigenetic cell states in breast cancer. Nucleic Acids Research, gkac908. https://doi.org/10.1093/nar/gkac908
Garrison, Z., Chang, M., Hornick, N., Yu, W. Y., Cheng, J. B., & Kulkarni, R. P. (2022). A Novel Potential Role for Monocytes Revealed by Single Cell Analysis of Immunotherapy Induced Immune Related Adverse Events. Cancers, 14(21), 5407. https://doi.org/10.3390/cancers14215407
David, J. K., Maden, S. K., Wood, M. A., Thompson, R. F., & Nellore, A. (2022). Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads. Genome Biology, 23(1), 240. https://doi.org/10.1186/s13059-022-02789-6
Sepe, J. J., Gardner, R. T., Blake, M. R., Brooks, D. M., Staffenson, M. A., Betts, C. B., Sivagnanam, S., Larson, W., Kumar, S., Bayles, R. G., Jin, H., Cohen, M. S., Coussens, L. M., & Habecker, B. A. (2022). Therapeutics That Promote Sympathetic Reinnervation Modulate the Inflammatory Response After Myocardial Infarction. JACC. Basic to Translational Science, 7(9), 915–930. https://doi.org/10.1016/j.jacbts.2022.04.009
Fankhauser, R., Chang, M., Garrison, Z., Berryman, R., Lucero, O. M., Fuiten, A., DePatie, N., Seifert, H., & Kulkarni, R. P. (2022). Single-Cell Identification of Melanoma Biomarkers in Circulating Tumor Cells. Cancers, 14(19), 4921. https://doi.org/10.3390/cancers14194921
Brown, S. Z., McCarthy, G. A., Carroll, J. R., Di Niro, R., Pelz, C., Jain, A., Sutton, T. L., Holly, H. D., Nevler, A., Schultz, C. W., McCoy, M. D., Cozzitorto, J. A., Jiang, W., Yeo, C. J., Dixon, D. A., Sears, R. C., & Brody, J. R. (2022). The RNA-Binding Protein HuR Posttranscriptionally Regulates the Protumorigenic Activator YAP1 in Pancreatic Ductal Adenocarcinoma. Molecular and Cellular Biology, 42(7), e00018-22. https://doi.org/10.1128/mcb.00018-22
Hill, J. H., Massaquoi, M. S., Sweeney, E. G., Wall, E. S., Jahl, P., Bell, R., Kallio, K., Derrick, D., Murtaugh, L. C., Parthasarathy, R., Remington, S. J., Round, J. L., & Guillemin, K. (2022). BefA, a microbiota-secreted membrane disrupter, disseminates to the pancreas and increases β cell mass. Cell Metabolism, S1550-4131(22)00391-6. https://doi.org/10.1016/j.cmet.2022.09.001
Gross, S. M., Dane, M. A., Smith, R. L., Devlin, K. L., McLean, I. C., Derrick, D. S., Mills, C. E., Subramanian, K., London, A. B., Torre, D., Evangelista, J. E., Clarke, D. J. B., Xie, Z., Erdem, C., Lyons, N., Natoli, T., Pessa, S., Lu, X., Mullahoo, J., … Heiser, L. M. (2022). A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses. Communications Biology, 5(1), 1066. https://doi.org/10.1038/s42003-022-03975-9
Haynes, D., Reiter, T., Velasco, R., Chang, M., Kulkarni, R., Kent, G., Strunck, J., Cassidy, P., & Greiling, T. M. (2022). Pityriasis rubra pilaris transcriptomics implicate Th17 signaling and correlate with response to ixekizumab, with distinct gene expression profiles in non-responders. The Journal of Investigative Dermatology, S0022-202X(22)01938-8. https://doi.org/10.1016/j.jid.2022.09.005
Le, Q., Hadland, B., Smith, J. L., Leonti, A., Huang, B. J., Ries, R., Hylkema, T. A., Castro, S., Tang, T. T., McKay, C. N., Perkins, L., Pardo, L., Sarthy, J., Beckman, A. K., Williams, R., Idemmili, R., Furlan, S., Ishida, T., Call, L., … Meshinchi, S. (2022). CBFA2T3-GLIS2 model of pediatric acute megakaryoblastic leukemia identifies FOLR1 as a CAR T cell target. The Journal of Clinical Investigation, 132(22), e157101. https://doi.org/10.1172/JCI157101
Loeb, K. R., Le, Q. H., Tang, T., Castro, S. K., Pardo, L., McKay, C. N., Perkins, L., Smith, J. L., Kirkey, D. C., Abrahams, C., Bedard, K., Molina, A., Eidenschink Brodersen, L., Loken, M. R., Tarlock, K., & Meshinchi, S. (2022). Targeting FOLR1 in high-risk CBF2AT3-GLIS2 Pediatric AML with STRO-002 FOLR1-Antibody-Drug Conjugate. Blood Advances, bloodadvances.2022008503. https://doi.org/10.1182/bloodadvances.2022008503
Denans, N., Tran, N. T. T., Swall, M. E., Diaz, D. C., Blanck, J., & Piotrowski, T. (2022). An anti-inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish. Nature Communications, 13(1), 5356. https://doi.org/10.1038/s41467-022-33015-3
Bailon-Zambrano, R., Sucharov, J., Mumme-Monheit, A., Murry, M., Stenzel, A., Pulvino, A. T., Mitchell, J. M., Colborn, K. L., & Nichols, J. (2022). Variable paralog expression underlies phenotype variation. ELife, 11, e79247. https://doi.org/10.7554/eLife.79247
Huang, B. J., Smith, J. L., Farrar, J. E., Wang, Y.-C., Umeda, M., Ries, R. E., Leonti, A. R., Crowgey, E., Furlan, S. N., Tarlock, K., Armendariz, M., Liu, Y., Shaw, T. I., Wei, L., Gerbing, R. B., Cooper, T. M., Gamis, A. S., Aplenc, R., Kolb, E. A., … Meshinchi, S. (2022). Integrated stem cell signature and cytomolecular risk determination in pediatric acute myeloid leukemia. Nature Communications, 13(1), 5487. https://doi.org/10.1038/s41467-022-33244-6
Zimmerman, S. M., Fropf, R., Kulasekara, B. R., Griswold, M., Appelbe, O., Bahrami, A., Boykin, R., Buhr, D. L., Fuhrman, K., Hoang, M. L., Huynh, Q., Isgur, L., Klock, A., Kutchma, A., Lasley, A. E., Liang, Y., McKay-Fleisch, J., Nelson, J. S., Nguyen, K., … Beechem, J. M. (2022). Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling. Genome Research, 32(10), 1892–1905. https://doi.org/10.1101/gr.276206.121
Kieran Blair, S. R., Hull, J., Escalona, M., Finger, A., Joslin, S. E. K., Sahasrabudhe, R., Marimuthu, M. P. A., Nguyen, O., Chumchim, N., Morris, E. R., Velazquez, S., & Schreier, A. (2022). The reference genome of the Vernal Pool Tadpole Shrimp, Lepidurus packardi. The Journal of Heredity, 113(6), 706–711. https://doi.org/10.1093/jhered/esac051
Carratt, S. A., Kong, G. L., Curtiss, B. M., Schonrock, Z., Maloney, L., Maniaci, B. N., Blaylock, H. Z., Baris, A., Druker, B. J., Braun, T. P., & Maxson, J. E. (2022). Mutated SETBP1 activates transcription of Myc programs to accelerate CSF3R-driven myeloproliferative neoplasms. Blood, 140(6), 644–658. https://doi.org/10.1182/blood.2021014777
Tsui, D. C. C., Drusbosky, L. M., Wienke, S., Gao, D., Bubie, A., Barbacioru, C., & Camidge, D. R. (2022). Oncogene Overlap Analysis of Circulating Cell-free Tumor DNA to Explore the Appropriate Criteria for Defining MET Copy Number-Driven Lung Cancer. Clinical Lung Cancer, S1525-7304(22)00159-0. https://doi.org/10.1016/j.cllc.2022.07.002
Xu, Y., Twarog, M., Li, N., Banks, A., Schustak, J., Bao, Y., Huang, Q., & Medley, Q. G. (2022). Zinc transport from the endoplasmic reticulum to the cytoplasm via Zip7 is necessary for barrier dysfunction mediated by inflammatory signaling in RPE cells. PloS One, 17(7), e0271656. https://doi.org/10.1371/journal.pone.0271656
Yashar, W. M., Kong, G., VanCampen, J., Curtiss, B. M., Coleman, D. J., Carbone, L., Yardimci, G. G., Maxson, J. E., & Braun, T. P. (2022). GoPeaks: Histone modification peak calling for CUT&Tag. Genome Biology, 23(1), 144. https://doi.org/10.1186/s13059-022-02707-w
Sanders, C. K., Biondi, T. C., Eng, W., Kunde, Y. A., Hovde, B. T., & Dale, T. (2022). High-Quality Genome Assembly of Nannochloris desiccata 2437 and Its Associated Bacterial Community. Microbiology Resource Announcements, 11(7), e0071021. https://doi.org/10.1128/mra.00710-21
Gutierrez, J., Davis, B. A., Nevonen, K. A., Ward, S., Carbone, L., & Maslen, C. L. (2022). DNA Methylation Analysis of Turner Syndrome BAV. Frontiers in Genetics, 13, 872750. https://doi.org/10.3389/fgene.2022.872750
Claridge, S. E., & Hopkins, B. D. (2022). PI3King the Environment for Growth: PI3K Activation Drives Transcriptome Changes That Support Oncogenic Growth. Cancer Research, 82(12), 2216–2218. https://doi.org/10.1158/0008-5472.CAN-22-1466
Curtiss, B. M., VanCampen, J., Macaraeg, J., Kong, G. L., Taherinasab, A., Tsuchiya, M., Yashar, W. M., Tsang, Y. H., Horton, W., Coleman, D. J., Estabrook, J., Lusardi, T. A., Mills, G. B., Druker, B. J., Maxson, J. E., & Braun, T. P. (2022). PU.1 and MYC transcriptional network defines synergistic drug responses to KIT and LSD1 inhibition in acute myeloid leukemia. Leukemia, 36(7), 1781–1793. https://doi.org/10.1038/s41375-022-01594-1
Bruce, M., DeWees, D., Harmon, J., Cates, L., Khaing, Z. Z., & Hofstetter, C. P. (2022). Blood Flow Changes Associated with Spinal Cord Injury Assessed by Non-linear Doppler Contrast-Enhanced Ultrasound. Ultrasound in Medicine & Biology, 48(8), 1410–1419. https://doi.org/10.1016/j.ultrasmedbio.2022.03.004
Blair, T. C., Bambina, S., Kramer, G. F., Dowdell, A. K., Alice, A. F., Baird, J. R., Lund, A. W., Piening, B. D., Crittenden, M. R., & Gough, M. J. (2022). Fluorescent tracking identifies key migratory dendritic cells in the lymph node after radiotherapy. Life Science Alliance, 5(9), e202101337. https://doi.org/10.26508/lsa.202101337
James, C. A., Yu, K. K. Q., Mayer-Blackwell, K., Fiore-Gartland, A., Smith, M. T., Layton, E. D., Johnson, J. L., Hanekom, W. A., Scriba, T. J., & Seshadri, C. (2022). Durable Expansion of TCR-δ Meta-Clonotypes After BCG Revaccination in Humans. Frontiers in Immunology, 13, 834757. https://doi.org/10.3389/fimmu.2022.834757
Driskill, M., Pardee, K., Hummer, K. E., Zurn, J. D., Amundsen, K., Wiles, A., Wiedow, C., Patzak, J., Henning, J. A., & Bassil, N. V. (2022). Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers. PloS One, 17(4), e0257746. https://doi.org/10.1371/journal.pone.0257746
Willcox, A. C., Sung, K., Garrett, M. E., Galloway, J. G., Erasmus, J. H., Logue, J. K., Hawman, D. W., Chu, H. Y., Hasenkrug, K. J., Fuller, D. H., Matsen Iv, F. A., & Overbaugh, J. (2022). Detailed analysis of antibody responses to SARS-CoV-2 vaccination and infection in macaques. PLoS Pathogens, 18(4), e1010155. https://doi.org/10.1371/journal.ppat.1010155
Oladeinde, A., Abdo, Z., Zwirzitz, B., Woyda, R., Lakin, S. M., Press, M. O., Cox, N. A., Thomas, J. C., Looft, T., Rothrock, M. J., Zock, G., Plumblee Lawrence, J., Cudnik, D., Ritz, C., Aggrey, S. E., Liachko, I., Grove, J. R., & Wiersma, C. (2022). Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens. Applied and Environmental Microbiology, 88(9), e0251721. https://doi.org/10.1128/aem.02517-21
Uppala, J. K., Sathe, L., Chakraborty, A., Bhattacharjee, S., Pulvino, A. T., & Dey, M. (2022). The cap-proximal RNA secondary structure inhibits preinitiation complex formation on HAC1 mRNA. Journal of Biological Chemistry, 298(3). https://doi.org/10.1016/j.jbc.2022.101648
Claridge, S. E., & Hopkins, B. D. (2022). Circling back to PTEN: Fumarate inhibits canonical tumor suppressor. Molecular Cell, 82(7), 1244–1245. https://doi.org/10.1016/j.molcel.2022.03.013
Lee, K.-Y., Seah, C., Li, C., Chen, Y.-F., Chen, C.-Y., Wu, C.-I., Liao, P.-C., Shyu, Y.-C., Olafson, H. R., McKee, K. K., Wang, E. T., Yeh, C.-H., & Wang, C.-H. (2022). Mice lacking MBNL1 and MBNL2 exhibit sudden cardiac death and molecular signatures recapitulating myotonic dystrophy. Human Molecular Genetics, 31(18), 3144–3160. https://doi.org/10.1093/hmg/ddac108
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., Aganezov, S., Hoyt, S. J., Diekhans, M., Logsdon, G. A., Alonge, M., Antonarakis, S. E., Borchers, M., Bouffard, G. G., Brooks, S. Y., … Phillippy, A. M. (2022). The complete sequence of a human genome. Science, 376(6588), 44–53. https://doi.org/10.1126/science.abj6987
Brooks, K. E., Daughtry, B. L., Davis, B., Yan, M. Y., Fei, S. S., Shepherd, S., Carbone, L., & Chavez, S. L. (2022). Molecular contribution to embryonic aneuploidy and karyotypic complexity in initial cleavage divisions of mammalian development. Development (Cambridge, England), 149(7), dev198341. https://doi.org/10.1242/dev.198341
Baek, S., Tran, N. T. T., Diaz, D. C., Tsai, Y.-Y., Acedo, J. N., Lush, M. E., & Piotrowski, T. (2022). Single-cell transcriptome analysis reveals three sequential phases of gene expression during zebrafish sensory hair cell regeneration. Developmental Cell, 57(6), 799-819.e6. https://doi.org/10.1016/j.devcel.2022.03.001
Guan, X., Polesso, F., Wang, C., Sehrawat, A., Hawkins, R. M., Murray, S. E., Thomas, G. V., Caruso, B., Thompson, R. F., Wood, M. A., Hipfinger, C., Hammond, S. A., Graff, J. N., Xia, Z., & Moran, A. E. (2022). Androgen receptor activity in T cells limits checkpoint blockade efficacy. Nature. https://doi.org/10.1038/s41586-022-04522-6
Piening, B. D., Dowdell, A. K., Zhang, M., Loza, B.-L., Walls, D., Gao, H., Mohebnasab, M., Li, Y. R., Elftmann, E., Wei, E., Gandla, D., Lad, H., Chaib, H., Sweitzer, N. K., Deng, M., Pereira, A. C., Cadeiras, M., Shaked, A., Snyder, M. P., & Keating, B. J. (2022). Whole transcriptome profiling of prospective endomyocardial biopsies reveals prognostic and diagnostic signatures of cardiac allograft rejection. The Journal of Heart and Lung Transplantation: The Official Publication of the International Society for Heart Transplantation, 41(6), 840–848. https://doi.org/10.1016/j.healun.2022.01.1377
Ravisankar, S., Murphy, M. J., Redmayne-Titley, N., Davis, B., Luo, F., Takahashi, D., Hennebold, J. D., & Chavez, S. L. (2022). Long-term Hyperandrogenemia and/or Western-style Diet in Rhesus Macaque Females Impairs Preimplantation Embryogenesis. Endocrinology, 163(4), bqac019. https://doi.org/10.1210/endocr/bqac019
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, 43(8), 998–1011. 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
O’Brien, T. D., Campbell, N. E., Potter, A. B., Letaw, J. H., Kulkarni, A., & Richards, C. S. (2022). Artificial intelligence (AI)-assisted exome reanalysis greatly aids in the identification of new positive cases and reduces analysis time in a clinical diagnostic laboratory. Genetics in Medicine: Official Journal of the American College of Medical Genetics, 24(1), 192–200. https://doi.org/10.1016/j.gim.2021.09.007
Fachko, D. N., Chen, Y., & Skalsky, R. L. (2022). Epstein-Barr Virus miR-BHRF1-3 Targets the BZLF1 3’UTR and Regulates the Lytic Cycle. Journal of Virology, 96(4), e0149521. https://doi.org/10.1128/JVI.01495-21
2021
Burns, A. M., & Gräff, J. (2021). Cognitive epigenetic priming: Leveraging histone acetylation for memory amelioration. Current Opinion in Neurobiology, 67, 75–84. https://doi.org/10.1016/j.conb.2020.08.011
Cheng, C., Reis, S. A., Adams, E. T., Fass, D. M., Angus, S. P., Stuhlmiller, T. J., Richardson, J., Olafson, H., Wang, E. T., Patnaik, D., Beauchamp, R. L., Feldman, D. A., Silva, M. C., Sur, M., Johnson, G. L., Ramesh, V., Miller, B. L., Temple, S., Kosik, K. S., … Haggarty, S. J. (2021). High-content image-based analysis and proteomic profiling identifies Tau phosphorylation inhibitors in a human iPSC-derived glutamatergic neuronal model of tauopathy. Scientific Reports, 11(1), 17029. https://doi.org/10.1038/s41598-021-96227-5
Hana, S., Peterson, M., McLaughlin, H., Marshall, E., Fabian, A. J., McKissick, O., Koszka, K., Marsh, G., Craft, M., Xu, S., Sorets, A., Torregrosa, T., Sun, C., Henderson, C. E., & Lo, S.-C. (2021). Highly efficient neuronal gene knockout in vivo by CRISPR-Cas9 via neonatal intracerebroventricular injection of AAV in mice. Gene Therapy, 28(10–11), 646–658. https://doi.org/10.1038/s41434-021-00224-2
Bouvet, M., Voigt, S., Tagawa, T., Albanese, M., Chen, Y.-F. A., Chen, Y., Fachko, D. N., Pich, D., Göbel, C., Skalsky, R. L., & Hammerschmidt, W. (2021). Multiple Viral microRNAs Regulate Interferon Release and Signaling Early during Infection with Epstein-Barr Virus. MBio, 12(2), e03440-20. https://doi.org/10.1128/mBio.03440-20
Oakes, M., Arastu, A., Kato, C., Somers, J., Holly, H. D., Elstrott, B. K., Dy, G. W., Kohs, T. C. L., Patel, R. R., McCarty, O. J. T., DeLoughery, T. G., Milano, C., Raghunathan, V., & Shatzel, J. J. (2021). Erythrocytosis and thromboembolic events in transgender individuals receiving gender-affirming testosterone. Thrombosis Research, 207, 96–98. https://doi.org/10.1016/j.thromres.2021.09.005
Chen, Y., Fachko, D. N., Ivanov, N. S., & Skalsky, R. L. (2021). B Cell Receptor-Responsive miR-141 Enhances Epstein-Barr Virus Lytic Cycle via FOXO3 Inhibition. MSphere, 6(2), e00093-21. https://doi.org/10.1128/mSphere.00093-21
Wilkerson, B. A., Zebroski, H. L., Finkbeiner, C. R., Chitsazan, A. D., Beach, K. E., Sen, N., Zhang, R. C., & Bermingham-McDonogh, O. (2021). Novel cell types and developmental lineages revealed by single-cell RNA-seq analysis of the mouse crista ampullaris. ELife, 10, e60108. https://doi.org/10.7554/eLife.60108
Silva, B. A., Astori, S., Burns, A. M., Heiser, H., van den Heuvel, L., Santoni, G., Martinez-Reza, M. F., Sandi, C., & Gräff, J. (2021). A thalamo-amygdalar circuit underlying the extinction of remote fear memories. Nature Neuroscience, 24(7), 964–974. https://doi.org/10.1038/s41593-021-00856-y
Groot, J., Zhou, Y., Marshall, E., Cullen, P., Carlile, T., Lin, D., Xu, C.-F., Crisafulli, J., Sun, C., Casey, F., Zhang, B., & Alves, C. (2021). Benchmarking and optimization of a high-throughput sequencing based method for transgene sequence variant analysis in biotherapeutic cell line development. Biotechnology Journal, 16(8), e2000548. https://doi.org/10.1002/biot.202000548
Rubin, J. D., Stanley, J. T., Sigauke, R. F., Levandowski, C. B., Maas, Z. L., Westfall, J., Taatjes, D. J., & Dowell, R. D. (2021). Transcription factor enrichment analysis (TFEA) quantifies the activity of multiple transcription factors from a single experiment. Communications Biology, 4(1), 661. https://doi.org/10.1038/s42003-021-02153-7
Smith, J., Shi, Y., Benedikt, M., & Nikolic, M. (2021). Scalable analysis of multi-modal biomedical data. GigaScience, 10(9), giab058. https://doi.org/10.1093/gigascience/giab058
Raghavan, S., Winter, P. S., Navia, A. W., Williams, H. L., DenAdel, A., Lowder, K. E., Galvez-Reyes, J., Kalekar, R. L., Mulugeta, N., Kapner, K. S., Raghavan, M. S., Borah, A. A., Liu, N., Väyrynen, S. A., Costa, A. D., Ng, R. W. S., Wang, J., Hill, E. K., Ragon, D. Y., … Shalek, A. K. (2021). Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer. Cell, 184(25), 6119-6137.e26. https://doi.org/10.1016/j.cell.2021.11.017
Bush, J. A., Aikawa, H., Fuerst, R., Li, Y., Ursu, A., Meyer, S. M., Benhamou, R. I., Chen, J. L., Khan, T., Wagner-Griffin, S., Van Meter, M. J., Tong, Y., Olafson, H., McKee, K. K., Childs-Disney, J. L., Gendron, T. F., Zhang, Y., Coyne, A. N., Wang, E. T., … Disney, M. D. (2021). Ribonuclease recruitment using a small molecule reduced c9ALS/FTD r(G4C2) repeat expansion in vitro and in vivo ALS models. Science Translational Medicine, 13(617), eabd5991. https://doi.org/10.1126/scitranslmed.abd5991
Eksi, S. E., Chitsazan, A., Sayar, Z., Thomas, G. V., Fields, A. J., Kopp, R. P., Spellman, P. T., & Adey, A. C. (2021). Epigenetic loss of heterogeneity from low to high grade localized prostate tumours. Nature Communications, 12(1), 7292. https://doi.org/10.1038/s41467-021-27615-8
Hu, B., Canon, S., Eloe-Fadrosh, E. A., Anubhav, null, Babinski, M., Corilo, Y., Davenport, K., Duncan, W. D., Fagnan, K., Flynn, M., Foster, B., Hays, D., Huntemann, M., Jackson, E. K. P., Kelliher, J., Li, P.-E., Lo, C.-C., Mans, D., McCue, L. A., … Chain, P. S. G. (2021). Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale. Frontiers in Bioinformatics, 1, 826370. https://doi.org/10.3389/fbinf.2021.826370
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
Grzadkowski, M. R., Holly, H. D., Somers, J., & Demir, E. (2021). Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes. BMC Bioinformatics, 22(1), 233. https://doi.org/10.1186/s12859-021-04147-y
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
Wang, E. T., Treacy, D., Eichinger, K., Struck, A., Estabrook, J., Olafson, H., Wang, T. T., Bhatt, K., Westbrook, T., Sedehizadeh, S., Ward, A., Day, J., Brook, D., Berglund, J. A., Cooper, T., Housman, D., Thornton, C., & Burge, C. (2019). Transcriptome alterations in myotonic dystrophy skeletal muscle and heart. Human Molecular Genetics, 28(8), 1312–1321. https://doi.org/10.1093/hmg/ddy432
Dropulic, L. K., Oestreich, M. C., Pietz, H. L., Laing, K. J., Hunsberger, S., Lumbard, K., Garabedian, D., Turk, S. P., Chen, A., Hornung, R. L., Seshadri, C., Smith, M. T., Hosken, N. A., Phogat, S., Chang, L.-J., Koelle, D. M., Wang, K., & Cohen, J. I. (2019). A Randomized, Double-Blinded, Placebo-Controlled, Phase 1 Study of a Replication-Defective Herpes Simplex Virus (HSV) Type 2 Vaccine, HSV529, in Adults With or Without HSV Infection. The Journal of Infectious Diseases, 220(6), 990–1000. https://doi.org/10.1093/infdis/jiz225
Hoshino, A., Horvath, S., Sridhar, A., Chitsazan, A., & Reh, T. A. (2019). Synchrony and asynchrony between an epigenetic clock and developmental timing. Scientific Reports, 9(1), 3770. https://doi.org/10.1038/s41598-019-39919-3
Angelbello, A. J., Rzuczek, S. G., Mckee, K. K., Chen, J. L., Olafson, H., Cameron, M. D., Moss, W. N., Wang, E. T., & Disney, M. D. (2019). Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model. Proceedings of the National Academy of Sciences of the United States of America, 116(16), 7799–7804. https://doi.org/10.1073/pnas.1901484116
Braun, T. P., Okhovat, M., Coblentz, C., Carratt, S. A., Foley, A., Schonrock, Z., Curtiss, B. M., Nevonen, K., Davis, B., Garcia, B., LaTocha, D., Weeder, B. R., Grzadkowski, M. R., Estabrook, J. C., Manning, H. G., Watanabe-Smith, K., Jeng, S., Smith, J. L., Leonti, A. R., … Maxson, J. E. (2019). Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia. Nature Communications, 10(1), Article 1. https://doi.org/10.1038/s41467-019-13364-2
Lu, L. L., Smith, M. T., Yu, K. K. Q., Luedemann, C., Suscovich, T. J., Grace, P. S., Cain, A., Yu, W. H., McKitrick, T. R., Lauffenburger, D., Cummings, R. D., Mayanja-Kizza, H., Hawn, T. R., Boom, W. H., Stein, C. M., Fortune, S. M., Seshadri, C., & Alter, G. (2019). IFN-γ-independent immune markers of Mycobacterium tuberculosis exposure. Nature Medicine, 25(6), 977–987. https://doi.org/10.1038/s41591-019-0441-3
Lush, M. E., Diaz, D. C., Koenecke, N., Baek, S., Boldt, H., St Peter, M. K., Gaitan-Escudero, T., Romero-Carvajal, A., Busch-Nentwich, E. M., Perera, A. G., Hall, K. E., Peak, A., Haug, J. S., & Piotrowski, T. (2019). ScRNA-Seq reveals distinct stem cell populations that drive hair cell regeneration after loss of Fgf and Notch signaling. ELife, 8. https://doi.org/10.7554/eLife.44431
Okoye, A. A., DeGottardi, M. Q., Fukazawa, Y., Vaidya, M., Abana, C. O., Konfe, A. L., Fachko, D. N., Duell, D. M., Li, H., Lum, R., Gao, L., Park, B. S., Skalsky, R. L., Lewis, A. D., Axthelm, M. K., Lifson, J. D., Wong, S. W., & Picker, L. J. (2019). Role of IL-15 Signaling in the Pathogenesis of Simian Immunodeficiency Virus Infection in Rhesus Macaques. Journal of Immunology (Baltimore, Md.: 1950), 203(11), 2928–2943. https://doi.org/10.4049/jimmunol.1900792
Raboin, M. J., Letaw, J., Mitchell, A. D., Toffey, D., McKelvey, J., Roberts, C. T., Curran, J. E., & Vinson, A. (2019). Genetic Architecture of Human Obesity Traits in the Rhesus Macaque. Obesity (Silver Spring, Md.), 27(3), 479–488. https://doi.org/10.1002/oby.22392
Tettey, T. T., Gao, X., Shao, W., Li, H., Story, B. A., Chitsazan, A. D., Glaser, R. L., Goode, Z. H., Seidel, C. W., Conaway, R. C., Zeitlinger, J., Blanchette, M., & Conaway, J. W. (2019). A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing. Cell Reports, 27(13), 3770-3779.e7. https://doi.org/10.1016/j.celrep.2019.05.099
Tsujikawa, T., Thibault, G., Azimi, V., Sivagnanam, S., Banik, G., Means, C., Kawashima, R., Clayburgh, D. R., Gray, J. W., Coussens, L. M., & Chang, Y. H. (2019). Robust Cell Detection and Segmentation for Image Cytometry Reveal Th17 Cell Heterogeneity. Cytometry. Part A: The Journal of the International Society for Analytical Cytology, 95(4), 389–398. https://doi.org/10.1002/cyto.a.23726
Wilkerson, B. A., Chitsazan, A. D., VandenBosch, L. S., Wilken, M. S., Reh, T. A., & Bermingham-McDonogh, O. (2019). Open chromatin dynamics in prosensory cells of the embryonic mouse cochlea. Scientific Reports, 9(1), 9060. https://doi.org/10.1038/s41598-019-45515-2
Wood, M. A., Nellore, A., & Thompson, R. F. (2019). Tumor Mutation Burden-From Doubts to Concerns. JAMA Oncology. https://doi.org/10.1001/jamaoncol.2019.4138
Yu, K. K. Q., Wilburn, D. B., Hackney, J. A., Darrah, P. A., Foulds, K. E., James, C. A., Smith, M. T., Jing, L., Seder, R. A., Roederer, M., Koelle, D. M., Swanson, W. J., & Seshadri, C. (2019). Conservation of molecular and cellular phenotypes of invariant NKT cells between humans and non-human primates. Immunogenetics, 71(7), 465–478. https://doi.org/10.1007/s00251-019-01118-9
2018
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.