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    • 39648
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    1990 …2024

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    • 2024

      The response of Dual-leucine zipper kinase (DLK) to nocodazole: Evidence for a homeostatic cytoskeletal repair mechanism

      DeVault, L., Mateusiak, C., Palucki, J., Brent, M., Milbrandt, J. & DiAntonio, A., Apr 2024, In: PloS one. 19, 4 April, e0300539.

      Research output: Contribution to journalArticlepeer-review

      Open Access
    • 2023

      Calling Cards: A Customizable Platform to Longitudinally Record Protein-DNA Interactions Over Time in Cells and Tissues

      Yen, A., Mateusiak, C., Sarafinovska, S., Gachechiladze, M. A., Guo, J., Chen, X., Moudgil, A., Cammack, A. J., Hoisington-Lopez, J., Crosby, M. L., Brent, M. R., Mitra, R. D. & Dougherty, J. D., Sep 2023, In: Current Protocols. 3, 9, e883.

      Research output: Contribution to journalArticlepeer-review

    • NetProphet 3: a machine learning framework for transcription factor network mapping and multi-omics integration

      Abid, D. & Brent, M. R., Feb 1 2023, In: Bioinformatics. 39, 2, btad038.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      1 Scopus citations
    • Unbiased discovery of natural sequence variants that influence fungal virulence

      Agustinho, D. P., Brown, H. L., Chen, G., Gaylord, E. A., Geddes-McAlister, J., Brent, M. R. & Doering, T. L., Nov 8 2023, In: Cell Host and Microbe. 31, 11, p. 1910-1920.e5

      Research output: Contribution to journalArticlepeer-review

      Open Access
    • 2022

      Predicting which genes will respond to transcription factor perturbations

      Kang, Y., Jung, W. J. & Brent, M. R., Aug 2022, In: G3: Genes, Genomes, Genetics. 12, 8, jkac144.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      1 Scopus citations
    • The Programmed Death-1 Signaling Axis Modulates Inflammation and LV Structure/Function in a Stress-Induced Cardiomyopathy Model

      Hayashi, T., Tiwary, S. K., Lavine, K. J., Acharya, S., Brent, M., Adamo, L., Kovacs, A. & Mann, D., Nov 2022, In: JACC: Basic to Translational Science. 7, 11, p. 1120-1139 20 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      14 Scopus citations
    • 2021

      Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data

      Ma, C. Z. & Brent, M. R., May 1 2021, In: Bioinformatics. 37, 9, p. 1234-1245 12 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      11 Scopus citations
    • The transcription factor pdr802 regulates titan cell formation and pathogenicity of cryptococcus neoformans

      Reuwsaat, J. C. V., Agustinho, D. P., Motta, H., Chang, A. L., Brown, H., Brent, M. R., Kmetzsch, L. & Doering, T. L., Mar 1 2021, In: mBio. 12, 2, p. 1-20 20 p., e03457-20.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      11 Scopus citations
    • 2020

      Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses

      Kang, Y., Patel, N. R., Shively, C., Recio, P. S., Chen, X., Wranik, B. J., Kim, G., Scott McIsaac, R., Mitra, R. & Brent, M. R., 2020, In: Genome research. 30, 3, p. 459-471 13 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      15 Scopus citations
    • 2018

      NetProphet 2.0: Mapping transcription factor networks by exploiting scalable data resources

      Kang, Y., Liow, H. H., Maier, E. J. & Brent, M. R., Jan 15 2018, In: Bioinformatics. 34, 2, p. 249-257 9 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      10 Scopus citations
    • Seven-up is a novel regulator of insulin signaling

      Musselman, L. P., Fink, J. L., Maier, E. J., Gatto, J. A., Brent, M. R. & Baranski, T. J., Apr 2018, In: Genetics. 208, 4, p. 1643-1656 14 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      11 Scopus citations
    • Unintended side effects of transformation are very rare in Cryptococcus neoformans

      Friedman, R. Z., Gish, S. R., Brown, H., Brier, L., Howard, N., Doering, T. L. & Brent, M. R., Mar 1 2018, In: G3: Genes, Genomes, Genetics. 8, 3, p. 815-822 8 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      10 Scopus citations
    • 2016

      Computational analysis reveals a key regulator of cryptococcal virulence and determinant of host response

      Gish, S. R., Maier, E. J., Haynes, B. C., Santiago-Tirado, F. H., Srikanta, D. L., Ma, C. Z., Li, L. X., Williams, M., Crouch, E. C., Khader, S. A., Brent, M. R. & Doering, T. L., Apr 19 2016, In: mBio. 7, 2, e00313-16.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      33 Scopus citations
    • Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast

      Michael, D. G., Maier, E. J., Brown, H., Gish, S. R., Fiore, C., Brown, R. H. & Brent, M. R., Nov 22 2016, In: Proceedings of the National Academy of Sciences of the United States of America. 113, 47, p. E7428-E7437

      Research output: Contribution to journalArticlepeer-review

      Open Access
      28 Scopus citations
    • 2015

      Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation

      Maier, E. J., Haynes, B. C., Gish, S. R., Wang, Z. A., Skowyra, M. L., Marulli, A. L., Doering, T. L. & Brent, M. R., May 1 2015, In: Genome research. 125, 5, p. 690-700 11 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      37 Scopus citations
    • SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers

      Hass, M. R., Liow, H. H., Chen, X., Sharma, A., Inoue, Y. U., Inoue, T., Reeb, A., Martens, A., Fulbright, M., Raju, S., Stevens, M., Boyle, S., Park, J. S., Weirauch, M. T., Brent, M. R. & Kopan, R., Aug 20 2015, In: Molecular cell. 59, 4, p. 685-697 13 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      39 Scopus citations
    • 2014

      Cryptococcus neoformans Dual GDP-mannose transporters and their role in biology and virulence

      Wang, Z. A., Griffith, C. L., Skowyra, M. L., Salinas, N., Williams, M., Maier, E. J., Gish, S. R., Liu, H., Brent, M. R. & Doering, T. L., Jun 2014, In: Eukaryotic Cell. 13, 6, p. 832-842 11 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      20 Scopus citations
    • 2013

      Mapping functional transcription factor networks from gene expression data

      Haynes, B. C., Maier, E. J., Kramer, M. H., Wang, P. I., Brown, H. & Brent, M. R., Aug 2013, In: Genome research. 23, 8, p. 1319-1328 10 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      33 Scopus citations
    • Role of fat body lipogenesis in protection against the effects of caloric overload in drosophila

      Musselman, L. P., Fink, J. L., Ramachandran, P. V., Patterson, B. W., Okunade, A. L., Maier, E., Brent, M. R., Turk, J. & Baranski, T. J., Mar 22 2013, In: Journal of Biological Chemistry. 288, 12, p. 8028-8042 15 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      94 Scopus citations
    • 2012

      An integrated encyclopedia of DNA elements in the human genome

      Principal investigators (steering committee), Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis), Broad Institute Group (data production and analysis), Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis), Data coordination center at UC Santa Cruz (production data coordination), Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis), Genome Institute of Singapore group (data production and analysis), HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis), Lawrence Berkeley National Laboratory group (targeted experimental validation), NHGRI groups (data production and analysis), Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis), Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis), University of Albany SUNY group (data production and analysis), University of Chicago Stanford group (data production and analysis), University of Heidelberg group (targeted experimental validation), University of Massachusetts Medical School Bioinformatics group (data production and analysis), University of Washington University of Massachusetts Medical Center group (data production and analysis), Data Analysis Center (data analysis), The ENCODE Project Consortium, Data production leads (data production), & 3 othersLead analysts (data analysis), Writing Group & NHGRI project management (scientific management), Sep 6 2012, In: Nature. 489, 7414, p. 57-74 18 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      12257 Scopus citations
    • GENCODE: The reference human genome annotation for the ENCODE project

      Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., Barnes, I., Bignell, A., Boychenko, V., Hunt, T., Kay, M., Mukherjee, G., Rajan, J., Despacio-Reyes, G., Saunders, G., Steward, C., & 21 othersHarte, R., Lin, M., Howald, C., Tanzer, A., Derrien, T., Chrast, J., Walters, N., Balasubramanian, S., Pei, B., Tress, M., Rodriguez, J. M., Ezkurdia, I., Van Baren, J., Brent, M., Haussler, D., Kellis, M., Valencia, A., Reymond, A., Gerstein, M., Guigó, R. & Hubbard, T. J., Sep 2012, In: Genome research. 22, 9, p. 1760-1774 15 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      3289 Scopus citations
    • Reduced DICER1 elicits an interferon response in endometrial cancer cells

      Chiappinelli, K. B., Haynes, B. C., Brent, M. R. & Goodfellow, P. J., Mar 2012, In: Molecular Cancer Research. 10, 3, p. 316-325 10 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      13 Scopus citations
    • 2011

      A user's guide to the Encyclopedia of DNA elements (ENCODE)

      Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., Gingeras, T. R., Kent, W. J., Birney, E., Wold, B., Crawford, G. E., Epstein, C. B., Shoresh, N., Ernst, J., Mikkelsen, T. S., Kheradpour, P., Zhang, X., Wang, L., Issner, R., Coyne, M. J., & 295 othersDurham, T., Ku, M., Truong, T., Ward, L. D., Altshuler, R. C., Lin, M. F., Kellis, M., Davis, C. A., Kapranov, P., Dobin, A., Zaleski, C., Schlesinger, F., Batut, P., Chakrabortty, S., Jha, S., Lin, W., Drenkow, J., Wang, H., Bell, K., Bell, I., Gao, H., Dumais, E., Dumais, J., Antonarakis, S. E., Ucla, C., Borel, C., Guigo, R., Djebali, S., Lagarde, J., Kingswood, C., Ribeca, P., Sammeth, M., Alioto, T., Merkel, A., Tilgner, H., Carninci, P., Hayashizaki, Y., Lassmann, T., Takahashi, H., Abdelhamid, R. F., Hannon, G., Fejes, K. T., Preall, J., Gordon, A., Sotirova, V., Reymond, A., Howald, C., Graison, E. A. Y., Chrast, J., Ruan, Y., Ruan, X., Shahab, A., Poh, W. T., Wei, C. L., Furey, T. S., Boyle, A. P., Sheffield, N. C., Song, L., Shibata, Y., Vales, T., Winter, D., Zhang, Z., London, D., Wang, T., Keefe, D., Iyer, V. R., Lee, B. K., McDaniell, R. M., Liu, Z., Battenhouse, A., Bhinge, A. A., Lieb, J. D., Grasfeder, L. L., Showers, K. A., Giresi, P. G., Kim, S. K. C., Shestak, C., Pauli, F., Reddy, T. E., Gertz, J., Partridge, E. C., Jain, P., Sprouse, R. O., Bansal, A., Pusey, B., Muratet, M. A., Varley, K. E., Bowling, K. M., Newberry, K. M., Nesmith, A. S., Dilocker, J. A., Parker, S. L., Waite, L. L., Thibeault, K., Roberts, K., Absher, D. M., Mortazavi, A., Williams, B., Marinov, G., Trout, D., King, B., McCue, K., Kirilusha, A., DeSalvo, G., Fisher, K. A., Amrhein, H., Pepke, S., Vielmetter, J., Sherlock, G., Sidow, A., Batzoglou, S., Rauch, R., Kundaje, A., Libbrecht, M., Margulies, E. H., Parker, S. C. J., Elnitski, L., Green, E. D., Hubbard, T., Harrow, J., Searle, S., Kokocinski, F., Aken, B., Frankish, A., Hunt, T., Despacio-Reyes, G., Kay, M., Mukherjee, G., Bignell, A., Saunders, G., Boychenko, V., Brent, M., van Baren, M. J., Brown, R. H., Gerstein, M., Khurana, E., Balasubramanian, S., Lam, H., Cayting, P., Robilotto, R., Lu, Z., Derrien, T., Tanzer, A., Knowles, D. G., Mariotti, M., Haussler, D., Harte, R., Diekhans, M., Lin, M., Valencia, A., Tress, M., Landt, S. G., Raha, D., Shi, M., Euskirchen, G., Grubert, F., Kasowski, M., Lian, J., Lacroute, P., Xu, Y., Monahan, H., Patacsil, D., Slifer, T., Yang, X., Charos, A., Reed, B., Wu, L., Auerbach, R. K., Habegger, L., Hariharan, M., Rozowsky, J., Abyzov, A., Weissman, S. M., Struhl, K., Lamarre-Vincent, N., Lindahl-Allen, M., Miotto, B., Moqtaderi, Z., Fleming, J. D., Newburger, P., Farnham, P. J., Frietze, S., O'Geen, H., Xu, X., Blahnik, K. R., Cao, A. R., Iyengar, S., Kaul, R., Thurman, R. E., Wang, H., Navas, P. A., Sandstrom, R., Sabo, P. J., Weaver, M., Canfield, T., Lee, K., Neph, S., Roach, V., Reynolds, A., Johnson, A., Rynes, E., Giste, E., Vong, S., Neri, J., Frum, T., Nguyen, E. D., Ebersol, A. K., Sanchez, M. E., Sheffer, H. H., Lotakis, D., Haugen, E., Humbert, R., Kutyavin, T., Shafer, T., Noble, W. S., Dekker, J., Lajoie, B. R., Sanyal, A., Rosenbloom, K. R., Dreszer, T. R., Raney, B. J., Barber, G. P., Meyer, L. R., Sloan, C. A., Malladi, V. S., Cline, M. S., Learned, K., Swing, V. K., Zweig, A. S., Rhead, B., Fujita, P. A., Roskin, K., Karolchik, D., Kuhn, R. M., Wilder, S. P., Sobral, D., Herrero, J., Beal, K., Lukk, M., Brazma, A., Vaquerizas, J. M., Luscombe, N. M., Bickel, P. J., Boley, N., Brown, J. B., Li, Q., Huang, H., Sboner, A., Yip, K. Y., Cheng, C., Yan, K. K., Bhardwaj, N., Wang, J., Lochovsky, L., Jee, J., Gibson, T., Leng, J., Du, J., Harris, R. S., Song, G., Miller, W., Suh, B., Paten, B., Hoffman, M. M., Buske, O. J., Weng, Z., Dong, X., Wang, J., Xi, H., Tenenbaum, S. A., Doyle, F., Chittur, S., Penalva, L. O., Tullius, T. D., White, K. P., Karmakar, S., Victorsen, A., Jameel, N., Bild, N., Grossman, R. L., Collins, P. J., Trinklein, N. D., Giddings, M. C., Khatun, J., Maier, C., Wang, T., Whitfield, T. W., Chen, X., Yu, Y., Gunawardena, H., Feingold, E. A., Lowdon, R. F., Dillon, L. A. L., Good, P. J. & Risk, B., Apr 1 2011, In: PLoS biology. 9, 4, e1001046.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      1166 Scopus citations
    • The developmental transcriptome of Drosophila melanogaster

      Graveley, B. R., Brooks, A. N., Carlson, J. W., Duff, M. O., Landolin, J. M., Yang, L., Artieri, C. G., Van Baren, M. J., Boley, N., Booth, B. W., Brown, J. B., Cherbas, L., Davis, C. A., Dobin, A., Li, R., Lin, W., Malone, J. H., Mattiuzzo, N. R., Miller, D., Sturgill, D., & 27 othersTuch, B. B., Zaleski, C., Zhang, D., Blanchette, M., Dudoit, S., Eads, B., Green, R. E., Hammonds, A., Jiang, L., Kapranov, P., Langton, L., Perrimon, N., Sandler, J. E., Wan, K. H., Willingham, A., Zhang, Y., Zou, Y., Andrews, J., Bickel, P. J., Brenner, S. E., Brent, M. R., Cherbas, P., Gingeras, T. R., Hoskins, R. A., Kaufman, T. C., Oliver, B. & Celniker, S. E., Mar 24 2011, In: Nature. 471, 7339, p. 473-479 7 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      1126 Scopus citations
    • The transcriptional diversity of 25 Drosophila cell lines

      Cherbas, L., Willingham, A., Zhang, D., Yang, L., Zou, Y., Eads, B. D., Carlson, J. W., Landolin, J. M., Kapranov, P., Dumais, J., Samsonova, A., Choi, J. H., Roberts, J., Davis, C. A., Tang, H., Van Baren, M. J., Ghosh, S., Dobin, A., Bell, K., Lin, W., & 13 othersLangton, L., Duff, M. O., Tenney, A. E., Zaleski, C., Brent, M. R., Hoskins, R. A., Kaufman, T. C., Andrews, J., Graveley, B. R., Perrimon, N., Celniker, S. E., Gingeras, T. R. & Cherbas, P., Feb 2011, In: Genome research. 21, 2, p. 301-314 14 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      190 Scopus citations
    • Toward an integrated model of capsule regulation in Cryptococcus neoformans

      Haynes, B. C., Skowyra, M. L., Spencer, S. J., Gish, S. R., Williams, M., Held, E. P., Brent, M. R. & Doering, T. L., Dec 2011, In: PLoS pathogens. 7, 12, e1002411.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      74 Scopus citations
    • 2010

      A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription

      Kuttykrishnan, S., Sabina, J., Langton, L. L., Johnston, M. & Brent, M. R., Sep 21 2010, In: Proceedings of the National Academy of Sciences of the United States of America. 107, 38, p. 16743-16748 6 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      32 Scopus citations
    • Identification of functional elements and regulatory circuits by Drosophila modENCODE

      Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N., Eaton, M. L., Landolin, J. M., Bristow, C. A., Ma, L., Lin, M. F., Washietl, S., Arshinoff, B. I., Ay, F., Meyer, P. E., Robine, N., Washington, N. L., Di Stefano, L., Berezikov, E., Brown, C. D., Candeias, R., & 166 othersCarlson, J. W., Carr, A., Jungreis, I., Marbach, D., Sealfon, R., Tolstorukov, M. Y., Will, S., Alekseyenko, A. A., Artieri, C., Booth, B. W., Brooks, A. N., Dai, Q., Davis, C. A., Duff, M. O., Feng, X., Gorchakov, A. A., Gu, T., Henikoff, J. G., Kapranov, P., Li, R., MacAlpine, H. K., Malone, J., Minoda, A., Nordman, J., Okamura, K., Perry, M., Powell, S. K., Riddle, N. C., Sakai, A., Samsonova, A., Sandler, J. E., Schwartz, Y. B., Sher, N., Spokony, R., Sturgill, D., van Baren, M., Wan, K. H., Yang, L., Yu, C., Feingold, E., Good, P., Guyer, M., Lowdon, R., Ahmad, K., Andrews, J., Berger, B., Brenner, S. E., Brent, M. R., Cherbas, L., Elgin, S. C. R., Gingeras, T. R., Grossman, R., Hoskins, R. A., Kaufman, T. C., Kent, W., Kuroda, M. I., Orr-Weaver, T., Perrimon, N., Pirrotta, V., Posakony, J. W., Ren, B., Russell, S., Cherbas, P., Graveley, B. R., Lewis, S., Micklem, G., Oliver, B., Park, P. J., Celniker, S. E., Henikoff, S., Karpen, G. H., Lai, E. C., MacAlpine, D. M., Stein, L. D., White, K. P., Kellis, M., Booth, B., Comstock, C. L. G., Dobin, A., Drenkow, J., Dudoit, S., Dumais, J., Fagegaltier, D., Ghosh, S., Hansen, K. D., Jha, S., Langton, L., Lin, W., Miller, D., Tenney, A. E., Wang, H., Willingham, A. T., Zaleski, C., Zhang, D., Acevedo, D., Bishop, E. P., Gadel, S. E., Jung, Y. L., Kennedy, C. D., Lee, O. K., Linder-Basso, D., Marchetti, S. E., Shanower, G., Nègre, N., Grossman, R. L., Auburn, R., Bellen, H. J., Chen, J., Domanus, M. H., Hanley, D., Heinz, E., Li, Z., Meyer, F., Miller, S. W., Morrison, C. A., Scheftner, D. A., Senderowicz, L., Shah, P. K., Suchy, S., Tian, F., Venken, K. J. T., White, R., Wilkening, J., Zieba, J., Nordman, J. T., Orr-Weaver, T. L., DeNapoli, L. C., Ding, Q., Eng, T., Kashevsky, H., Li, S., Prinz, J. A., Hannon, G. J., Hirst, M., Marra, M., Rooks, M., Zhao, Y., Bryson, T. D., Perry, M. D., Kent, W. J., Lewis, S. E., Barber, G., Chateigner, A., Clawson, H., Contrino, S., Guillier, F., Hinrichs, A. S., Kephart, E. T., Lloyd, P., Lyne, R., McKay, S., Moore, R. A., Mungall, C., Rutherford, K. M., Ruzanov, P., Smith, R., Stinson, E. O., Zha, Z., Artieri, C. G., Malone, J. H., Jiang, L., Mattiuzzo, N., Feingold, E. A., Good, P. J., Guyer, M. S. & Lowdon, R. F., Dec 24 2010, In: Science. 330, 6012, p. 1787-1797 11 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      957 Scopus citations
    • 2009

      Benchmarking regulatory network reconstruction with GRENDEL

      Haynes, B. C. & Brent, M. R., Mar 2009, In: Bioinformatics. 25, 6, p. 801-807 7 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      23 Scopus citations
    • Pairagon: A highly accurate, HMM-based cDNA-to-genome aligner

      Lu, D. V., Brown, R. H., Arumugam, M. & Brent, M. R., 2009, In: Bioinformatics. 25, 13, p. 1587-1593 7 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      6 Scopus citations
    • The completion of the Mammalian Gene Collection

      Temple, G., Gerhard, D. S., Rasooly, R., Feingold, E. A., Good, P. J., Robinson, C., Mandich, A., Derge, J. G., Lewis, J., Shoaf, D., Collins, F. S., Jang, W., Wagner, L., Shenmen, C. M., Misquitta, L., Schaefer, C. F., Buetow, K. H., Bonner, T. I., Yankie, L., Ward, M., & 107 othersPhan, L., Astashyn, A., Brown, G., Farrell, C., Hart, J., Landrum, M., Maidak, B. L., Murphy, M., Murphy, T., Rajput, B., Riddick, L., Webb, D., Weber, J., Wu, W., Pruitt, K. D., Maglott, D., Siepel, A., Brejova, B., Diekhans, M., Harte, R., Baertsch, R., Kent, J., Haussler, D., Brent, M., Langton, L., Comstock, C. L. G., Stevens, M., Wei, C., Van Baren, M. J., Salehi-Ashtiani, K., Murray, R. R., Ghamsari, L., Mello, E., Lin, C., Pennacchio, C., Schreiber, K., Shapiro, N., Marsh, A., Pardes, E., Moore, T., Lebeau, A., Muratet, M., Simmons, B., Kloske, D., Sieja, S., Hudson, J., Sethupathy, P., Brownstein, M., Bhat, N., Lazar, J., Jacob, H., Gruber, C. E., Smith, M. R., McPherson, J., Garcia, A. M., Gunaratne, P. H., Wu, J., Muzny, D., Gibbs, R. A., Young, A. C., Bouffard, G. G., Blakesley, R. W., Mullikin, J., Green, E. D., Dickson, M. C., Rodriguez, A. C., Grimwood, J., Schmutz, J., Myers, R. M., Hirst, M., Zeng, T., Tse, K., Moksa, M., Deng, M., Ma, K., Mah, D., Pang, J., Taylor, G., Chuah, E., Deng, A., Fichter, K., Go, A., Lee, S., Wang, J., Griffith, M., Morin, R., Moore, R. A., Mayo, M., Munro, S., Wagner, S., Jones, S. J. M., Holt, R. A., Marra, M. A., Lu, S., Yang, S., Hartigan, J., Graf, M., Wagner, R., Letovksy, S., Pulido, J. C., Robison, K., Esposito, D., Hartley, J., Wall, V. E., Hopkins, R. F., Ohara, O. & Wiemann, S., Dec 2009, In: Genome research. 19, 12, p. 2324-2333 10 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      108 Scopus citations
    • 2008

      wuHMM: A robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data

      Cahan, P., Godfrey, L. E., Eis, P. S., Richmond, T. A., Selzer, R. R., Brent, M., Mcleod, H. L., Ley, T. J. & Graubert, T. A., Apr 2008, In: Nucleic acids research. 36, 7, e41.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      24 Scopus citations
    • 2007

      A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices

      Tenney, A. E., Jia, Q. W., Langton, L., Klueh, P., Quatrano, R. & Brent, M. R., Feb 2007, In: Genome research. 17, 2, p. 212-218 7 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      12 Scopus citations
    • Evolution of genes and genomes on the Drosophila phylogeny

      Clark, A. G., Eisen, M. B., Smith, D. R., Bergman, C. M., Oliver, B., Markow, T. A., Kaufman, T. C., Kellis, M., Gelbart, W., Iyer, V. N., Pollard, D. A., Sackton, T. B., Larracuente, A. M., Singh, N. D., Abad, J. P., Abt, D. N., Adryan, B., Aguade, M., Akashi, H., Anderson, W. W., & 395 othersAquadro, C. F., Ardell, D. H., Arguello, R., Artieri, C. G., Barbash, D. A., Barker, D., Barsanti, P., Batterham, P., Batzoglou, S., Begun, D., Bhutkar, A., Blanco, E., Bosak, S. A., Bradley, R. K., Brand, A. D., Brent, M. R., Brooks, A. N., Brown, R. H., Butlin, R. K., Caggese, C., Calvi, B. R., Bernardo De Carvalho, A., Caspi, A., Castrezana, S., Celniker, S. E., Chang, J. L., Chapple, C., Chatterji, S., Chinwalla, A., Civetta, A., Clifton, S. W., Comeron, J. M., Costello, J. C., Coyne, J. A., Daub, J., David, R. G., Delcher, A. L., Delehaunty, K., Do, C. B., Ebling, H., Edwards, K., Eickbush, T., Evans, J. D., Filipski, A., Findeiß, S., Freyhult, E., Fulton, L., Fulton, R., Garcia, A. C. L., Gardiner, A., Garfield, D. A., Garvin, B. E., Gibson, G., Gilbert, D., Gnerre, S., Godfrey, J., Good, R., Gotea, V., Gravely, B., Greenberg, A. J., Griffiths-Jones, S., Gross, S., Guigo, R., Gustafson, E. A., Haerty, W., Hahn, M. W., Halligan, D. L., Halpern, A. L., Halter, G. M., Han, M. V., Heger, A., Hillier, L. D., Hinrichs, A. S., Holmes, I., Hoskins, R. A., Hubisz, M. J., Hultmark, D., Huntley, M. A., Jaffe, D. B., Jagadeeshan, S., Jeck, W. R., Johnson, J., Jones, C. D., Jordan, W. C., Karpen, G. H., Kataoka, E., Keightley, P. D., Kheradpour, P., Kirkness, E. F., Koerich, L. B., Kristiansen, K., Kudrna, D., Kulathinal, R. J., Kumar, S., Kwok, R., Lander, E., Langley, C. H., Lapoint, R., Lazzaro, B. P., Lee, S. J., Levesque, L., Li, R., Lin, C. F., Lin, M. F., Lindblad-Toh, K., Llopart, A., Long, M., Low, L., Lozovsky, E., Lu, J., Luo, M., Machado, C. A., Makalowski, W., Marzo, M., Matsuda, M., Matzkin, L., McAllister, B., McBride, C. S., McKernan, B., McKernan, K., Mendez-Lago, M., Minx, P., Mollenhauer, M. U., Montooth, K., Mount, S. M., Mu, X., Myers, E., Negre, B., Newfeld, S., Nielsen, R., Noor, M. A. F., O'Grady, P., Pachter, L., Papaceit, M., Parisi, M. J., Parisi, M., Parts, L., Pedersen, J. S., Pesole, G., Phillippy, A. M., Ponting, C. P., Pop, M., Porcelli, D., Powell, J. R., Prohaska, S., Pruitt, K., Puig, M., Quesneville, H., Ravi Ram, K., Rand, D., Rasmussen, M. D., Reed, L. K., Reenan, R., Reily, A., Remington, K. A., Rieger, T. T., Ritchie, M. G., Robin, C., Rogers, Y. H., Rohde, C., Rozas, J., Rubenfield, M. J., Ruiz, A., Russo, S., Salzberg, S. L., Sanchez-Gracia, A., Saranga, D. J., Sato, H., Schaeffer, S. W., Schatz, M. C., Schlenke, T., Schwartz, R., Segarra, C., Singh, R. S., Sirot, L., Sirota, M., Sisneros, N. B., Smith, C. D., Smith, T. F., Spieth, J., Stage, D. E., Stark, A., Stephan, W., Strausberg, R. L., Strempel, S., Sturgill, D., Sutton, G., Sutton, G. 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      Research output: Contribution to journalArticlepeer-review

      Open Access
      1573 Scopus citations
    • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

      Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J. A., Andrews, R. M., Flicek, P., & 291 othersBoyle, P. J., Cao, H., Carter, N. P., Clelland, G. K., Davis, S., Day, N., Dhami, P., Dillon, S. C., Dorschner, M. O., Fiegler, H., Giresi, P. G., Goldy, J., Hawrylycz, M., Haydock, A., Humbert, R., James, K. D., Johnson, B. E., Johnson, E. M., Frum, T. T., Rosenzweig, E. R., Karnani, N., Lee, K., Lefebvre, G. C., Navas, P. A., Neri, F., Parker, S. C. J., Sabo, P. J., Sandstrom, R., Shafer, A., Vetrie, D., Weaver, M., Wilcox, S., Yu, M., Collins, F. S., Dekker, J., Lieb, J. D., Tullius, T. D., Crawford, G. E., Sunyaev, S., Noble, W. S., Dunham, I., Denoeud, F., Reymond, A., Kapranov, P., Rozowsky, J., Zheng, D., Castelo, R., Frankish, A., Harrow, J., Ghosh, S., Sandelin, A., Hofacker, I. L., Baertsch, R., Keefe, D., Dike, S., Cheng, J., Hirsch, H. A., Sekinger, E. A., Lagarde, J., Abril, J. F., Shahab, A., Flamm, C., Fried, C., Hackermüller, J., Hertel, J., Lindemeyer, M., Missal, K., Tanzer, A., Washietl, S., Korbel, J., Emanuelsson, O., Pedersen, J. S., Holroyd, N., Taylor, R., Swarbreck, D., Matthews, N., Dickson, M. C., Thomas, D. J., Weirauch, M. T., Gilbert, J., Drenkow, J., Bell, I., Zhao, X., Srinivasan, K. G., Sung, W. K., Ooi, H. S., Chiu, K. P., Foissac, S., Alioto, T., Brent, M., Pachter, L., Tress, M. L., Valencia, A., Choo, S. W., Choo, C. Y., Ucla, C., Manzano, C., Wyss, C., Cheung, E., Clark, T. G., Brown, J. B., Ganesh, M., Patel, S., Tammana, H., Chrast, J., Henrichsen, C. N., Kai, C., Kawai, J., Nagalakshmi, U., Wu, J., Lian, Z., Lian, J., Newburger, P., Zhang, X., Bickel, P., Mattick, J. S., Carninci, P., Hayashizaki, Y., Weissman, S., Hubbard, T., Myers, R. M., Rogers, J., Stadler, P. F., Lowe, T. M., Wei, C. L., Ruan, Y., Struhl, K., Gerstein, M., Antonarakis, S. E., Fu, Y., Green, E. D., Karaöz, U., Siepel, A., Taylor, J., Liefer, L. A., Wetterstrand, K. A., Good, P. J., Feingold, E. A., Guyer, M. S., Cooper, G. M., Asimenos, G., Dewey, C. N., Hou, M., Nikolaev, S., Montoya-Burgos, J. I., Löytynoja, A., Whelan, S., Pardi, F., Massingham, T., Huang, H., Zhang, N. R., Holmes, I., Mullikin, J. C., Ureta-Vidal, A., Paten, B., Seringhaus, M., Church, D., Rosenbloom, K., Kent, W. J., Stone, E. A., Batzoglou, S., Goldman, N., Hardison, R. C., Haussler, D., Miller, W., Sidow, A., Trinklein, N. D., Zhang, Z. D., Barrera, L., Stuart, R., King, D. C., Ameur, A., Enroth, S., Bieda, M. C., Kim, J., Bhinge, A. A., Jiang, N., Liu, J., Yao, F., Vega, V. B., Lee, C. W. H., Ng, P., Yang, A., Moqtaderi, Z., Zhu, Z., Xu, X., Squazzo, S., Oberley, M. J., Inman, D., Singer, M. A., Richmond, T. A., Munn, K. J., Rada-Iglesias, A., Wallerman, O., Komorowski, J., Fowler, J. C., Couttet, P., Bruce, A. W., Dovey, O. M., Ellis, P. D., Langford, C. F., Nix, D. A., Euskirchen, G., Hartman, S., Urban, A. E., Kraus, P., Van Calcar, S., Heintzman, N., Hoon Kim, T., Wang, K., Qu, C., Hon, G., Luna, R., Glass, C. K., Rosenfeld, M. G., Aldred, S. F., Cooper, S. J., Halees, A., Lin, J. M., Shulha, H. P., Zhang, X., Xu, M., Haidar, J. N. S., Yu, Y., Iyer, V. R., Green, R. D., Wadelius, C., Farnham, P. J., Ren, B., Harte, R. A., Hinrichs, A. S., Trumbower, H., Clawson, H., Hillman-Jackson, J., Zweig, A. S., Smith, K., Thakkapallayil, A., Barber, G., Kuhn, R. M., Karolchik, D., Armengol, L., Bird, C. P., De Bakker, P. I. W., Kern, A. D., Lopez-Bigas, N., Martin, J. D., Stranger, B. E., Woodroffe, A., Davydov, E., Dimas, A., Eyras, E., Hallgrímsdóttir, I. B., Huppert, J., Zody, M. C., Abecasis, G. R., Estivill, X., Bouffard, G. G., Guan, X., Hansen, N. F., Idol, J. R., Maduro, V. V. B., Maskeri, B., McDowell, J. C., Park, M., Thomas, P. J., Young, A. C., Blakesley, R. W., Muzny, D. M., Sodergren, E., Wheeler, D. A., Worley, K. C., Jiang, H., Weinstock, G. M., Gibbs, R. A., Graves, T., Fulton, R., Mardis, E. R., Wilson, R. K., Clamp, M., Cuff, J., Gnerre, S., Jaffe, D. B., Chang, J. L., Lindblad-Toh, K., Lander, E. S., Koriabine, M., Nefedov, M., Osoegawa, K., Yoshinaga, Y., Zhu, B. & De Jong, P. J., Jun 14 2007, In: Nature. 447, 7146, p. 799-816 18 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      4268 Scopus citations
    • Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping

      Vermeirssen, V., Deplancke, B., Barrasa, M. I., Reece-Hoyes, J. S., Arda, H. E., Grove, C. A., Martinez, N. J., Sequerra, R., Doucette-Stamm, L., Brent, M. R. & Walhout, A. J. M., Aug 2007, In: Nature Methods. 4, 8, p. 659-664 6 p.

      Research output: Contribution to journalArticlepeer-review

      57 Scopus citations
    • Targeted discovery of novel human exons by comparative genomics

      Siepel, A., Diekhans, M., Brejová, B., Langton, L., Stevens, M., Comstock, C. L. G., Davis, C., Ewing, B., Oommen, S., Lau, C., Yu, H. C., Li, J., Roe, B. A., Green, P., Gerhard, D. S., Temple, G., Haussler, D. & Brent, M. R., Dec 2007, In: Genome research. 17, 12, p. 1763-1773 11 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      38 Scopus citations
    • The Treeterbi and Parallel Treeterbi algorithms: Efficient, optimal decoding for ordinary, generalized and pair HMMs

      Keibler, E., Arumugam, M. & Brent, M. R., Mar 2007, In: Bioinformatics. 23, 5, p. 545-554 10 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      7 Scopus citations
    • Using N-SCAN or TWINSCAN to predict gene structures in genomic DNA sequences.

      van Baren, M. J., Koebbe, B. C. & Brent, M. R., Dec 2007, In: Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]. Chapter 4, p. Unit 4.8

      Research output: Contribution to journalArticlepeer-review

      16 Scopus citations
    • 2006

      Iterative gene prediction and pseudogene removal improves genome annotation

      Van Baren, M. J. & Brent, M. R., May 2006, In: Genome research. 16, 5, p. 678-685 8 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      56 Scopus citations
    • Molecular properties of adult mouse gastric and intestinal epithelial progenitors in their niches

      Giannakis, M., Stappenbeck, T., Mills, J. C., Leip, D. G., Lovett, M., Clifton, S. W., Ippolito, J. E., Glasscock, J. I., Arumugam, M., Brent, M. R. & Gordon, J. I., Apr 21 2006, In: Journal of Biological Chemistry. 281, 16, p. 11292-11300 9 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      158 Scopus citations
    • Pairagon+N-SCAN_EST: a model-based gene annotation pipeline.

      Arumugam, M., Wei, C., Brown, R. H. & Brent, M. R., 2006, In: Genome biology. 7 Suppl 1, p. S5.1-10

      Research output: Contribution to journalArticlepeer-review

      11 Scopus citations
    • Using ESTs to improve the accuracy of de novo gene prediction

      Wei, C. & Brent, M. R., Jul 3 2006, In: BMC bioinformatics. 7, 327.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      35 Scopus citations
    • Using multiple alignments to improve gene prediction

      Gross, S. S. & Brent, M. R., Mar 2006, In: Journal of Computational Biology. 13, 2, p. 379-393 15 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      93 Scopus citations
    • Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.

      Flicek, P. & Brent, M. R., 2006, In: Genome biology. 7 Suppl 1, p. S8.1-9

      Research output: Contribution to journalArticlepeer-review

      4 Scopus citations
    • 2005

      Begin at the beginning: Predicting genes with 5′ UTRs

      Brown, R. H., Gross, S. S. & Brent, M. R., May 2005, In: Genome research. 15, 5, p. 742-747 6 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      25 Scopus citations
    • Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions

      Wei, C., Lamesch, P., Arumugam, M., Rosenberg, J., Hu, P., Vidal, M. & Brent, M. R., Apr 2005, In: Genome research. 15, 4, p. 577-582 6 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      32 Scopus citations
    • Gene finding in the chicken genome

      Eyras, E., Reymond, A., Castelo, R., Bye, J. M., Camara, F., Flicek, P., Huckle, E. J., Parra, G., Shteynberg, D. D., Wyss, C., Rogers, J., Antonarakis, S. E., Birney, E., Guigo, R. & Brent, M. R., May 30 2005, In: BMC bioinformatics. 6, 131.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      28 Scopus citations
    • The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans

      Loftus, B. J., Fung, E., Roncaglia, P., Rowley, D., Amedeo, P., Bruno, D., Vamathevan, J., Miranda, M., Anderson, I. J., Fraser, J. A., Allen, J. E., Bosdet, I. E., Brent, M. R., Chiu, R., Doering, T. L., Donlin, M. J., D'Souza, C. A., Fox, D. S., Grinberg, V., Fu, J., & 34 othersFukushima, M., Haas, B. J., Huang, J. C., Janbon, G., Jones, S. J. M., Koo, H. L., Krzywinski, M. I., Kwon-Chung, J. K., Lengeler, K. B., Maiti, R., Marra, M. A., Marra, R. E., Mathewson, C. A., Mitchell, T. G., Pertea, M., Riggs, F. R., Salzberg, S. L., Schein, J. E., Shvartsbeyn, A., Shin, H., Shumway, M., Specht, C. A., Suh, B. B., Tenney, A., Utterback, T. R., Wickes, B. L., Wortman, J. R., Wye, N. H., Kronstad, J. W., Lodge, J. K., Heitman, J., Davis, R. W., Fraser, C. M. & Hyman, R. W., Feb 25 2005, In: Science. 307, 5713, p. 1321-1324 4 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      577 Scopus citations
    • 2004

      Gene prediction and verification in a compact genome with numerous small introns

      Tenney, A. E., Brown, R. H., Vaske, C., Lodge, J. K., Doering, T. L. & Brent, M. R., Nov 2004, In: Genome research. 14, 11, p. 2330-2335 6 p.

      Research output: Contribution to journalArticlepeer-review

      Open Access
      33 Scopus citations