Browse by CSHL Author

Paper

Williams, Jason, Nash, Bruce, Ghiban, Cornel, Khalfan, Mohammed, Hilgert, Uwe, Lauter, Susan, Yang, Chun-Hua, Micklos, David Andrew (April 2024) Analysis of DNA Barcodes Using DNA Subway. Methods in molecular biology (Clifton, N.J.), 2744. pp. 551-560. ISSN 1064-3745

Swetnam, Tyson L, Antin, Parker B, Bartelme, Ryan, Bucksch, Alexander, Camhy, David, Chism, Greg, Choi, Illyoung, Cooksey, Amanda M, Cosi, Michele, Cowen, Cindy, Culshaw-Maurer, Michael, Davey, Robert, Davey, Sean, Devisetty, Upendra, Edgin, Tony, Edmonds, Andy, Fedorov, Dmitry, Frady, Jeremy, Fonner, John, Gillan, Jeffrey K, Hossain, Iqbal, Joyce, Blake, Lang, Konrad, Lee, Tina, Littin, Shelley, McEwen, Ian, Merchant, Nirav, Micklos, David, Nelson, Andrew, Ramsey, Ashley, Roberts, Sarah, Sarando, Paul, Skidmore, Edwin, Song, Jawon, Sprinkle, Mary Margaret, Srinivasan, Sriram, Stanzione, Dan, Strootman, Jonathan D, Stryeck, Sarah, Tuteja, Reetu, Vaughn, Matthew, Wali, Mojib, Wall, Mariah, Walls, Ramona, Wang, Liya, Wickizer, Todd, Williams, Jason, Wregglesworth, John, Lyons, Eric (February 2024) CyVerse: Cyberinfrastructure for open science. PLoS Computational Biology, 20 (2). e1011270. ISSN 1553-734X

Swetnam, Tyson L, Antin, Parker B, Bartelme, Ryan, Bucksch, Alexander, Camhy, David, Chism, Greg, Choi, Illyoung, Cooksey, Amanda M, Cosi, Michele, Cowen, Cindy, Culshaw-Maurer, Michael, Davey, Robert, Davey, Sean, Devisetty, Upendra, Edgin, Tony, Edmonds, Andy, Fedorov, Dmitry, Frady, Jeremy, Fonner, John, Gillan, Jeffrey K, Hossain, Iqbal, Joyce, Blake, Lang, Konrad, Lee, Tina, Littin, Shelley, Mcewen, Ian, Merchant, Nirav, Micklos, David, Nelson, Andrew, Ramsey, Ashley, Roberts, Sarah, Sarando, Paul, Skidmore, Edwin, Song, Jawon, Sprinkle, Mary Margaret, Srinivasan, Sriram, Strootman, Jonathan D, Stryeck, Sarah, Tuteja, Reetu, Vaughn, Matthew, Wali, Mojib, Wall, Mariah, Walls, Ramona, Wang, Liya, Wickizer, Todd, Williams, Jason, Wregglesworth, John, Lyons, Eric (June 2023) CyVerse: Cyberinfrastructure for Open Science. (Submitted)

Drew, J, Morgan, W, Galindo, S, Kleinschmit, AJ, McWilliams, M, Pauley, M, Triplett, EW, Williams, J, Murdoch, B, Rosenwald, A (January 2023) Revisiting barriers to implementation of bioinformatics into life sciences education. Frontiers in Education, 8. ISSN 2504-284X

Harris, Nomi L, Fields, Christopher J, Hokamp, Karsten, Just, Jérémy, Khetani, Radhika, Maia, Jessica, Ménager, Hervé, Munoz-Torres, Monica C, Unni, Deepak, Williams, Jason (2023) BOSC 2023, the 24th annual Bioinformatics Open Source Conference. F1000Research, 12. p. 1568. ISSN 2046-1402

Williams, Jason J, Tractenberg, Rochelle E, Batut, Bérénice, Becker, Erin A, Brown, Anne M, Burke, Melissa L, Busby, Ben, Cooch, Nisha K, Dillman, Allissa A, Donovan, Samuel S, Doyle, Maria A, van Gelder, Celia WG, Hall, Christina R, Hertweck, Kate L, Jordan, Kari L, Jungck, John R, Latour, Ainsley R, Lindvall, Jessica M, Lloret-Llinares, Marta, McDowell, Gary S, Morris, Rana, Mourad, Teresa, Nisselle, Amy, Ordóñez, Patricia, Paladin, Lisanna, Palagi, Patricia M, Sukhai, Mahadeo A, Teal, Tracy K, Woodley, Louise (2023) An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond. PLoS One, 18 (11). e0293879. ISSN 1932-6203

Handelsman, Jo, Elgin, Sarah, Estrada, Mica, Hays, Shan, Johnson, Tracy, Miller, Sarah, Mingo, Vida, Shaffer, Christopher, Williams, Jason (June 2022) Achieving STEM diversity: Fix the classrooms. Science, 376 (6597). pp. 1057-1059. ISSN 0036-8075

Harris, Nomi L, Hokamp, Karsten, Ménager, Hervé, Munoz-Torres, Monica, Unni, Deepak, Vasilevsky, Nicole, Williams, Jason (2022) BOSC 2022: the first hybrid and 23rd annual Bioinformatics Open Source Conference. F1000Research, 11. p. 1034. ISSN 2046-1402

Williams, Jason (2022) CyVerse for Reproducible Research: RNA-Seq Analysis. Methods in Molecular Biology, 2443. pp. 57-79. ISSN 1064-3745

Harris, Nomi L, Cock, Peter JA, Fields, Christopher J, Hokamp, Karsten, Maia, Jessica, Munoz-Torres, Monica, Sharan, Malvika, Williams, Jason (October 2021) BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference. F1000Research, 10. p. 1054. ISSN 2046-1402

Elgin, Sarah CR, Hays, Shan, Mingo, Vida, Shaffer, Christopher D, Williams, Jason (June 2021) Building Back More Equitable STEM Education: Teach Science by Engaging Students in Doing Science. BioRxiv. (Unpublished)

Williams, J. J., Drew, J. C., Galindo-Gonzalez, S., Robic, S., Dinsdale, E., Morgan, W. R., Triplett, E. W., Burnette, J. M., Donovan, S. S., Fowlks, E. R., Goodman, A. L., Grandgenett, N. F., Goller, C. C., Hauser, C., Jungck, J. R., Newman, J. D., Pearson, W. R., Ryder, E. F., Sierk, M., Smith, T. M., Tosado-Acevedo, R., Tapprich, W., Tobin, T. C., Toro-Martinez, A., Welch, L. R., Wilson, M. A., Ebenbach, D., McWilliams, M., Rosenwald, A. G., Pauley, M. A. (November 2019) Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction. PLoS One, 14 (11). e0224288. ISSN 1932-6203

Clarke, D. J. B., Wang, L., Jones, A., Wojciechowicz, M. L., Torre, D., Jagodnik, K. M., Jenkins, S. L., McQuilton, P., Flamholz, Z., Silverstein, M. C., Schilder, B. M., Robasky, K., Castillo, C., Idaszak, R., Ahalt, S. C., Williams, J., Schurer, S., Cooper, D. J., de Miranda Azevedo, R., Klenk, J. A., Haendel, M. A., Nedzel, J., Avillach, P., Shimoyama, M. E., Harris, R. M., Gamble, M., Poten, R., Charbonneau, A. L., Larkin, J., Brown, C. T., Bonazzi, V. R., Dumontier, M. J., Sansone, S. A., Ma'ayan, A. (October 2019) FAIRshake: Toolkit to Evaluate the FAIRness of Research Digital Resources. Cell Syst, 9 (5). pp. 417-421. ISSN 2405-4712

Clarke, Daniel JB, Wang, Lily, Jones, Alex, Wojciechowicz, Megan L, Torre, Denis, Jagodnik, Kathleen M, Jenkins, Sherry L, McQuilton, Peter, Flamholz, Zachary, Silverstein, Moshe C, Schilder, Brian M, Robasky, Kimberly, Castillo, Claris, Idaszak, Ray, Ahalt, Stanley C, Williams, Jason, Schurer, Stephan, Cooper, Daniel J, de Miranda Azevedo, Ricardo, Klenk, Juergen A, Haendel, Melissa A, Nedzel, Jared, Avillach, Paul, Shimoyama, Mary E, Harris, Rayna M, Gamble, Meredith, Poten, Rudy, Charbonneau, Amanda L, Larkin, Jennie, Brown, C Titus, Bonazzi, Vivien R, Dumontier, Michel J, Sansone, Susanna-Assunta, Ma’ayan, Avi (June 2019) FAIRshake: toolkit to evaluate the findability, accessibility, interoperability, and reusability of research digital resources. BioRxiv. (Unpublished)

Wilson Sayres, M. A., Hauser, C., Sierk, M., Robic, S., Rosenwald, A. G., Smith, T. M., Triplett, E. W., Williams, J. J., Dinsdale, E., Morgan, W. R., Burnette, J. M., Donovan, S. S., Drew, J. C., Elgin, S. C. R., Fowlks, E. R., Galindo-Gonzalez, S., Goodman, A. L., Grandgenett, N. F., Goller, C. C., Jungck, J. R., Newman, J. D., Pearson, W., Ryder, E. F., Tosado-Acevedo, R., Tapprich, W., Tobin, T. C., Toro-Martinez, A., Welch, L. R., Wright, R., Barone, L., Ebenbach, D., McWilliams, M., Olney, K. C., Pauley, M. A. (June 2018) Bioinformatics core competencies for undergraduate life sciences education. PLoS One, 13 (6). e0196878. ISSN 1932-6203

Williams, Jason J, Drew, Jennifer C, Galindo-Gonzalez, Sebastian, Robic, Srebrenka, Dinsdale, Elizabeth, Morgan, William, Triplett, Eric W, Burnette, James, Donovan, Samuel, Elgin, Sarah, Fowlks, Edison R, Goodman, Anya L, Grandgenett, Nealy F, Goller, Carlos, Hauser, Charles, Jungck, John R, Newman, Jeffrey D, Pearson, William, Ryder, Elizabeth, Wilson Sayres, Melissa A, Sierk, Michael, Smith, Todd, Tosado-Acevedo, Rafael, Tapprich, William, Tobin, Tammy C, Toro, Arlín, Welch, Lonnie, Wright, Robin, Ebenbach, David, McWilliams, Mindy, Rosenwald, Anne G, Pauley, Mark A (October 2017) Barriers to Integration of Bioinformatics into Undergraduate Life Sciences Education. BioRxiv. (Unpublished)

Barone, L., Williams, J., Micklos, D. (October 2017) Unmet needs for analyzing biological big data: A survey of 704 NSF principal investigators. PLoS Comput Biol, 13 (10). e1005755. ISSN 1553-734x

Wilson Sayres, Melissa A, Hauser, Charles, Sierk, Michael, Robic, Srebrenka, Rosenwald, Anne G, Smith, Todd M, Triplett, Eric W, Williams, Jason J, Dinsdale, Elizabeth, Morgan, William, Burnette, James M, Donovan, Samuel S, Drew, Jennifer C, Elgin, Sarah CR, Fowlks, Edison R, Galindo-Gonzalez, Sebastian, Goodman, Anya L, Grandgenett, Neal F, Goller, Carlos C, Jungck, John, Newman, Jeffrey D, Pearson, William, Ryder, Elizabeth, Tosado-Acevedo, Rafael, Tapprich, William, Tobin, Tammy C, Toro-Martínez, Arlín, Welch, Lonnie R, Wright, Robin, Ebenbach, David, Olney, Kimberly C, McWilliams, Mindy, Pauley, Mark A (August 2017) Bioinformatics Core Competencies for Undergraduate Life Sciences Education. BioRxiv. (Unpublished)

Barone, Lindsay, Williams, Jason, Micklos, David (February 2017) Unmet Needs for Analyzing Biological Big Data: A Survey of 704 NSF Principal Investigators. BioRxiv. (Unpublished)

Williams, J. J., Teal, T. K. (January 2017) A vision for collaborative training infrastructure for bioinformatics. Ann N Y Acad Sci, 1387 (1). pp. 54-60. ISSN 1749-6632 (Electronic)0077-8923 (Linking)

Martin, L., Cook, C., Matasci, N., Williams, J., Bastow, R. (2015) Data mining with iPlant: A meeting report from the 2013 GARNet workshop, Data mining with iPlant. Journal of Experimental Botany, 66 (1). pp. 1-6. ISSN 0022-0957

Flint, S. J., Sambrook, J., Williams, J. F., Sharp, P. A. (July 1976) Viral nucleic acid sequences in transformed cells. IV. A study of the sequences of adenovirus 5 DNA and RNA in four lines of adenovirus 5-transformed rodent cells using specific fragments of the viral genome. Virology, 72 (2). pp. 456-70.

Conference or Workshop Item

Grodzicker, T., Williams, J., Sharp, P., Sambrook, J. (1974) Physical mapping of temperature-sensitive mutations of adenoviruses. In: Cold Spring Harbor Symposia on Quantitative Biology XXXIX: Tumor Viruses, Cold Spring Harbor, N. Y..

Book

Hilgert, U., McKay, S., Ghiban, C., Khalfan, M., Micklos, D., Williams, J. (July 2014) DNA Subway: Making genome analysis egalitarian. ACM International Conference Proceeding Series . Association for Computing Machinery, Article number 70. ISBN 978-145032893-7