Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins

by Yan Koon-Kiu, Axelsen Jacob, Maslov Sergei
Published 2007-11-01

Upstream plasticity and downstream robustness in evolution of molecular networks

by Eriksen Kasper, Sneppen Kim, Maslov Sergei, Yan Koon-Kiu
Published 2004-03-01

Detecting modules in multiplex networks – an application for integrating expression profiles across multiple species

by Yan, Koon-Kiu, Wang, Daifeng, Rozowsky, Joel, Zheng, Henry, Pei, Baikang, Gerstein, Mark
Published 2013

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation.

by Sethi, Anurag, Gu, Mengting, Gumusgoz, Emrah, Chan, Landon, Yan, Koon-Kiu, Rozowsky, Joel, Barozzi, Iros, Afzal, Veena, Akiyama, Jennifer A, Plajzer-Frick, Ingrid, Yan, Chengfei, Novak, Catherine S, Kato, Momoe, Garvin, Tyler H, Pham, Quan, Harrington, Anne, Mannion, Brandon J, Lee, Elizabeth A, Fukuda-Yuzawa, Yoko, Visel, Axel, Dickel, Diane E, Yip, Kevin Y, Sutton, Richard, Pennacchio, Len A, Gerstein, Mark
Published 2020

A cross-organism framework for supervised enhancer prediction with epigenetic pattern recognition and targeted validation

by Sethi, Anurag, Gu, Mengting, Gumusgoz, Emrah, Chan, Landon, Yan, Koon-Kiu, Rozowsky, Joel, Barozzi, Iros, Afzal, Veena, Akiyama, Jennifer, Plajzer-Frick, Ingrid, Yan, Chengfei, Pickle, Catherine, Kato, Momoe, Garvin, Tyler, Pham, Quan, Harrington, Anne, Mannion, Brandon, Lee, Elizabeth, Fukuda-Yuzawa, Yoko, Visel, Axel, Dickel, Diane, Yip, Kevin, Sutton, Richard, Pennacchio, Len, Gerstein, Mark
Published 2018

Comparative analysis of regulatory information and circuits across distant species.

by Boyle, Alan P, Araya, Carlos L, Brdlik, Cathleen, Cayting, Philip, Cheng, Chao, Cheng, Yong, Gardner, Kathryn, Hillier, LaDeana W, Janette, Judith, Jiang, Lixia, Kasper, Dionna, Kawli, Trupti, Kheradpour, Pouya, Kundaje, Anshul, Li, Jingyi Jessica, Ma, Lijia, Niu, Wei, Rehm, E Jay, Rozowsky, Joel, Slattery, Matthew, Spokony, Rebecca, Terrell, Robert, Vafeados, Dionne, Wang, Daifeng, Weisdepp, Peter, Wu, Yi-Chieh, Xie, Dan, Yan, Koon-Kiu, Feingold, Elise A, Good, Peter J, Pazin, Michael J, Huang, Haiyan, Bickel, Peter J, Brenner, Steven E, Reinke, Valerie, Waterston, Robert H, Gerstein, Mark, White, Kevin P, Kellis, Manolis, Snyder, Michael
Published 2014

Comparative Analysis of the Transcriptome across Distant Species

by Gerstein, Mark B., Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B., Davis, Carrie A, Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O., Duff, Michael O., Djebali, Sarah, Alexander, Roger P., Alver, Burak H., Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J., Boeck, Max E., Boley, Nathan P., Booth, Benjamin W., Cherbas, Lucy, Cherbas, Peter, Di, Chao, Dobin, Alex, Drenkow, Jorg, Ewing, Brent, Fang, Gang, Fastuca, Megan, Feingold, Elise A., Frankish, Adam, Gao, Guanjun, Good, Peter J., Guigó, Roderic, Hammonds, Ann, Harrow, Jen, Hoskins, Roger A., Howald, Cédric, Hu, Long, Huang, Haiyan, Hubbard, Tim J. P., Huynh, Chau, Jha, Sonali, Kasper, Dionna, Kato, Masaomi, Kaufman, Thomas C., Kitchen, Robert R., Ladewig, Erik, Lagarde, Julien, Lai, Eric, Leng, Jing, Lu, Zhi, MacCoss, Michael, May, Gemma, McWhirter, Rebecca, Merrihew, Gennifer, Miller, David M., Mortazavi, Ali, Murad, Rabi, Oliver, Brian, Olson, Sara, Park, Peter J., Pazin, Michael J., Perrimon, Norbert, Pervouchine, Dmitri, Reinke, Valerie, Reymond, Alexandre, Robinson, Garrett, Samsonova, Anastasia, Saunders, Gary I., Schlesinger, Felix, Sethi, Anurag, Slack, Frank J., Spencer, William C., Stoiber, Marcus H., Strasbourger, Pnina, Tanzer, Andrea, Thompson, Owen A., Wan, Kenneth H., Wang, Guilin, Wang, Huaien, Watkins, Kathie L., Wen, Jiayu, Wen, Kejia, Xue, Chenghai, Yang, Li, Yip, Kevin, Zaleski, Chris, Zhang, Yan, Zheng, Henry, Brenner, Steven E., Graveley, Brenton R., Celniker, Susan E., Gingeras, Thomas R, Waterston, Robert
Published 2015

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors.

by Kudron, Michelle M, Victorsen, Alec, Gevirtzman, Louis, Hillier, LaDeana W, Fisher, William W, Vafeados, Dionne, Kirkey, Matt, Hammonds, Ann S, Gersch, Jeffery, Ammouri, Haneen, Wall, Martha L, Moran, Jennifer, Steffen, David, Szynkarek, Matt, Seabrook-Sturgis, Samantha, Jameel, Nader, Kadaba, Madhura, Patton, Jaeda, Terrell, Robert, Corson, Mitch, Durham, Timothy J, Park, Soo, Samanta, Swapna, Han, Mei, Xu, Jinrui, Yan, Koon-Kiu, Celniker, Susan E, White, Kevin P, Ma, Lijia, Gerstein, Mark, Reinke, Valerie, Waterston, Robert H
Published 2018

Comparative analysis of the transcriptome across distant species.

by Gerstein, Mark B, Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B, Davis, Carrie A, Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O, Duff, Michael O, Djebali, Sarah, Alexander, Roger P, Alver, Burak H, Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J, Boeck, Max E, Boley, Nathan P, Booth, Benjamin W, Cherbas, Lucy, Cherbas, Peter, Di, Chao, Dobin, Alex, Drenkow, Jorg, Ewing, Brent, Fang, Gang, Fastuca, Megan, Feingold, Elise A, Frankish, Adam, Gao, Guanjun, Good, Peter J, Guigó, Roderic, Hammonds, Ann, Harrow, Jen, Hoskins, Roger A, Howald, Cédric, Hu, Long, Huang, Haiyan, Hubbard, Tim JP, Huynh, Chau, Jha, Sonali, Kasper, Dionna, Kato, Masaomi, Kaufman, Thomas C, Kitchen, Robert R, Ladewig, Erik, Lagarde, Julien, Lai, Eric, Leng, Jing, Lu, Zhi, MacCoss, Michael, May, Gemma, McWhirter, Rebecca, Merrihew, Gennifer, Miller, David M, Mortazavi, Ali, Murad, Rabi, Oliver, Brian, Olson, Sara, Park, Peter J, Pazin, Michael J, Perrimon, Norbert, Pervouchine, Dmitri, Reinke, Valerie, Reymond, Alexandre, Robinson, Garrett, Samsonova, Anastasia, Saunders, Gary I, Schlesinger, Felix, Sethi, Anurag, Slack, Frank J, Spencer, William C, Stoiber, Marcus H, Strasbourger, Pnina, Tanzer, Andrea, Thompson, Owen A, Wan, Kenneth H, Wang, Guilin, Wang, Huaien, Watkins, Kathie L, Wen, Jiayu, Wen, Kejia, Xue, Chenghai, Yang, Li, Yip, Kevin, Zaleski, Chris, Zhang, Yan, Zheng, Henry, Brenner, Steven E, Graveley, Brenton R, Celniker, Susan E, Gingeras, Thomas R, Waterston, Robert
Published 2014

Comparative Analysis of the Transcriptome Across Distant Species

by Gerstein, Mark B., Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B., Davis, Carrie A., Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O., Duff, Michael O., Djebali, Sarah, Alexander, Roger P., Alver, Burak, Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J., Boeck, Max E., Boley, Nathan P., Booth, Benjamin W., Cherbas, Lucy, Cherbas, Peter, Di, Chao, Dobin, Alex, Drenkow, Jorg, Ewing, Brent, Fang, Gang, Fastuca, Megan, Feingold, Elise A., Frankish, Adam, Gao, Guanjun, Good, Peter J., Guigó, Roderic, Hammonds, Ann, Harrow, Jen, Hoskins, Roger A., Howald, Cédric, Hu, Long, Huang, Haiyan, Hubbard, Tim J. P., Huynh, Chau, Jha, Sonali, Kasper, Dionna, Kato, Masaomi, Kaufman, Thomas C., Kitchen, Robert R., Ladewig, Erik, Lagarde, Julien, Lai, Eric, Leng, Jing, Lu, Zhi, MacCoss, Michael, May, Gemma, McWhirter, Rebecca, Merrihew, Gennifer, Miller, David M., Mortazavi, Ali, Murad, Rabi, Oliver, Brian, Olson, Sara, Park, Peter, Pazin, Michael J., Perrimon, Norbert, Pervouchine, Dmitri, Reinke, Valerie, Reymond, Alexandre, Robinson, Garrett, Samsonova, Anastasia, Saunders, Gary I., Schlesinger, Felix, Sethi, Anurag, Slack, Frank J., Spencer, William C., Stoiber, Marcus H., Strasbourger, Pnina, Tanzer, Andrea, Thompson, Owen A., Wan, Kenneth H., Wang, Guilin, Wang, Huaien, Watkins, Kathie L., Wen, Jiayu, Wen, Kejia, Xue, Chenghai, Yang, Li, Yip, Kevin, Zaleski, Chris, Zhang, Yan, Zheng, Henry, Brenner, Steven E., Graveley, Brenton R., Celniker, Susan E., Gingeras, Thomas R., Waterston, Robert
Published 2022