Tiling array data analysis: a multiscale approach using wavelets

by Rozowsky Joel, Karpikov Alexander, Gerstein Mark
Published 2011-02-01

An approach to compare genome tiling microarray and MPSS sequencing data for transcript mapping

by Rozowsky Joel, Agarwal Ashish, Sasidharan Rajkumar, Gerstein Mark
Published 2009-10-01

An approach to comparing tiling array and high throughput sequencing technologies for genomic transcript mapping

by Rozowsky Joel, Agarwal Ashish, Sasidharan Rajkumar, Gerstein Mark
Published 2009-07-01

Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays

by Jee Justin, Nagalakshmi Ugrappa, Royce Thomas, Rozowsky Joel, Seringhaus Michael, Snyder Michael, Gerstein Mark
Published 2008-12-01

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

by Yellman Christopher M, Gibson Theodore, Rozowsky Joel, Auerbach Raymond K, Euskirchen Ghia M, Lefrançois Philippe, Gerstein Mark, Snyder Michael
Published 2009-01-01

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

by Reinke Valerie, Sasidharan Rajkumar, Hillier LaDeana W, Habegger Lukas, Sboner Andrea, Rozowsky Joel, Koppstein David, Agarwal Ashish, Waterston Robert H, Gerstein Mark
Published 2010-06-01

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

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

by Yip, Kevin Y, Cheng, Chao, Bhardwaj, Nitin, Brown, James B, Leng, Jing, Kundaje, Anshul, Rozowsky, Joel, Birney, Ewan, Bickel, Peter, Snyder, Michael, Gerstein, Mark
Published 2012

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

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

by Altshuler, Robert Charles, Onuchic, Vitor, Lurie, Eugene, Carrero, Ivenise, Pawliczek, Piotr, Patel, Ronak Y., Rozowsky, Joel, Galeev, Timur, Huang, Zhuoyi, Harris, R. Alan, Coarfa, Cristian, Ashmore, Lillian, Bertol, Jessica W., Fakhouri, Walid D., Yu, Fuli, Kellis, Manolis, Gerstein, Mark, Milosavljevic, Aleksandar
Published 2019

A Novel Tissue Atlas and Online Tool for the Interrogation of Small RNA Expression in Human Tissues and Biofluids.

by Alsop, Eric, Meechoovet, Bessie, Kitchen, Robert, Sweeney, Thadryan, Beach, Thomas G, Serrano, Geidy E, Hutchins, Elizabeth, Ghiran, Ionita, Reiman, Rebecca, Syring, Michael, Hsieh, Michael, Courtright-Lim, Amanda, Valkov, Nedyalka, Whitsett, Timothy G, Rakela, Jorge, Pockros, Paul, Rozowsky, Joel, Gallego, Juan, Huentelman, Matthew J, Shah, Ravi, Nakaji, Peter, Kalani, M Yashar S, Laurent, Louise, Das, Saumya, Van Keuren-Jensen, Kendall
Published 2022

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

exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids.

by Murillo, Oscar D, Thistlethwaite, William, Rozowsky, Joel, Subramanian, Sai Lakshmi, Lucero, Rocco, Shah, Neethu, Jackson, Andrew R, Srinivasan, Srimeenakshi, Chung, Allen, Laurent, Clara D, Kitchen, Robert R, Galeev, Timur, Warrell, Jonathan, Diao, James A, Welsh, Joshua A, Hanspers, Kristina, Riutta, Anders, Burgstaller-Muehlbacher, Sebastian, Shah, Ravi V, Yeri, Ashish, Jenkins, Lisa M, Ahsen, Mehmet E, Cordon-Cardo, Carlos, Dogra, Navneet, Gifford, Stacey M, Smith, Joshua T, Stolovitzky, Gustavo, Tewari, Ashutosh K, Wunsch, Benjamin H, Yadav, Kamlesh K, Danielson, Kirsty M, Filant, Justyna, Moeller, Courtney, Nejad, Parham, Paul, Anu, Simonson, Bridget, Wong, David K, Zhang, Xuan, Balaj, Leonora, Gandhi, Roopali, Sood, Anil K, Alexander, Roger P, Wang, Liang, Wu, Chunlei, Wong, David TW, Galas, David J, Van Keuren-Jensen, Kendall, Patel, Tushar, Jones, Jennifer C, Das, Saumya, Cheung, Kei-Hoi, Pico, Alexander R, Su, Andrew I, Raffai, Robert L, Laurent, Louise C, Roth, Matthew E, Gerstein, Mark B, Milosavljevic, Aleksandar
Published 2019

Extending gene ontology in the context of extracellular RNA and vesicle communication.

by Cheung, Kei-Hoi, Keerthikumar, Shivakumar, Roncaglia, Paola, Subramanian, Sai Lakshmi, Roth, Matthew E, Samuel, Monisha, Anand, Sushma, Gangoda, Lahiru, Gould, Stephen, Alexander, Roger, Galas, David, Gerstein, Mark B, Hill, Andrew F, Kitchen, Robert R, Lötvall, Jan, Patel, Tushar, Procaccini, Dena C, Quesenberry, Peter, Rozowsky, Joel, Raffai, Robert L, Shypitsyna, Aleksandra, Su, Andrew I, Théry, Clotilde, Vickers, Kasey, Wauben, Marca HM, Mathivanan, Suresh, Milosavljevic, Aleksandar, Laurent, Louise C
Published 2016

Extending gene ontology in the context of extracellular RNA and vesicle communication.

by Cheung, Kei-Hoi, Keerthikumar, Shivakumar, Roncaglia, Paola, Subramanian, Sai Lakshmi, Roth, Matthew E, Samuel, Monisha, Anand, Sushma, Gangoda, Lahiru, Gould, Stephen, Alexander, Roger, Galas, David, Gerstein, Mark B, Hill, Andrew F, Kitchen, Robert R, Lötvall, Jan, Patel, Tushar, Procaccini, Dena C, Quesenberry, Peter, Rozowsky, Joel, Raffai, Robert L, Shypitsyna, Aleksandra, Su, Andrew I, Théry, Clotilde, Vickers, Kasey, Wauben, Marca HM, Mathivanan, Suresh, Milosavljevic, Aleksandar, Laurent, Louise C
Published 2016

Expanded encyclopaedias of DNA elements in the human and mouse genomes.

by ENCODE Project Consortium, Moore, Jill E, Purcaro, Michael J, Pratt, Henry E, Epstein, Charles B, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie A, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric L, Freese, Peter, Gorkin, David U, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian A, Mortazavi, Ali, Keller, Cheryl A, Zhang, Xiao-Ou, Elhajjajy, Shaimae I, Huey, Jack, Dickel, Diane E, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan Carlos, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya B, Zhang, Jialing, Victorsen, Alec, White, Kevin P, Visel, Axel, Yeo, Gene W, Burge, Christopher B, Lécuyer, Eric, Gilbert, David M, Dekker, Job, Rinn, John, Mendenhall, Eric M, Ecker, Joseph R, Kellis, Manolis, Klein, Robert J, Noble, William S, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy J, Cherry, J Michael, Myers, Richard M, Ren, Bing, Graveley, Brenton R, Gerstein, Mark B, Pennacchio, Len A, Snyder, Michael P, Bernstein, Bradley E, Wold, Barbara, Hardison, Ross C, Gingeras, Thomas R, Stamatoyannopoulos, John A, Weng, Zhiping
Published 2020

Landscape of transcription in human cells.

by Djebali, Sarah, Davis, Carrie A, Merkel, Angelika, Dobin, Alex, Lassmann, Timo, Mortazavi, Ali, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Schlesinger, Felix, Xue, Chenghai, Marinov, Georgi K, Khatun, Jainab, Williams, Brian A, Zaleski, Chris, Rozowsky, Joel, Röder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F, Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T, Bar, Nadav S, Batut, Philippe, Bell, Kimberly, Bell, Ian, Chakrabortty, Sudipto, Chen, Xian, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jacqueline, Duttagupta, Radha, Falconnet, Emilie, Fastuca, Meagan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J, Gao, Hui, Gonzalez, David, Gordon, Assaf, Gunawardena, Harsha, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Luo, Oscar J, Park, Eddie, Persaud, Kimberly, Preall, Jonathan B, Ribeca, Paolo, Risk, Brian, Robyr, Daniel, Sammeth, Michael, Schaffer, Lorian, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Wrobel, John, Yu, Yanbao, Ruan, Xiaoan, Hayashizaki, Yoshihide, Harrow, Jennifer, Gerstein, Mark, Hubbard, Tim, Reymond, Alexandre, Antonarakis, Stylianos E, Hannon, Gregory, Giddings, Morgan C, Ruan, Yijun, Wold, Barbara, Carninci, Piero, Guigó, Roderic, Gingeras, Thomas R
Published 2012

Evaluation of commercially available small RNASeq library preparation kits using low input RNA

by Yeri, Ashish, Courtright, Amanda, Danielson, Kirsty, Hutchins, Elizabeth, Alsop, Eric, Carlson, Elizabeth, Hsieh, Michael, Ziegler, Olivia, Das, Avash, Shah, Ravi V., Rozowsky, Joel, Das, Saumya, Van Keuren-Jensen, Kendall
Published 2018