Tiling array data analysis: a multiscale approach using wavelets

by Karpikov, Alexander, Rozowsky, Joel, Gerstein, Mark
Published 2011

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework

by Harmanci, Arif, Rozowsky, Joel, Gerstein, Mark
Published 2014

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification

by Royce, Thomas E., Rozowsky, Joel S., Gerstein, Mark B.
Published 2007

Tilescope: online analysis pipeline for high-density tiling microarray data

by Zhang, Zhengdong D, Rozowsky, Joel, Lam, Hugo YK, Du, Jiang, Snyder, Michael, Gerstein, Mark
Published 2007

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

by Cheng, Chao, Yan, Koon-Kiu, Yip, Kevin Y, Rozowsky, Joel, Alexander, Roger, Shou, Chong, Gerstein, Mark
Published 2011

Loregic: A Method to Characterize the Cooperative Logic of Regulatory Factors

by Wang, Daifeng, Yan, Koon-Kiu, Sisu, Cristina, Cheng, Chao, Rozowsky, Joel, Meyerson, William, Gerstein, Mark B.
Published 2015

OrthoClust: an orthology-based network framework for clustering data across multiple species

by Yan, Koon-Kiu, Wang, Daifeng, Rozowsky, Joel, Zheng, Henry, Cheng, Chao, Gerstein, Mark
Published 2014

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data

by Cheng, Chao, Yan, Koon-Kiu, Hwang, Woochang, Qian, Jiang, Bhardwaj, Nitin, Rozowsky, Joel, Lu, Zhi John, Niu, Wei, Alves, Pedro, Kato, Masaomi, Snyder, Michael, Gerstein, Mark
Published 2011

ACT: aggregation and correlation toolbox for analyses of genome tracks

by Jee, Justin, Rozowsky, Joel, Yip, Kevin Y., Lochovsky, Lucas, Bjornson, Robert, Zhong, Guoneng, Zhang, Zhengdong, Fu, Yutao, Wang, Jie, Weng, Zhiping, Gerstein, Mark
Published 2011

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

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

AlleleSeq: analysis of allele-specific expression and binding in a network framework

by Rozowsky, Joel, Abyzov, Alexej, Wang, Jing, Alves, Pedro, Raha, Debasish, Harmanci, Arif, Leng, Jing, Bjornson, Robert, Kong, Yong, Kitabayashi, Naoki, Bhardwaj, Nitin, Rubin, Mark, Snyder, Michael, Gerstein, Mark
Published 2011

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

Discordant Expression of Circulating microRNA from Cellular and Extracellular Sources

by Shah, Ravi, Tanriverdi, Kahraman, Levy, Daniel, Larson, Martin, Gerstein, Mark, Mick, Eric, Rozowsky, Joel, Kitchen, Robert, Murthy, Venkatesh, Mikalev, Ekaterina, Freedman, Jane E.
Published 2016

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation

by Muir, Paul, Li, Shantao, Lou, Shaoke, Wang, Daifeng, Spakowicz, Daniel J., Salichos, Leonidas, Zhang, Jing, Weinstock, George M., Isaacs, Farren, Rozowsky, Joel, Gerstein, Mark
Published 2016

The real cost of sequencing: scaling computation to keep pace with data generation

by Muir, Paul, Li, Shantao, Lou, Shaoke, Wang, Daifeng, Spakowicz, Daniel J, Salichos, Leonidas, Zhang, Jing, Weinstock, George M., Isaacs, Farren, Rozowsky, Joel, Gerstein, Mark
Published 2016

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

by Chen, Jieming, Rozowsky, Joel, Galeev, Timur R., Harmanci, Arif, Kitchen, Robert, Bedford, Jason, Abyzov, Alexej, Kong, Yong, Regan, Lynne, Gerstein, Mark
Published 2016

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

by Sboner, Andrea, Habegger, Lukas, Pflueger, Dorothee, Terry, Stephane, Chen, David Z, Rozowsky, Joel S, Tewari, Ashutosh K, Kitabayashi, Naoki, Moss, Benjamin J, Chee, Mark S, Demichelis, Francesca, Rubin, Mark A, Gerstein, Mark B
Published 2010

Integration of extracellular RNA profiling data using metadata, biomedical ontologies and Linked Data technologies

by Subramanian, Sai Lakshmi, Kitchen, Robert R., Alexander, Roger, Carter, Bob S., Cheung, Kei-Hoi, Laurent, Louise C., Pico, Alexander, Roberts, Lewis R., Roth, Matthew E., Rozowsky, Joel S., Su, Andrew I., Gerstein, Mark B., Milosavljevic, Aleksandar
Published 2015

The Reality of Pervasive Transcription

by Clark, Michael B., Amaral, Paulo P., Schlesinger, Felix J., Dinger, Marcel E., Taft, Ryan J., Rinn, John L., Ponting, Chris P., Stadler, Peter F., Morris, Kevin V., Morillon, Antonin, Rozowsky, Joel S., Gerstein, Mark B., Wahlestedt, Claes, Hayashizaki, Yoshihide, Carninci, Piero, Gingeras, Thomas R., Mattick, John S.
Published 2011

Diverse human extracellular RNAs are widely detected in human plasma

by Freedman, Jane E., Gerstein, Mark, Mick, Eric, Rozowsky, Joel, Levy, Daniel, Kitchen, Robert, Das, Saumya, Shah, Ravi, Danielson, Kirsty, Beaulieu, Lea, Navarro, Fabio C. P., Wang, Yaoyu, Galeev, Timur R., Holman, Alex, Kwong, Raymond Y., Murthy, Venkatesh, Tanriverdi, Selim E., Koupenova, Milka, Mikhalev, Ekaterina, Tanriverdi, Kahraman
Published 2016