Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity von Zhang, Jingli A., Mortazavi, Ali, Williams, Brian A., Wold, Barbara J., Rothenberg, Ellen V.

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation von Pachter, Lior, Trapnell, Cole, Williams, Brian A, Pertea, Geo, Mortazavi, Ali, Kwan, Gordon, van Baren, Marijke J, Salzberg, Steven L, Wold, Barbara J

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From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing von Marinov, Georgi K, Williams, Brian A, McCue, Ken, Schroth, Gary P, Gertz, Jason, Myers, Richard M, Wold, Barbara J

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Dynamic DNA methylation across diverse human cell lines and tissues von Varley, Katherine E, Gertz, Jason, Bowling, Kevin M, Parker, Stephanie L, Reddy, Timothy E, Pauli-Behn, Florencia, Cross, Marie K, Williams, Brian A, Stamatoyannopoulos, John A, Crawford, Gregory E, Absher, Devin M, Wold, Barbara J, Myers, Richard M

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The changing mouse embryo transcriptome at whole tissue and single-cell resolution von He, Peng, Williams, Brian A., Trout, Diane, Marinov, Georgi K., Amrhein, Henry, Berghella, Libera, Goh, Say-Tar, Plajzer-Frick, Ingrid, Afzal, Veena, Pennacchio, Len A., Dickel, Diane E., Visel, Axel, Ren, Bing, Hardison, Ross C., Zhang, Yu, Wold, Barbara J.

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Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming von Kim, Daniel H., Marinov, Georgi K., Pepke, Shirley, Singer, Zakary S., He, Peng, Williams, Brian, Schroth, Gary P., Elowitz, Michael B., Wold, Barbara J.

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RNA editing in the human ENCODE RNA-seq data von Park, Eddie, Williams, Brian, Wold, Barbara J, Mortazavi, Ali

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Occupancy maps of 208 chromatin-associated proteins in one human cell type von Partridge, E. Christopher, Chhetri, Surya B., Prokop, Jeremy W., Ramaker, Ryne C., Jansen, Camden S., Goh, Say-Tar, Mackiewicz, Mark, Newberry, Kimberly M., Brandsmeier, Laurel A., Meadows, Sarah K., Messer, C. Luke, Hardigan, Andrew A., Coppola, Candice J., Dean, Emma C., Jiang, Shan, Savic, Daniel, Mortazavi, Ali, Wold, Barbara J., Myers, Richard M., Mendenhall, Eric M.

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Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq von Rebboah, Elisabeth, Reese, Fairlie, Williams, Katherine, Balderrama-Gutierrez, Gabriela, McGill, Cassandra, Trout, Diane, Rodriguez, Isaryhia, Liang, Heidi, Wold, Barbara J., Mortazavi, Ali

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Systematic evaluation of factors influencing ChIP-seq fidelity von Chen, Yiwen, Negre, Nicolas, Li, Qunhua, Mieczkowska, Joanna O, Slattery, Matthew, Liu, Tao, Zhang, Yong, Kim, Tae-Kyung, He, Housheng Hansen, Zieba, Jennifer, Ruan, Yijun, Bickel, Peter J, Myers, Richard M, Wold, Barbara J, White, Kevin P, Lieb, Jason D, Liu, X Shirley

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Large-scale quality analysis of published ChIP-seq data von Marinov, Georgi K, Kundaje, Anshul, Park, Peter J, Wold, Barbara J

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Genome-wide analysis reveals coating of the mitochondrial genome by TFAM von Wang, Yun E, Marinov, Georgi K, Wold, Barbara J, Chan, David C

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Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors von Marinov, Georgi K, Wang, Yun E, Chan, David, Wold, Barbara J

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Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps von Mortazavi, Ali, Pepke, Shirley, Jansen, Camden, Marinov, Georgi K, Ernst, Jason, Kellis, Manolis, Hardison, Ross C, Myers, Richard M, Wold, Barbara J

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Spatiometabolic Stratification of Shewanella oneidensis Biofilms von Teal, Tracy K, Lies, Douglas P, Wold, Barbara J, Newman, Dianne K

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Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi’s Genomic Targets Still Not Identified von Marinov, Georgi K., Wang, Jie, Handler, Dominik, Wold, Barbara J., Weng, Zhiping, Hannon, Gregory J., Aravin, Alexei A., Zamore, Phillip D., Brennecke, Julius, Toth, Katalin Fejes

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High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation von Ozdemir, Anil, Fisher-Aylor, Katherine I, Pepke, Shirley, Samanta, Manoj, Dunipace, Leslie, McCue, Kenneth, Zeng, Lucy, Ogawa, Nobuo, Wold, Barbara J, Stathopoulos, Angelike

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Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint von Budd, Martin E., Antoshechkin, Igor A., Reis, Clara, Wold, Barbara J., Campbell, Judith L.

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p62 overexpression in breast tumors and regulation by prostate-derived Ets factor in breast cancer cells von THOMPSON, H. Garrett R, HARRIS, Joseph W, WOLD, Barbara J, LIN, Fritz, BRODY, James P

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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia von Landt, Stephen G, Marinov, Georgi K, Kundaje, Anshul, Kheradpour, Pouya, Pauli, Florencia, Batzoglou, Serafim, Bernstein, Bradley E, Bickel, Peter, Brown, James B, Cayting, Philip, Chen, Yiwen, DeSalvo, Gilberto, Epstein, Charles, Fisher-Aylor, Katherine I, Euskirchen, Ghia, Gerstein, Mark, Gertz, Jason, Hartemink, Alexander J, Hoffman, Michael M, Iyer, Vishwanath R, Jung, Youngsook L, Karmakar, Subhradip, Kellis, Manolis, Kharchenko, Peter V, Li, Qunhua, Liu, Tao, Liu, X Shirley, Ma, Lijia, Milosavljevic, Aleksandar, Myers, Richard M, Park, Peter J, Pazin, Michael J, Perry, Marc D, Raha, Debasish, Reddy, Timothy E, Rozowsky, Joel, Shoresh, Noam, Sidow, Arend, Slattery, Matthew, Stamatoyannopoulos, John A, Tolstorukov, Michael Y, White, Kevin P, Xi, Simon, Farnham, Peggy J, Lieb, Jason D, Wold, Barbara J, Snyder, Michael

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