Connectivity in the Yeast Cell Cycle Transcription Network: Inferences from Neural Networks

por Hart, Christopher E, Mjolsness, Eric, Wold, Barbara J
Publicado 2006

RNA editing in the human ENCODE RNA-seq data

por Park, Eddie, Williams, Brian, Wold, Barbara J., Mortazavi, Ali
Publicado 2012

Evidence for Site-Specific Occupancy of the Mitochondrial Genome by Nuclear Transcription Factors

por Marinov, Georgi K., Wang, Yun E., Chan, David, Wold, Barbara J.
Publicado 2014

Large-Scale Quality Analysis of Published ChIP-seq Data

por Marinov, Georgi K., Kundaje, Anshul, Park, Peter J., Wold, Barbara J.
Publicado 2013

Transcription factor redundancy and tissue-specific regulation: Evidence from functional and physical network connectivity

por Kuntz, Steven G., Williams, Brian A., Sternberg, Paul W., Wold, Barbara J.
Publicado 2012

Genome-Wide Analysis Reveals Coating of the Mitochondrial Genome by TFAM

por Wang, Yun E., Marinov, Georgi K., Wold, Barbara J., Chan, David C.
Publicado 2013

A ratiometric-based measure of gene co-expression

por Abelin, Anna CT, Marinov, Georgi K, Williams, Brian A, McCue, Kenneth, Wold, Barbara J
Publicado 2014

Mining gene expression data by interpreting principal components

por Roden, Joseph C, King, Brandon W, Trout, Diane, Mortazavi, Ali, Wold, Barbara J, Hart, Christopher E
Publicado 2006

A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data

por Hart, Christopher E., Sharenbroich, Lucas, Bornstein, Benjamin J., Trout, Diane, King, Brandon, Mjolsness, Eric, Wold, Barbara J.
Publicado 2005

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

por Marinov, Georgi K., Williams, Brian A., McCue, Ken, Schroth, Gary P., Gertz, Jason, Myers, Richard M., Wold, Barbara J.
Publicado 2014

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

por Mortazavi, Ali, Pepke, Shirley, Jansen, Camden, Marinov, Georgi K., Ernst, Jason, Kellis, Manolis, Hardison, Ross C., Myers, Richard M., Wold, Barbara J.
Publicado 2013

Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms

por Trapnell, Cole, Williams, Brian A., Pertea, Geo, Mortazavi, Ali, Kwan, Gordon, van Baren, Marijke J., Salzberg, Steven L., Wold, Barbara J., Pachter, Lior
Publicado 2010

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

por Rebboah, Elisabeth, Reese, Fairlie, Williams, Katherine, Balderrama-Gutierrez, Gabriela, McGill, Cassandra, Trout, Diane, Rodriguez, Isaryhia, Liang, Heidi, Wold, Barbara J., Mortazavi, Ali
Publicado 2021

Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies

por Gasper, William C., Marinov, Georgi K., Pauli-Behn, Florencia, Scott, Max T., Newberry, Kimberly, DeSalvo, Gilberto, Ou, Susan, Myers, Richard M., Vielmetter, Jost, Wold, Barbara J.
Publicado 2014

RNAget: an API to securely retrieve RNA quantifications

por Upchurch, Sean, Palumbo, Emilio, Adams, Jeremy, Bujold, David, Bourque, Guillaume, Nedzel, Jared, Graham, Keenan, Kagda, Meenakshi S, Assis, Pedro, Hitz, Benjamin, Righi, Emilio, Guigó, Roderic, Wold, Barbara J
Publicado 2023

Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer

por Tai, Phillip WL, Fisher-Aylor, Katherine I, Himeda, Charis L, Smith, Catherine L, MacKenzie, Alexandra P, Helterline, Deri L, Angello, John C, Welikson, Robert E, Wold, Barbara J, Hauschka, Stephen D
Publicado 2011

Dynamic DNA methylation across diverse human cell lines and tissues

por 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.
Publicado 2013

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

por 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.
Publicado 2020

Systematic evaluation of factors influencing ChIP-seq fidelity

por 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
Publicado 2012

Dynamics of microRNA expression during mouse prenatal development

por Rahmanian, Sorena, Murad, Rabi, Breschi, Alessandra, Zeng, Weihua, Mackiewicz, Mark, Williams, Brian, Davis, Carrie A., Roberts, Brian, Meadows, Sarah, Moore, Dianna, Trout, Diane, Zaleski, Chris, Dobin, Alex, Sei, Lei-Hoon, Drenkow, Jorg, Scavelli, Alex, Gingeras, Thomas R., Wold, Barbara J., Myers, Richard M., Guigó, Roderic, Mortazavi, Ali
Publicado 2019