Transcriptional profiling of cells sorted by transcript abundance

by Klemm, Sandy Lee, Semrau, Stefan, Wiebrands, Kay, Mooijman, Dylan, Jaenisch, Rudolf, van Oudenaarden, Alexander, Faddah, Dina A.
Published 2015

Numerous recursive sites contribute to accuracy of splicing in long introns in flies

by Adelman, Karen, Pai, Athma A., Paggi, Joseph M., Yang, Paul L, Burge, Christopher B
Published 2018

A combinatorial extracellular matrix platform identifies cell-extracellular matrix interactions that correlate with metastasis

by Reticker-Flynn, Nathan E., Malta, David F. Braga, Underhill, Gregory H., Xu, Mary Jue, Winslow, Monte Meier, Hynes, Richard O, Jacks, Tyler E, Bhatia, Sangeeta N, Lamar, John
Published 2014

Identifying Recent Adaptations in Large-Scale Genomic Data

by Andersen, Kristian G., Tabrizi, Shervin, Winnicki, Sarah, Yen, Angela, Park, Daniel J, Griesemer, Dustin, Karlsson, Elinor K., Wong, Sunny H, Cabili, Moran N., Adegbola, Richard A, Bamezai, Rameshwar N.K, Hill, Adrian V. S., Vannberg, Fredrik O, Rinn, John L., Schaffner, Stephen F, Sabeti, Pardis C, Grossman, Sharon Rachel, Shlyakhter, Ilya 1975-, Lander, Eric Steven
Published 2014

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

by Raychowdhury, Raktima, Jovanovic, Marko, Stumpo, Deborah J, Pauli, Andrea, Hacohen, Nir, Schier, Alexander F, Blackshear, Perry J, Friedman, Nir, Amit, Ido, Rabani, Michal, Rooney, Michael Steven, Regev, Aviv
Published 2016

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

by Kheradpour, Pouya, Bristow, Christopher A., Mag Washietl, Stefan, Ay, Ferhat, Jungreis, Irwin, Marbach, Daniel, Sealfon, Rachel Sima, Will, Sebastian, Berger, Bonnie, Kellis, Manolis, Roy, Sushmita, Ernst, Jason, Lin, Michael F., Meyer, Patrick E., Di Stefano, Luisa, Candeias, Rogerio, Nordman, Jared T., Orr-Weaver, Terry L.
Published 2013

Integrative analysis of 111 reference human epigenomes

by Kundaje, Anshul, Meuleman, Wouter, Ernst, Jason, Yen, Angela, Kheradpour, Pouya, Zhang, Zhizhuo, Wang, Jianrong, Ward, Lucas D., Sarkar, Abhishek Kulshreshtha, Quon, Gerald, Eaton, Matthew Lucas, Wu, Yi-Chieh, Pfenning, Andreas R., Wang, Xinchen, Claussnitzer, Melina, Liu, Yaping, Bansal, Mukul S., Kim, Ah Ram, Cowper Sal-lari, Richard, Sinnott-Armstrong, Nicholas A., Gjoneska, Elizabeta, Tsai, Li-Huei, Kellis, Manolis, Feizi- Khankandi, Soheil, Boyer, Laurie Ann
Published 2016

Synchronized cycles of bacterial lysis for in vivo delivery

by Din, M. Omar, Prindle, Arthur, Selimkhanov, Jangir, Julio, Ellixis, Tsimring, Lev S., Hasty, Jeff, Danino, Tal, Skalak, Matthew T., Allen, Kaitlin N., Atolia, Eta, Bhatia, Sangeeta N
Published 2017

Arboretum: Reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

by Kellis, Manolis, Regev, Aviv, Roy, Sushmita, Wapinski, Ilan, Pfiffner, Jenna, French, Courtney, Socha, Amanda, Konieczka, Jay, Habib, Naomi, Thompson, Dawn
Published 2014

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

by Goggin, Sarah M., Saadat, Alham, Wang, Li, Sinnott-Armstrong, Nasa, Wang, Xinchen, He, Liang, Kellis, Manolis, Claussnitzer, Melina
Published 2019

Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas

by Farzadfard, Fahim, Perli, Samuel David, Lu, Timothy K
Published 2013

Control of Transcription by Cell Size

by Wu, Chia-Yung, Rolfe, Philip Alexander, Gifford, David K, Fink, Gerald R
Published 2011

Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay

by Melnikov, Alexandre, Murugan, Anand, Zhang, Xiaolan, Tesileanu, Tiberiu, Wang, Li, Rogov, Peter, Feizi-Khankandi, Soheil, Gnirke, Andreas, Callan Jr, Curtis G., Kinney, Justin B., Kellis, Manolis, Lander, Eric S., Mikkelsen, Tarjei Sigurd 1978-
Published 2012

Discovering Regulatory Overlapping RNA Transcripts

by Danford, Timothy William, Dowell, Robin D., Agarwala, Sundeep, Grisafi, Paula, Fink, Gerald R., Gifford, David K.
Published 2012

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

by Cabili, Moran N., Trapnell, Cole, Goff, Loyal, Koziol, Magdalena J., Tazon-Vega, Barbara, Regev, Aviv, Rinn, John L.
Published 2014

Rapid modelling of cooperating genetic events in cancer through somatic genome editing

by Papagiannakopoulos, Thales, Romero, Rodrigo, Tammela, Tuomas, Bauer, Matthew R., Subbaraj, Lakshmipriya, Bronson, Roderick T., Xue, Wen, Sanchez-Rivera, Francisco Jav, Joshi, Nik, Bhutkar, Arjun, Jacks, Tyler E
Published 2015

In Vitro-In Vivo Translation of Lipid Nanoparticles for Hepatocellular siRNA Delivery

by Matthews, Jonathan, Chang, Philip H., Niroui, Farnaz, Severgnini, Mariano, Whitehead, Kathryn Ann, Dorkin, Joseph Robert, Anderson, Daniel Griffith
Published 2014

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

by Ram, Oren, Goren, Alon, Amit, Ido, Shoresh, Noam, Yosef, Nir, Ernst, Jason, Kellis, Manolis, Issner, Robbyn, Durham, Timothy, Zhang, Xiaolan, Donaghey, Julie, Epstein, Charles B., Regev, Aviv, Bernstein, Bradley E., Gymrek, Melissa A., Coyne, Michael J.
Published 2014

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

by Mazzoni, Esteban O., Mahony, Shaun, Peljto, Mirza, Patel, Tulsi, McCuine, Scott, Wichterle, Hynek, Thornton, Seraphim R., Young, Richard A., Reeder, Christopher, Gifford, David K, Boyer, Laurie Ann
Published 2014

GeNets: a unified web platform for network-based genomic analyses

by Li, Taibo, Kim, April, Rosenbluh, Joseph, Horn, Heiko, Greenfeld, Liraz, An, David, Zimmer, Andrew, Liberzon, Arthur, Bistline, Jon, Natoli, Ted, Li, Yang, Tsherniak, Aviad, Narayan, Rajiv, Subramanian, Aravind, Liefeld, Ted, Wong, Bang, Thompson, Dawn, Calvo, Sarah, Carr, Steve, Boehm, Jesse, Jaffe, Jake, Mesirov, Jill, Hacohen, Nir, Regev, Aviv, Lage, Kasper
Published 2018