Spectrogram Analysis of Genomes

by David Sussillo, Anshul Kundaje, Dimitris Anastassiou
Published 2004-01-01

mtDNA Chromatin-like Organization Is Gradually Established during Mammalian Embryogenesis

by Shani Marom, Amit Blumberg, Anshul Kundaje, Dan Mishmar
Published 2019-02-01

MTSplice predicts effects of genetic variants on tissue-specific splicing

by Jun Cheng, Muhammed Hasan Çelik, Anshul Kundaje, Julien Gagneur
Published 2021-03-01

Publisher Correction: MTSplice predicts effects of genetic variants on tissue-specific splicing

by Jun Cheng, Muhammed Hasan Çelik, Anshul Kundaje, Julien Gagneur
Published 2021-04-01

Deciphering the impact of genetic variation on human polyadenylation using APARENT2

by Johannes Linder, Samantha E. Koplik, Anshul Kundaje, Georg Seelig
Published 2022-11-01

Protocol for mapping the three-dimensional organization of dinoflagellate genomes

by Georgi K. Marinov, Anshul Kundaje, William J. Greenleaf, Arthur R. Grossman
Published 2024-06-01

Vicus: Exploiting local structures to improve network-based analysis of biological data.

by Bo Wang, Lin Huang, Yuke Zhu, Anshul Kundaje, Serafim Batzoglou, Anna Goldenberg
Published 2017-10-01

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays.

by Rajiv Movva, Peyton Greenside, Georgi K Marinov, Surag Nair, Avanti Shrikumar, Anshul Kundaje
Published 2019-01-01

The chromatin landscape of the euryarchaeon Haloferax volcanii

by Georgi K. Marinov, S. Tansu Bagdatli, Tong Wu, Chuan He, Anshul Kundaje, William J. Greenleaf
Published 2023-11-01

A predictive model of the oxygen and heme regulatory network in yeast.

by Anshul Kundaje, Xiantong Xin, Changgui Lan, Steve Lianoglou, Mei Zhou, Li Zhang, Christina Leslie
Published 2008-11-01

The chromatin organization of a chlorarachniophyte nucleomorph genome

by Georgi K. Marinov, Xinyi Chen, Tong Wu, Chuan He, Arthur R. Grossman, Anshul Kundaje, William James Greenleaf
Published 2022-03-01

Homogeneity in the association of body mass index with type 2 diabetes across the UK Biobank: A Mendelian randomization study.

by Michael Wainberg, Anubha Mahajan, Anshul Kundaje, Mark I McCarthy, Erik Ingelsson, Nasa Sinnott-Armstrong, Manuel A Rivas
Published 2019-12-01

Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis

by Xin Liu, Tao Sun, Anna Shcherbina, Qin Li, Inga Jarmoskaite, Kalli Kappel, Gokul Ramaswami, Rhiju Das, Anshul Kundaje, Jin Billy Li
Published 2021-04-01

CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping

by Georgi K. Marinov, Samuel H. Kim, S. Tansu Bagdatli, Soon Il Higashino, Alexandro E. Trevino, Josh Tycko, Tong Wu, Lacramioara Bintu, Michael C. Bassik, Chuan He, Anshul Kundaje, William J. Greenleaf
Published 2023-04-01

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens

by David W. Morgens, Michael Wainberg, Evan A. Boyle, Oana Ursu, Carlos L. Araya, C. Kimberly Tsui, Michael S. Haney, Gaelen T. Hess, Kyuho Han, Edwin E. Jeng, Amy Li, Michael P. Snyder, William J. Greenleaf, Anshul Kundaje, Michael C. Bassik
Published 2017-05-01

Genetic Effects on Transcriptome Profiles in Colon Epithelium Provide Functional Insights for Genetic Risk LociSummary

by Virginia Díez-Obrero, Christopher H. Dampier, Ferran Moratalla-Navarro, Matthew Devall, Sarah J. Plummer, Anna Díez-Villanueva, Ulrike Peters, Stephanie Bien, Jeroen R. Huyghe, Anshul Kundaje, Gemma Ibáñez-Sanz, Elisabeth Guinó, Mireia Obón-Santacana, Robert Carreras-Torres, Graham Casey, Víctor Moreno
Published 2021-01-01

Measuring the reproducibility and quality of Hi-C data

by Galip Gürkan Yardımcı, Hakan Ozadam, Michael E. G. Sauria, Oana Ursu, Koon-Kiu Yan, Tao Yang, Abhijit Chakraborty, Arya Kaul, Bryan R. Lajoie, Fan Song, Ye Zhan, Ferhat Ay, Mark Gerstein, Anshul Kundaje, Qunhua Li, James Taylor, Feng Yue, Job Dekker, William S. Noble
Published 2019-03-01

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements

by Josh Tycko, Michael Wainberg, Georgi K. Marinov, Oana Ursu, Gaelen T. Hess, Braeden K. Ego, Aradhana, Amy Li, Alisa Truong, Alexandro E. Trevino, Kaitlyn Spees, David Yao, Irene M. Kaplow, Peyton G. Greenside, David W. Morgens, Douglas H. Phanstiel, Michael P. Snyder, Lacramioara Bintu, William J. Greenleaf, Anshul Kundaje, Michael C. Bassik
Published 2019-09-01

Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data.

by Stephanie A Bien, Paul L Auer, Tabitha A Harrison, Conghui Qu, Charles M Connolly, Peyton G Greenside, Sai Chen, Sonja I Berndt, Stéphane Bézieau, Hyun M Kang, Jeroen Huyghe, Hermann Brenner, Graham Casey, Andrew T Chan, John L Hopper, Barbara L Banbury, Jenny Chang-Claude, Stephen J Chanock, Robert W Haile, Michael Hoffmeister, Christian Fuchsberger, Mark A Jenkins, Suzanne M Leal, Mathieu Lemire, Polly A Newcomb, Steven Gallinger, John D Potter, Robert E Schoen, Martha L Slattery, Joshua D Smith, Loic Le Marchand, Emily White, Brent W Zanke, Goncalo R Abeçasis, Christopher S Carlson, Ulrike Peters, Deborah A Nickerson, Anshul Kundaje, Li Hsu, GECCO and CCFR
Published 2017-01-01

The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles

by Jacob Schreiber, Carles Boix, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Schölkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y. Yip, Jeffrey P. Spence, Sanjit Singh Batra, Yun S. Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard Sandstrom, Nina Farrell, Jessica Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles Epstein, J. Seth Strattan, Bradley Bernstein, Michael Snyder, Manolis Kellis, William Stafford, Anshul Kundaje, ENCODE Imputation Challenge Participants
Published 2023-04-01