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Author Anshul Kundaje

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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Mathys Grapotte, Manu Saraswat, Chloé Bessière, Christophe Menichelli, Jordan A Ramilowski, Jessica Severin, Yoshihide Hayashizaki, Masayoshi Itoh, Michihira Tagami, Mitsuyoshi Murata, Miki Kojima-Ishiyama, Shohei Noma, Shuhei Noguchi, Takeya Kasukawa, Akira Hasegawa, Harukazu Suzuki, Hiromi Nishiyori-Sueki, Martin C Frith, , Clément Chatelain, Piero Carninci, Michiel J L de Hoon, Wyeth W Wasserman, Laurent Bréhélin, Charles-Henri Lecellier,

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe ... Read more >>

Nat Commun (Nature communications)
[2021, 12(1):3297]

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Cell-specific chromatin landscape of human coronary artery resolves regulatory mechanisms of disease risk

Adam Turner, Sheng’en Hu, Jose Verdezoto Mosquera, Wei Feng Ma, Chani Hodonsky, Doris Wong, Gaëlle Auguste, Katia Sol-Church, Emily Farber, Soumya Kundu, Anshul Kundaje, Nicolas Lopez, Lijiang Ma, Saikat Kumar Ghosh, Suna Onengut-Gumuscu, Euan Ashley, Thomas Quertermous, Aloke Finn, Nicholas Leeper, Jason Kovacic, Johan L.M. Björkgren, Chongzhi Zang, Clint Miller,

Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across several cell types. Genome-wide association studies (GWAS) have identified over 170 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis -regulatory elements (CREs). Here, we applied single-cell ATAC-seq to ... Read more >>

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AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency.

Glenn J Markov, Thach Mai, Surag Nair, Anna Shcherbina, Yu Xin Wang, David M Burns, Anshul Kundaje, Helen M Blau,

Somatic cell transcription factors are critical to maintaining cellular identity and constitute a barrier to human somatic cell reprogramming; yet a comprehensive understanding of the mechanism of action is lacking. To gain insight, we examined epigenome remodeling at the onset of human nuclear reprogramming by profiling human fibroblasts after fusion ... Read more >>

Proc Natl Acad Sci U S A (Proceedings of the National Academy of Sciences of the United States of America)
[2021, 118(23):]

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Direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping (CasKAS)

Georgi Marinov, Samuel Kim, Tansu Bagdatli, Alexandro Trevino, Josh Tycko, Tong Wu, Lacramioara Bintu, Michael Bassik, Chuan He, Anshul Kundaje, William Greenleaf,

Detecting and mitigating off-target activity is critical to the practical application of CRISPR-mediated genome and epigenome editing. While numerous methods have been developed to map Cas9 binding specificity genome-wide, they are generally time-consuming and/or expensive, and not applicable to catalytically dead CRISPR enzymes. We have developed a rapid, inexpensive, and ... Read more >>

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Multi-omic Analysis of Familial Adenomatous Polyposis Reveals Molecular Pathways and Polyclonal Spreading Associated with Early Tumorigenesis

Michael Snyder, Aaron Horning, Edward Esplin, Si Wu, Casey Hanson, Nasim Bararpour, Stephanie Nevins, Lihua Jiang, Kevin Contrepoi, Hayan Lee, Tuhin Guha, Zheng Hu, Rozelle Laquindanum, Meredith Mills, Hassan Chaib, Roxanne Chiu, Ruiqi Jian, Joanne Chan, Mathew Ellenberger, Aziz Khan, Basil Michael, Bahareh Bahmani, Glen Esplin, Jeanne Shen, Samuel Lancaster, Uri Ladabaum, Anshul Kundaje, Teri Longacre, William Greenleaf, Christina Curtis, James Ford, Winston Becker,

Familial adenomatous polyposis (FAP) is a genetic disease causing hundreds of premalignant polyps in affected patients, leading to colorectal cancer (CRC), and is an ideal model to study early transition to CRC. We performed deep multi-omic profiling of 135 normal mucosal, benign and dysplastic polyps and adenocarcinoma samples from 6 ... Read more >>

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A genome-wide atlas of co-essential modules assigns function to uncharacterized genes.

Michael Wainberg, Roarke A Kamber, Akshay Balsubramani, Robin M Meyers, Nasa Sinnott-Armstrong, Daniel Hornburg, Lihua Jiang, Joanne Chan, Ruiqi Jian, Mingxin Gu, Anna Shcherbina, Michael M Dubreuil, Kaitlyn Spees, Wouter Meuleman, Michael P Snyder, Michael C Bassik, Anshul Kundaje,

A central question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into 'co-essential' pathways, but this approach has been limited by ubiquitous false positives. In the present study, we develop a ... Read more >>

Nat Genet (Nature genetics)
[2021, 53(5):638-649]

Cited: 3 times

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Genome-wide enhancer maps link risk variants to disease genes.

Joseph Nasser, Drew T Bergman, Charles P Fulco, Philine Guckelberger, Benjamin R Doughty, Tejal A Patwardhan, Thouis R Jones, Tung H Nguyen, Jacob C Ulirsch, Fritz Lekschas, Kristy Mualim, Heini M Natri, Elle M Weeks, Glen Munson, Michael Kane, Helen Y Kang, Ang Cui, John P Ray, Thomas M Eisenhaure, Ryan L Collins, Kushal Dey, Hanspeter Pfister, Alkes L Price, Charles B Epstein, Anshul Kundaje, Ramnik J Xavier, Mark J Daly, Hailiang Huang, Hilary K Finucane, Nir Hacohen, Eric S Lander, Jesse M Engreitz,

Genome-wide association studies (GWAS) have identified thousands of noncoding loci that are associated with human diseases and complex traits, each of which could reveal insights into the mechanisms of disease<sup>1</sup>. Many of the underlying causal variants may affect enhancers<sup>2,3</sup>, but we lack accurate maps of enhancers and their target genes ... Read more >>

Nature (Nature)
[2021, 593(7858):238-243]

Cited: 2 times

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Chromatin accessibility dynamics of neurogenic niche cells reveal a reversible decline in neural stem cell migration during aging

Robin Yeo, Olivia Zhou, Brian Zhong, Mahfuza Sharmin, Tyson Ruetz, Anshul Kundaje, Alexander Dunn, Anne Brunet,

Aging is accompanied by a deterioration in the regenerative and repair potential of stem cell regions in the brain. However, the mechanisms underlying this decline are largely unknown. Here we profile the chromatin landscape of five different cell types freshly isolated from the subventricular zone neurogenic niche of young and ... Read more >>

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

Jun Cheng, Muhammed Hasan Çelik, Anshul Kundaje, Julien Gagneur,

Genome Biol (Genome biology)
[2021, 22(1):107]

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Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum.

Georgi K Marinov, Alexandro E Trevino, Tingting Xiang, Anshul Kundaje, Arthur R Grossman, William J Greenleaf,

Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state; are not packaged by histones; and contain genes organized into tandem gene arrays, with minimal transcriptional regulation. We analyze the three-dimensional genome of Breviolum minutum, and find large topological domains (dinoflagellate topologically associating ... Read more >>

Nat Genet (Nature genetics)
[2021, 53(5):613-617]

Cited: 1 time

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Single-cell analyses reveal a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Winston Becker, Stephanie Nevins, Derek Chen, Roxanne Chiu, Aaron Horning, Rozelle Laquindanum, Meredith Mills, Hassan Chaib, Uri Ladabaum, Teri Longacre, Jeanne Shen, Edward Esplin, Anshul Kundaje, James Ford, Christina Curtis, Michael Snyder, William Greenleaf,

<h4>ABSTRACT</h4> To chart cell composition and cell state changes that occur during the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated 451,886 single-cell chromatin accessibility profiles and 208,557 single-cell transcriptomes from 48 polyps, 27 normal tissues, and 6 CRCs collected from patients with and without ... Read more >>

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

Xin Liu, Tao Sun, Anna Shcherbina, Qin Li, Inga Jarmoskaite, Kalli Kappel, Gokul Ramaswami, Rhiju Das, Anshul Kundaje, Jin Billy Li,

Adenosine-to-inosine (A-to-I) RNA editing catalyzed by ADAR enzymes occurs in double-stranded RNAs. Despite a compelling need towards predictive understanding of natural and engineered editing events, how the RNA sequence and structure determine the editing efficiency and specificity (i.e., cis-regulation) is poorly understood. We apply a CRISPR/Cas9-mediated saturation mutagenesis approach to ... Read more >>

Nat Commun (Nature communications)
[2021, 12(1):2165]

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MTSplice predicts effects of genetic variants on tissue-specific splicing.

Jun Cheng, Muhammed Hasan Çelik, Anshul Kundaje, Julien Gagneur,

We develop the free and open-source model Multi-tissue Splicing (MTSplice) to predict the effects of genetic variants on splicing of cassette exons in 56 human tissues. MTSplice combines MMSplice, which models constitutive regulatory sequences, with a new neural network that models tissue-specific regulatory sequences. MTSplice outperforms MMSplice on predicting tissue-specific ... Read more >>

Genome Biol (Genome biology)
[2021, 22(1):94]

Cited: 1 time

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Genetic architectures of proximal and distal colorectal cancer are partly distinct.

Jeroen R Huyghe, Tabitha A Harrison, Stephanie A Bien, Heather Hampel, Jane C Figueiredo, Stephanie L Schmit, David V Conti, Sai Chen, Conghui Qu, Yi Lin, Richard Barfield, John A Baron, Amanda J Cross, Brenda Diergaarde, David Duggan, Sophia Harlid, Liher Imaz, Hyun Min Kang, David M Levine, Vittorio Perduca, Aurora Perez-Cornago, Lori C Sakoda, Fredrick R Schumacher, Martha L Slattery, Amanda E Toland, Fränzel J B van Duijnhoven, Bethany Van Guelpen, Antonio Agudo, Demetrius Albanes, M Henar Alonso, Kristin Anderson, Coral Arnau-Collell, Volker Arndt, Barbara L Banbury, Michael C Bassik, Sonja I Berndt, Stéphane Bézieau, D Timothy Bishop, Juergen Boehm, Heiner Boeing, Marie-Christine Boutron-Ruault, Hermann Brenner, Stefanie Brezina, Stephan Buch, Daniel D Buchanan, Andrea Burnett-Hartman, Bette J Caan, Peter T Campbell, Prudence R Carr, Antoni Castells, Sergi Castellví-Bel, Andrew T Chan, Jenny Chang-Claude, Stephen J Chanock, Keith R Curtis, Albert de la Chapelle, Douglas F Easton, Dallas R English, Edith J M Feskens, Manish Gala, Steven J Gallinger, W James Gauderman, Graham G Giles, Phyllis J Goodman, William M Grady, John S Grove, Andrea Gsur, Marc J Gunter, Robert W Haile, Jochen Hampe, Michael Hoffmeister, John L Hopper, Wan-Ling Hsu, Wen-Yi Huang, Thomas J Hudson, Mazda Jenab, Mark A Jenkins, Amit D Joshi, Temitope O Keku, Charles Kooperberg, Tilman Kühn, Sébastien Küry, Loic Le Marchand, Flavio Lejbkowicz, Christopher I Li, Li Li, Wolfgang Lieb, Annika Lindblom, Noralane M Lindor, Satu Männistö, Sanford D Markowitz, Roger L Milne, Lorena Moreno, Neil Murphy, Rami Nassir, Kenneth Offit, Shuji Ogino, Salvatore Panico, Patrick S Parfrey, Rachel Pearlman, Paul D P Pharoah, Amanda I Phipps, Elizabeth A Platz, John D Potter, Ross L Prentice, Lihong Qi, Leon Raskin, Gad Rennert, Hedy S Rennert, Elio Riboli, Clemens Schafmayer, Robert E Schoen, Daniela Seminara, Mingyang Song, Yu-Ru Su, Catherine M Tangen, Stephen N Thibodeau, Duncan C Thomas, Antonia Trichopoulou, Cornelia M Ulrich, Kala Visvanathan, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Korbinian Weigl, Stephanie J Weinstein, Emily White, Alicja Wolk, Michael O Woods, Anna H Wu, Goncalo R Abecasis, Deborah A Nickerson, Peter C Scacheri, Anshul Kundaje, Graham Casey, Stephen B Gruber, Li Hsu, Victor Moreno, Richard B Hayes, Polly A Newcomb, Ulrike Peters,

<h4>Objective</h4>An understanding of the etiologic heterogeneity of colorectal cancer (CRC) is critical for improving precision prevention, including individualized screening recommendations and the discovery of novel drug targets and repurposable drug candidates for chemoprevention. Known differences in molecular characteristics and environmental risk factors among tumors arising in different locations of the ... Read more >>

Gut (Gut)
[2021, 70(7):1325-1334]

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

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,

<h4>Background & aims</h4>The association of genetic variation with tissue-specific gene expression and alternative splicing guides functional characterization of complex trait-associated loci and may suggest novel genes implicated in disease. Here, our aims were as follows: (1) to generate reference profiles of colon mucosa gene expression and alternative splicing and compare ... Read more >>

Cell Mol Gastroenterol Hepatol (Cellular and molecular gastroenterology and hepatology)
[2021, 12(1):181-197]

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Domain adaptive neural networks improve cross-species prediction of transcription factor binding

Kelly Cochran, Divyanshi Srivastava, Avanti Shrikumar, Akshay Balsubramani, Anshul Kundaje, Shaun Mahony,

The intrinsic DNA sequence preferences and cell-type specific cooperative partners of transcription factors (TFs) are typically highly conserved. Hence, despite the rapid evolutionary turnover of individual TF binding sites, predictive sequence models of cell-type specific genomic occupancy of a TF in one species should generalize to closely matched cell types ... Read more >>

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Base-resolution models of transcription-factor binding reveal soft motif syntax.

Žiga Avsec, Melanie Weilert, Avanti Shrikumar, Sabrina Krueger, Amr Alexandari, Khyati Dalal, Robin Fropf, Charles McAnany, Julien Gagneur, Anshul Kundaje, Julia Zeitlinger,

The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that uses DNA sequence to predict base-resolution chromatin immunoprecipitation (ChIP)-nexus binding profiles of pluripotency TFs. We develop interpretation tools to learn predictive motif ... Read more >>

Nat Genet (Nature genetics)
[2021, 53(3):354-366]

Cited: 8 times

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High-Throughput Discovery and Characterization of Human Transcriptional Effectors.

Josh Tycko, Nicole DelRosso, Gaelen T Hess, Aradhana, Abhimanyu Banerjee, Aditya Mukund, Mike V Van, Braeden K Ego, David Yao, Kaitlyn Spees, Peter Suzuki, Georgi K Marinov, Anshul Kundaje, Michael C Bassik, Lacramioara Bintu,

Thousands of proteins localize to the nucleus; however, it remains unclear which contain transcriptional effectors. Here, we develop HT-recruit, a pooled assay where protein libraries are recruited to a reporter, and their transcriptional effects are measured by sequencing. Using this approach, we measure gene silencing and activation for thousands of ... Read more >>

Cell (Cell)
[2020, 183(7):2020-2035.e16]

Cited: 1 time

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Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution

Alexandro Trevino, Fabian Müller, Jimena Andersen, Laksshman Sundaram, Arwa Kathiria, Anna Shcherbina, Kyle Farh, Howard Chang, Anca Paşca, Anshul Kundaje, Sergiu Paşca, William Greenleaf,

<h4>ABSTRACT</h4> Genetic perturbations of cerebral cortical development can lead to neurodevelopmental disease, including autism spectrum disorder (ASD). To identify genomic regions crucial to corticogenesis, we mapped the activity of gene-regulatory elements generating a single-cell atlas of gene expression and chromatin accessibility both independently and jointly. This revealed waves of gene ... Read more >>

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fastISM: Performant in-silico saturation mutagenesis for convolutional neural networks

Surag Nair, Avanti Shrikumar, Anshul Kundaje,

Deep learning models such as convolutional neural networks are able to accurately map biological sequences to associated functional readouts and properties by learning predictive de novo representations. In-silico saturation mutagenesis (ISM) is a popular feature attribution technique for inferring contributions of all characters in an input sequence to the model’s ... Read more >>

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The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation

Daniel Kim, Viviana Risca, David Reynolds, James Chappell, Adam Rubin, Namyoung Jung, Laura Donohue, Arwa Kathiria, Minyi Shi, Zhixin Zhao, Harsh Deep, Howard Chang, Michael Snyder, William Greenleaf, Anshul Kundaje, Paul Khavari,

Transcription factors (TFs) bind DNA sequence motif vocabularies in cis-regulatory elements (CREs) to modulate chromatin state and gene expression during cell state transitions. A quantitative understanding of how motif lexicons influence dynamic regulatory activity has been elusive due to the combinatorial nature of the cis-regulatory code. To address this, we ... Read more >>

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Towards a Better Understanding of Reverse-Complement Equivariance for Deep Learning Models in Regulatory Genomics

Hannah Zhou, Avanti Shrikumar, Anshul Kundaje,

Predictive models mapping double-stranded DNA to signals of regulatory activity should, in principle, produce analogous (or “equivariant”) predictions whether the forward strand or its reverse complement (RC) is supplied as input. Unfortunately, standard neural networks can produce highly divergent predictions across strands, even when the training set is augmented with ... Read more >>

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Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases.

M Ryan Corces, Anna Shcherbina, Soumya Kundu, Michael J Gloudemans, Laure Frésard, Jeffrey M Granja, Bryan H Louie, Tiffany Eulalio, Shadi Shams, S Tansu Bagdatli, Maxwell R Mumbach, Boxiang Liu, Kathleen S Montine, William J Greenleaf, Anshul Kundaje, Stephen B Montgomery, Howard Y Chang, Thomas J Montine,

Genome-wide association studies of neurological diseases have identified thousands of variants associated with disease phenotypes. However, most of these variants do not alter coding sequences, making it difficult to assign their function. Here, we present a multi-omic epigenetic atlas of the adult human brain through profiling of single-cell chromatin accessibility ... Read more >>

Nat Genet (Nature genetics)
[2020, 52(11):1158-1168]

Cited: 10 times

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Transparency and reproducibility in artificial intelligence.

Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, , Levi Waldron, Bo Wang, Chris McIntosh, Anna Goldenberg, Anshul Kundaje, Casey S Greene, Tamara Broderick, Michael M Hoffman, Jeffrey T Leek, Keegan Korthauer, Wolfgang Huber, Alvis Brazma, Joelle Pineau, Robert Tibshirani, Trevor Hastie, John P A Ioannidis, John Quackenbush, Hugo J W L Aerts,

Nature (Nature)
[2020, 586(7829):E14-E16]

Cited: 6 times

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Size-independent mRNA synthesis and chromatin-based partitioning mechanisms generate and maintain constant amounts of protein per cell

Matthew Swaffer, Devon Chandler-Brown, Maurice Langhinrichs, Georgi Marinov, William Greenleaf, Anshul Kundaje, Kurt Schmoller, Jan Skotheim,

<h4>Summary</h4> Cell size and biosynthesis are inextricably linked. As cells grow, total protein synthesis increases in proportion to cell size so that protein concentrations remain constant. As an exception, the budding yeast cell-cycle inhibitor Whi5 is synthesized in a constant amount per cell cycle, so that it is diluted in ... Read more >>

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