Publications by authors named "Siddarth Selvaraj"

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Semi-automated assembly of high-quality diploid human reference genomes.
Erich D Jarvis, Giulio Formenti, Arang Rhie, Andrea Guarracino, Chentao Yang, Siddarth Selvaraj

Nature· November 2022

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Towards complete and error-free genome assemblies of all vertebrate species.
Arang Rhie, Shane A McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Siddarth Selvaraj

Nature· April 2021

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Telomere-to-telomere assembly of a complete human X chromosome.
Karen H Miga, Sergey Koren, Arang Rhie, Mitchell R Vollger, Ariel Gershman, Siddarth Selvaraj

Nature· September 2020

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Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
Jay Ghurye, Arang Rhie, Brian P Walenz, Anthony Schmitt, Siddarth Selvaraj

PLoS Comput Biol· August 2019

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Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression.
William W Greenwald, He Li, Paola Benaglio, David Jakubosky, Hiroko Matsui, Siddarth Selvaraj

Nat Commun· March 2019

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InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms.
Anand Patel, Peter Edge, Siddarth Selvaraj, Vikas Bansal, Vineet Bafna

Nucleic Acids Res· July 2016

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Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation.
Matthew D Schultz, Yupeng He, John W Whitaker, Manoj Hariharan, Eran A Mukamel, Siddarth Selvaraj

Nature· February 2016

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Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq.
Siddarth Selvaraj, Anthony D Schmitt, Jesse R Dixon, Bing Ren

BMC Genomics· November 2015

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CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells.
Yan Li, Chloe M Rivera, Haruhiko Ishii, Fulai Jin, Siddarth Selvaraj

PLoS One· August 2015

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Human body epigenome maps reveal noncanonical DNA methylation variation.
Matthew D Schultz, Yupeng He, John W Whitaker, Manoj Hariharan, Eran A Mukamel, Siddarth Selvaraj

Nature· July 2015

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Chromatin architecture reorganization during stem cell differentiation.
Jesse R Dixon, Inkyung Jung, Siddarth Selvaraj, Yin Shen, Jessica E Antosiewicz-Bourget

Nature· February 2015

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Integrative analysis of haplotype-resolved epigenomes across human tissues.
Danny Leung, Inkyung Jung, Nisha Rajagopal, Anthony Schmitt, Siddarth Selvaraj

Nature· February 2015

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5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation.
Gary C Hon, Chun-Xiao Song, Tingting Du, Fulai Jin, Siddarth Selvaraj

Mol Cell· October 2014

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Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.
Siddarth Selvaraj, Jesse R Dixon, Vikas Bansal, Bing Ren

Nat Biotechnol· December 2013

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A high-resolution map of the three-dimensional chromatin interactome in human cells.
Fulai Jin, Yan Li, Jesse R Dixon, Siddarth Selvaraj, Zhen Ye

Nature· November 2013

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Bayesian inference of spatial organizations of chromosomes.
Ming Hu, Ke Deng, Zhaohui Qin, Jesse Dixon, Siddarth Selvaraj

PLoS Comput Biol· June 2013

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HiCNorm: removing biases in Hi-C data via Poisson regression.
Ming Hu, Ke Deng, Siddarth Selvaraj, Zhaohui Qin, Bing Ren

Bioinformatics· December 2012

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Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Jesse R Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li

Nature· April 2012

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