I
Ido Machol
Researcher at Baylor College of Medicine
Publications - 17
Citations - 10948
Ido Machol is an academic researcher from Baylor College of Medicine. The author has contributed to research in topics: Chromatin & Genome. The author has an hindex of 11, co-authored 16 publications receiving 7429 citations. Previous affiliations of Ido Machol include Rice University.
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Journal ArticleDOI
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Suhas S.P. Rao,Miriam H. Huntley,Neva C. Durand,Elena K. Stamenova,Ivan D. Bochkov,James T. Robinson,James T. Robinson,Adrian L. Sanborn,Ido Machol,Ido Machol,Arina D. Omer,Arina D. Omer,Eric S. Lander,Eric S. Lander,Eric S. Lander,Erez Lieberman Aiden +15 more
TL;DR: In situ Hi-C is used to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types, identifying ∼10,000 loops that frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species.
Journal ArticleDOI
Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments
Neva C. Durand,Muhammad S. Shamim,Muhammad S. Shamim,Ido Machol,Ido Machol,Suhas S.P. Rao,Miriam H. Huntley,Eric S. Lander,Eric S. Lander,Erez Lieberman Aiden +9 more
TL;DR: Juicer as mentioned in this paper is an open-source tool for analyzing terabase-scale Hi-C datasets, which allows users without a computational background to transform raw sequence data into normalized contact maps with one click.
Journal ArticleDOI
De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
Olga Dudchenko,Sanjit S. Batra,Sanjit S. Batra,Arina D. Omer,Arina D. Omer,Sarah K. Nyquist,Sarah K. Nyquist,Marie Hoeger,Marie Hoeger,Neva C. Durand,Neva C. Durand,Muhammad S. Shamim,Muhammad S. Shamim,Ido Machol,Ido Machol,Eric S. Lander,Eric S. Lander,Aviva Presser Aiden,Erez Lieberman Aiden +18 more
TL;DR: In this paper, the authors combine Hi-C data with existing draft assemblies to generate chromosome-length scaffolds, which are then combined with draft sequences to create genome assemblies of the Aedes aegypti and Culex quinquefasciatus.
Journal ArticleDOI
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom.
Neva C. Durand,James T. Robinson,James T. Robinson,Muhammad S. Shamim,Muhammad S. Shamim,Ido Machol,Ido Machol,Jill P. Mesirov,Eric S. Lander,Eric S. Lander,Erez Lieberman Aiden +10 more
TL;DR: Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20 bp and as large as 200 Mb, and Juicebox, a tool for exploring Hi-C and other contact map data, is introduced.
Journal ArticleDOI
The Energetics and Physiological Impact of Cohesin Extrusion
Laura Vian,Aleksandra Pekowska,Suhas S.P. Rao,Suhas S.P. Rao,Kyong-Rim Kieffer-Kwon,Seolkyoung Jung,Laura Baranello,Su-Chen Huang,Laila El Khattabi,Marei Dose,Nathanael Pruett,Adrian L. Sanborn,Adrian L. Sanborn,Andres Canela,Yaakov Maman,Anna Oksanen,Wolfgang Resch,Xingwang Li,Byoungkoo Lee,Alexander L. Kovalchuk,Zhonghui Tang,Steevenson Nelson,Michele Di Pierro,Ryan R. Cheng,Ido Machol,Brian Glenn St Hilaire,Neva C. Durand,Muhammad S. Shamim,Elena Stamenova,José N. Onuchic,Yijun Ruan,André Nussenzweig,David Levens,Erez Lieberman Aiden,Erez Lieberman Aiden,Erez Lieberman Aiden,Rafael Casellas +36 more
TL;DR: It is proposed that higher organisms have coopted cohesin extrusion to enhance transcription and recombination, with implications for tumor development.