Literature DB >> 29489746

hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data.

Caleb A Lareau1,2,3, Martin J Aryee1,2,3,4.   

Abstract

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Year:  2018        PMID： 29489746     DOI： 10.1038/nmeth.4583

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  2 in total

1.  HiChIP: efficient and sensitive analysis of protein-directed genome architecture.

Authors:  Maxwell R Mumbach; Adam J Rubin; Ryan A Flynn; Chao Dai; Paul A Khavari; William J Greenleaf; Howard Y Chang
Journal:  Nat Methods       Date:  2016-09-19       Impact factor: 28.547

2.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.

Authors:  Nicolas Servant; Nelle Varoquaux; Bryan R Lajoie; Eric Viara; Chong-Jian Chen; Jean-Philippe Vert; Edith Heard; Job Dekker; Emmanuel Barillot
Journal:  Genome Biol       Date:  2015-12-01       Impact factor: 13.583
  2 in total
  53 in total

1.  Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis.

Authors:  Qian Qi; Li Cheng; Xing Tang; Yanghua He; Yichao Li; Tiffany Yee; Dewan Shrestha; Ruopeng Feng; Peng Xu; Xin Zhou; Shondra Pruett-Miller; Ross C Hardison; Mitchell J Weiss; Yong Cheng
Journal:  Blood       Date:  2021-03-11       Impact factor: 22.113

2.  IDR2D identifies reproducible genomic interactions.

Authors:  Konstantin Krismer; Yuchun Guo; David K Gifford
Journal:  Nucleic Acids Res       Date:  2020-04-06       Impact factor: 16.971

3.  Role of Systemic Lupus Erythematosus Risk Variants With Opposing Functional Effects as a Driver of Hypomorphic Expression of TNIP1 and Other Genes Within a Three-Dimensional Chromatin Network.

Authors:  Satish Pasula; Kandice L Tessneer; Yao Fu; Jaanam Gopalakrishnan; Richard C Pelikan; Jennifer A Kelly; Graham B Wiley; Mandi M Wiley; Patrick M Gaffney
Journal:  Arthritis Rheumatol       Date:  2020-03-30       Impact factor: 10.995

4.  An Activity-Mediated Transition in Transcription in Early Postnatal Neurons.

Authors:  Hume Stroud; Marty G Yang; Yael N Tsitohay; Christopher P Davis; Maxwell A Sherman; Sinisa Hrvatin; Emi Ling; Michael E Greenberg
Journal:  Neuron       Date:  2020-06-25       Impact factor: 17.173

5.  High resolution discovery of chromatin interactions.

Authors:  Yuchun Guo; Konstantin Krismer; Michael Closser; Hynek Wichterle; David K Gifford
Journal:  Nucleic Acids Res       Date:  2019-04-08       Impact factor: 16.971

6.  Chromatin Looping Shapes KLF5-Dependent Transcriptional Programs in Human Epithelial Cancers.

Authors:  Yanli Liu; Bingqian Guo; Estrella Aguilera-Jimenez; Vivian S Chu; Jin Zhou; Zhong Wu; Joshua M Francis; Xiaojun Yang; Peter S Choi; Swneke D Bailey; Xiaoyang Zhang
Journal:  Cancer Res       Date:  2020-10-28       Impact factor: 12.701

7.  Genetic analyses of gynecological disease identify genetic relationships between uterine fibroids and endometrial cancer, and a novel endometrial cancer genetic risk region at the WNT4 1p36.12 locus.

Authors:  Dylan M Glubb; Tracy A O'Mara; Pik Fang Kho; Sally Mortlock; Peter A W Rogers; Dale R Nyholt; Grant W Montgomery; Amanda B Spurdle
Journal:  Hum Genet       Date:  2021-07-15       Impact factor: 4.132

8.  Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.

Authors:  Sarah E Johnstone; Alejandro Reyes; Yifeng Qi; Carmen Adriaens; Esmat Hegazi; Karin Pelka; Jonathan H Chen; Luli S Zou; Yotam Drier; Vivian Hecht; Noam Shoresh; Martin K Selig; Caleb A Lareau; Sowmya Iyer; Son C Nguyen; Eric F Joyce; Nir Hacohen; Rafael A Irizarry; Bin Zhang; Martin J Aryee; Bradley E Bernstein
Journal:  Cell       Date:  2020-08-24       Impact factor: 41.582

9.  The connectome of neural crest enhancers reveals regulatory features of signaling systems.

Authors:  Ana Paula Azambuja; Marcos Simoes-Costa
Journal:  Dev Cell       Date:  2021-04-13       Impact factor: 12.270

10.  Variants on the UBE2L3/YDJC Autoimmune Disease Risk Haplotype Increase UBE2L3 Expression by Modulating CCCTC-Binding Factor and YY1 Binding.

Authors:  Jaanam Gopalakrishnan; Kandice L Tessneer; Yao Fu; Satish Pasula; Richard C Pelikan; Jennifer A Kelly; Graham B Wiley; Patrick M Gaffney
Journal:  Arthritis Rheumatol       Date:  2021-12-13       Impact factor: 10.995
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