Literature DB >> 26220134

Running spell-check to identify regulatory variants.

Martin Kircher1, Jay Shendure1.   

Abstract

A major challenge in human genetics is pinpointing which non-coding genetic variants affect gene expression and disease risk. A new study in this issue describes a broadly applicable approach for this task that explicitly models cell type-specific regulatory motifs and generates variant effect predictions that are more accurate and interpretable than those of alternative tools.

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Year:  2015        PMID: 26220134     DOI: 10.1038/ng.3364

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  15 in total

1.  Detection of nonneutral substitution rates on mammalian phylogenies.

Authors:  Katherine S Pollard; Melissa J Hubisz; Kate R Rosenbloom; Adam Siepel
Journal:  Genome Res       Date:  2009-10-26       Impact factor: 9.043

2.  Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases.

Authors:  Alexander Gusev; S Hong Lee; Gosia Trynka; Hilary Finucane; Bjarni J Vilhjálmsson; Han Xu; Chongzhi Zang; Stephan Ripke; Brendan Bulik-Sullivan; Eli Stahl; Anna K Kähler; Christina M Hultman; Shaun M Purcell; Steven A McCarroll; Mark Daly; Bogdan Pasaniuc; Patrick F Sullivan; Benjamin M Neale; Naomi R Wray; Soumya Raychaudhuri; Alkes L Price
Journal:  Am J Hum Genet       Date:  2014-11-06       Impact factor: 11.025

3.  FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.

Authors:  Yao Fu; Zhu Liu; Shaoke Lou; Jason Bedford; Xinmeng Jasmine Mu; Kevin Y Yip; Ekta Khurana; Mark Gerstein
Journal:  Genome Biol       Date:  2014       Impact factor: 13.583

4.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

Authors:  Adam Siepel; Gill Bejerano; Jakob S Pedersen; Angie S Hinrichs; Minmei Hou; Kate Rosenbloom; Hiram Clawson; John Spieth; Ladeana W Hillier; Stephen Richards; George M Weinstock; Richard K Wilson; Richard A Gibbs; W James Kent; Webb Miller; David Haussler
Journal:  Genome Res       Date:  2005-07-15       Impact factor: 9.043

5.  Chromatin marks identify critical cell types for fine mapping complex trait variants.

Authors:  Gosia Trynka; Cynthia Sandor; Buhm Han; Han Xu; Barbara E Stranger; X Shirley Liu; Soumya Raychaudhuri
Journal:  Nat Genet       Date:  2012-12-23       Impact factor: 38.330

6.  Massively parallel functional dissection of mammalian enhancers in vivo.

Authors:  Rupali P Patwardhan; Joseph B Hiatt; Daniela M Witten; Mee J Kim; Robin P Smith; Dalit May; Choli Lee; Jennifer M Andrie; Su-In Lee; Gregory M Cooper; Nadav Ahituv; Len A Pennacchio; Jay Shendure
Journal:  Nat Biotechnol       Date:  2012-02-26       Impact factor: 54.908

7.  Identifying a high fraction of the human genome to be under selective constraint using GERP++.

Authors:  Eugene V Davydov; David L Goode; Marina Sirota; Gregory M Cooper; Arend Sidow; Serafim Batzoglou
Journal:  PLoS Comput Biol       Date:  2010-12-02       Impact factor: 4.475

8.  A method to predict the impact of regulatory variants from DNA sequence.

Authors:  Dongwon Lee; David U Gorkin; Maggie Baker; Benjamin J Strober; Alessandro L Asoni; Andrew S McCallion; Michael A Beer
Journal:  Nat Genet       Date:  2015-06-15       Impact factor: 38.330

9.  A general framework for estimating the relative pathogenicity of human genetic variants.

Authors:  Martin Kircher; Daniela M Witten; Preti Jain; Brian J O'Roak; Gregory M Cooper; Jay Shendure
Journal:  Nat Genet       Date:  2014-02-02       Impact factor: 38.330

10.  Enhancer evolution across 20 mammalian species.

Authors:  Diego Villar; Camille Berthelot; Sarah Aldridge; Tim F Rayner; Margus Lukk; Miguel Pignatelli; Thomas J Park; Robert Deaville; Jonathan T Erichsen; Anna J Jasinska; James M A Turner; Mads F Bertelsen; Elizabeth P Murchison; Paul Flicek; Duncan T Odom
Journal:  Cell       Date:  2015-01-29       Impact factor: 41.582

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  3 in total

1.  Predicting regulatory variants with composite statistic.

Authors:  Mulin Jun Li; Zhicheng Pan; Zipeng Liu; Jiexing Wu; Panwen Wang; Yun Zhu; Feng Xu; Zhengyuan Xia; Pak Chung Sham; Jean-Pierre A Kocher; Miaoxin Li; Jun S Liu; Junwen Wang
Journal:  Bioinformatics       Date:  2016-06-06       Impact factor: 6.937

2.  regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants.

Authors:  Shijie Zhang; Yukun He; Huanhuan Liu; Haoyu Zhai; Dandan Huang; Xianfu Yi; Xiaobao Dong; Zhao Wang; Ke Zhao; Yao Zhou; Jianhua Wang; Hongcheng Yao; Hang Xu; Zhenglu Yang; Pak Chung Sham; Kexin Chen; Mulin Jun Li
Journal:  Nucleic Acids Res       Date:  2019-12-02       Impact factor: 16.971

Review 3.  Role of Non-Coding Variants in Brugada Syndrome.

Authors:  Adrian Pérez-Agustín; Mel Lina Pinsach-Abuin; Sara Pagans
Journal:  Int J Mol Sci       Date:  2020-11-13       Impact factor: 5.923

  3 in total

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