Literature DB >> 26418766

Diving deeper to predict noncoding sequence function.

Barbara E Engelhardt1, Christopher D Brown2.   

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Year:  2015        PMID: 26418766     DOI: 10.1038/nmeth.3604

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


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  13 in total

1.  Distribution and intensity of constraint in mammalian genomic sequence.

Authors:  Gregory M Cooper; Eric A Stone; George Asimenos; Eric D Green; Serafim Batzoglou; Arend Sidow
Journal:  Genome Res       Date:  2005-06-17       Impact factor: 9.043

2.  Joint analysis of functional genomic data and genome-wide association studies of 18 human traits.

Authors:  Joseph K Pickrell
Journal:  Am J Hum Genet       Date:  2014-04-03       Impact factor: 11.025

3.  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

4.  Predicting effects of noncoding variants with deep learning-based sequence model.

Authors:  Jian Zhou; Olga G Troyanskaya
Journal:  Nat Methods       Date:  2015-08-24       Impact factor: 28.547

5.  An atlas of active enhancers across human cell types and tissues.

Authors:  Robin Andersson; Claudia Gebhard; Michael Rehli; Albin Sandelin; Irene Miguel-Escalada; Ilka Hoof; Jette Bornholdt; Mette Boyd; Yun Chen; Xiaobei Zhao; Christian Schmidl; Takahiro Suzuki; Evgenia Ntini; Erik Arner; Eivind Valen; Kang Li; Lucia Schwarzfischer; Dagmar Glatz; Johanna Raithel; Berit Lilje; Nicolas Rapin; Frederik Otzen Bagger; Mette Jørgensen; Peter Refsing Andersen; Nicolas Bertin; Owen Rackham; A Maxwell Burroughs; J Kenneth Baillie; Yuri Ishizu; Yuri Shimizu; Erina Furuhata; Shiori Maeda; Yutaka Negishi; Christopher J Mungall; Terrence F Meehan; Timo Lassmann; Masayoshi Itoh; Hideya Kawaji; Naoto Kondo; Jun Kawai; Andreas Lennartsson; Carsten O Daub; Peter Heutink; David A Hume; Torben Heick Jensen; Harukazu Suzuki; Yoshihide Hayashizaki; Ferenc Müller; Alistair R R Forrest; Piero Carninci
Journal:  Nature       Date:  2014-03-27       Impact factor: 49.962

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.  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

8.  An integrated encyclopedia of DNA elements in the human genome.

Authors: 
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

9.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

10.  Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis.

Authors:  Michael N Weedon; Ines Cebola; Ann-Marie Patch; Sian Ellard; Jorge Ferrer; Andrew T Hattersley; Sarah E Flanagan; Elisa De Franco; Richard Caswell; Santiago A Rodríguez-Seguí; Charles Shaw-Smith; Candy H-H Cho; Hana Lango Allen; Jayne Al Houghton; Christian L Roth; Rongrong Chen; Khalid Hussain; Phil Marsh; Ludovic Vallier; Anna Murray
Journal:  Nat Genet       Date:  2013-11-10       Impact factor: 38.330

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  4 in total

Review 1.  Noncoding Variants Functional Prioritization Methods Based on Predicted Regulatory Factor Binding Sites.

Authors:  Haoyue Fu; Xiangde Zhang
Journal:  Curr Genomics       Date:  2017-08       Impact factor: 2.236

Review 2.  Conserved non-coding elements: developmental gene regulation meets genome organization.

Authors:  Dimitris Polychronopoulos; James W D King; Alexander J Nash; Ge Tan; Boris Lenhard
Journal:  Nucleic Acids Res       Date:  2017-12-15       Impact factor: 16.971

Review 3.  Brain transcriptome atlases: a computational perspective.

Authors:  Ahmed Mahfouz; Sjoerd M H Huisman; Boudewijn P F Lelieveldt; Marcel J T Reinders
Journal:  Brain Struct Funct       Date:  2016-12-01       Impact factor: 3.270

4.  Capturing variation in Lens (Fabaceae): Development and utility of an exome capture array for lentil.

Authors:  Ezgi Ogutcen; Larissa Ramsay; Eric Bishop von Wettberg; Kirstin E Bett
Journal:  Appl Plant Sci       Date:  2018-07-16       Impact factor: 1.936

  4 in total

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