Literature DB >> 27120444

Connecting the regulatory genome.

John Stamatoyannopoulos1.   

Abstract

Determining how the evolving genome-wide map of distal regulatory elements is connected with target genes has remained a significant challenge, despite progress in understanding chromatin architecture and regulation. A new study presents a computational approach for predicting distal element-gene interactions.

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Year:  2016        PMID： 27120444     DOI： 10.1038/ng.3553

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


  15 in total

Review 1.  A decade of 3C technologies: insights into nuclear organization.

Authors:  Elzo de Wit; Wouter de Laat
Journal:  Genes Dev       Date:  2012-01-01       Impact factor: 11.361

2.  A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors:  Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2014-12-11       Impact factor: 41.582

3.  FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.

Authors:  Melina Claussnitzer; Simon N Dankel; Kyoung-Han Kim; Gerald Quon; Wouter Meuleman; Christine Haugen; Viktoria Glunk; Isabel S Sousa; Jacqueline L Beaudry; Vijitha Puviindran; Nezar A Abdennur; Jannel Liu; Per-Arne Svensson; Yi-Hsiang Hsu; Daniel J Drucker; Gunnar Mellgren; Chi-Chung Hui; Hans Hauner; Manolis Kellis
Journal:  N Engl J Med       Date:  2015-08-19       Impact factor: 91.245

4.  HCF-1 self-association via an interdigitated Fn3 structure facilitates transcriptional regulatory complex formation.

Authors:  Jihye Park; Fabienne Lammers; Winship Herr; Ji-Joon Song
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-08       Impact factor: 11.205

5.  Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.

Authors:  Sean Whalen; Rebecca M Truty; Katherine S Pollard
Journal:  Nat Genet       Date:  2016-04-04       Impact factor: 38.330

6.  Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment.

Authors:  Jim R Hughes; Nigel Roberts; Simon McGowan; Deborah Hay; Eleni Giannoulatou; Magnus Lynch; Marco De Gobbi; Stephen Taylor; Richard Gibbons; Douglas R Higgs
Journal:  Nat Genet       Date:  2014-01-12       Impact factor: 38.330

Review 7.  Enabling functional genomics with genome engineering.

Authors:  Isaac B Hilton; Charles A Gersbach
Journal:  Genome Res       Date:  2015-10       Impact factor: 9.043

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

Review 10.  Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes.

Authors:  Lijing Yao; Benjamin P Berman; Peggy J Farnham
Journal:  Crit Rev Biochem Mol Biol       Date:  2015-10-08       Impact factor: 8.250
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  4 in total

Review 1.  How best to identify chromosomal interactions: a comparison of approaches.

Authors:  James O J Davies; A Marieke Oudelaar; Douglas R Higgs; Jim R Hughes
Journal:  Nat Methods       Date:  2017-01-31       Impact factor: 28.547

2.  The pharmacoepigenomics informatics pipeline defines a pathway of novel and known warfarin pharmacogenomics variants.

Authors:  Ari Allyn-Feuer; Alex Ade; Jasmine A Luzum; Gerald A Higgins; Brian D Athey
Journal:  Pharmacogenomics       Date:  2018-02-05       Impact factor: 2.533

3.  Association of environmental markers with childhood type 1 diabetes mellitus revealed by a long questionnaire on early life exposures and lifestyle in a case-control study.

Authors:  F Balazard; S Le Fur; S Valtat; A J Valleron; P Bougnères; Dominique Thevenieau; Corinne Fourmy Chatel; Rachel Desailloud; Hélène Bony-Trifunovic; Pierre-Henri Ducluzeau; Régis Coutant; Sophie Caudrelier; Armelle Pambou; Emmanuelle Dubosclard; Florence Joubert; Philippe Jan; Estelle Marcoux; Anne-Marie Bertrand; Brigitte Mignot; Alfred Penformis; Chantal Stuckens; Régis Piquemal; Pascal Barat; Vincent Rigalleau; Chantal Stheneur; Sylviane Fournier; Véronique Kerlan; Chantal Metz; Anne Fargeot-Espaliat; Yves Reznic; Frédérique Olivier; Iva Gueorguieva; Arnaud Monier; Catherine Radet; Vincent Gajdos; Daniel Terral; Christine Vervel; Djamel Bendifallah; Candace Ben Signor; Daniel Dervaux; Abdelkader Benmahammed; Guy-André Loeuille; Françoise Popelard; Agnès Guillou; Pierre-Yves Benhamou; Jamil Khoury; Jean-Pierre Brossier; Joachim Bassil; Sylvaine Clavel; Bernard Le Luyer; Pierre Bougnères; Françoise Labay; Isabelle Guemas; Jacques Weill; Jean-Pierre Cappoen; Sylvie Nadalon; Anne Lienhardt-Roussie; Anne Paoli; Claudie Kerouedan; Edwige Yollin; Marc Nicolino; Gilbert Simonin; Jacques Cohen; Catherine Atlan; Agnès Tamboura; Hervé Dubourg; Marie-Laure Pignol; Philippe Talon; Stéphanie Jellimann; Lucy Chaillous; Sabine Baron; Marie-Noëlle Bortoluzzi; Elisabeth Baechler; Randa Salet; Ariane Zelinsky-Gurung; Fabienne Dallavale; Etienne Larger; Marie Laloi-Michelin; Jean-François Gautier; Bénédicte Guérin; Laure Oilleau; Laetitia Pantalone; Céline Lukas; Isabelle Guilhem; Marc De Kerdanet; Marie-Claire Wielickzo; Mélanie Priou-Guesdon; Odile Richard; François Kurtz; Norbert Laisney; Déborah Ancelle; Guilhem Parlier; Catherine Boniface; Dominique Paris Bockel; Denis Dufillot; Berthe Razafimahefa; Pierre Gourdy; Pierre Lecomte; Myriam Pepin-Donat; Marie-Emmanuelle Combes-Moukhovsky; Brigitte Zymmermann; Marina Raoulx; Anne Gourdin Et Catherine Dumont
Journal:  BMC Public Health       Date:  2016-09-29       Impact factor: 3.295

4.  Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies.

Authors:  Li Tang; Matthew C Hill; Patrick T Ellinor; Min Li
Journal:  Genome Biol       Date:  2022-01-21       Impact factor: 13.583
  4 in total

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