Literature DB >> 23071271

MULTOVL: fast multiple overlaps of genomic regions.

András Aszódi1.   

Abstract

We present the MULTOVL application suite that detects and statistically analyses multiple overlaps of genomic regions in a fast and efficient manner. The package supports the detection of multiple region intersections, unions and 'solitary' genomic regions. The significance of actually observed overlaps is estimated by comparing them with empirical null distributions generated by random shuffling of the input regions.

Mesh：

Year:  2012        PMID： 23071271     DOI： 10.1093/bioinformatics/bts607

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  19 in total

1.  GINOM: A statistical framework for assessing interval overlap of multiple genomic features.

Authors:  Darshan Bryner; Stephen Criscione; Andrew Leith; Quyen Huynh; Fred Huffer; Nicola Neretti
Journal:  PLoS Comput Biol       Date:  2017-06-15       Impact factor: 4.475

2.  Local ancestry analysis reveals genomic convergence in extremophile fishes.

Authors:  Anthony P Brown; Kerry L McGowan; Enrique J Schwarzkopf; Ryan Greenway; Lenin Arias Rodriguez; Michael Tobler; Joanna L Kelley
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2019-06-03       Impact factor: 6.237

3.  Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.

Authors:  Gordana Wutz; Csilla Várnai; Kota Nagasaka; David A Cisneros; Roman R Stocsits; Wen Tang; Stefan Schoenfelder; Gregor Jessberger; Matthias Muhar; M Julius Hossain; Nike Walther; Birgit Koch; Moritz Kueblbeck; Jan Ellenberg; Johannes Zuber; Peter Fraser; Jan-Michael Peters
Journal:  EMBO J       Date:  2017-12-07       Impact factor: 11.598

4.  GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome.

Authors:  Boris Simovski; Daniel Vodák; Sveinung Gundersen; Diana Domanska; Abdulrahman Azab; Lars Holden; Marit Holden; Ivar Grytten; Knut Rand; Finn Drabløs; Morten Johansen; Antonio Mora; Christin Lund-Andersen; Bastian Fromm; Ragnhild Eskeland; Odd Stokke Gabrielsen; Egil Ferkingstad; Sigve Nakken; Mads Bengtsen; Alexander Johan Nederbragt; Hildur Sif Thorarensen; Johannes Andreas Akse; Ingrid Glad; Eivind Hovig; Geir Kjetil Sandve
Journal:  Gigascience       Date:  2017-07-01       Impact factor: 6.524

5.  OLOGRAM-MODL: mining enriched n-wise combinations of genomic features with Monte Carlo and dictionary learning.

Authors:  Quentin Ferré; Cécile Capponi; Denis Puthier
Journal:  NAR Genom Bioinform       Date:  2021-12-22

6.  Multifunctional role of the transcription factor Blimp-1 in coordinating plasma cell differentiation.

Authors:  Martina Minnich; Hiromi Tagoh; Peter Bönelt; Elin Axelsson; Maria Fischer; Beatriz Cebolla; Alexander Tarakhovsky; Stephen L Nutt; Markus Jaritz; Meinrad Busslinger
Journal:  Nat Immunol       Date:  2016-01-18       Impact factor: 25.606

7.  A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element.

Authors:  Veronika A Herzog; Adelheid Lempradl; Johanna Trupke; Helena Okulski; Christina Altmutter; Frank Ruge; Bernd Boidol; Stefan Kubicek; Gerald Schmauss; Karin Aumayr; Marius Ruf; Andrew Pospisilik; Andrew Dimond; Hasene Basak Senergin; Marcus L Vargas; Jeffrey A Simon; Leonie Ringrose
Journal:  Nat Genet       Date:  2014-08-10       Impact factor: 38.330

8.  Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl.

Authors:  Georg A Busslinger; Roman R Stocsits; Petra van der Lelij; Elin Axelsson; Antonio Tedeschi; Niels Galjart; Jan-Michael Peters
Journal:  Nature       Date:  2017-04-19       Impact factor: 49.962

9.  Stage-specific control of early B cell development by the transcription factor Ikaros.

Authors:  Tanja A Schwickert; Hiromi Tagoh; Sinan Gültekin; Aleksandar Dakic; Elin Axelsson; Martina Minnich; Anja Ebert; Barbara Werner; Mareike Roth; Luisa Cimmino; Ross A Dickins; Johannes Zuber; Markus Jaritz; Meinrad Busslinger
Journal:  Nat Immunol       Date:  2014-02-09       Impact factor: 25.606

10.  Chromatin regulator Asxl1 loss and Nf1 haploinsufficiency cooperate to accelerate myeloid malignancy.

Authors:  Peng Zhang; Fuhong He; Jie Bai; Shohei Yamamoto; Shi Chen; Lin Zhang; Mengyao Sheng; Lei Zhang; Ying Guo; Na Man; Hui Yang; Suyun Wang; Tao Cheng; Stephen D Nimer; Yuan Zhou; Mingjiang Xu; Qian-Fei Wang; Feng-Chun Yang
Journal:  J Clin Invest       Date:  2018-10-29       Impact factor: 14.808
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