Literature DB >> 29309061

GIGGLE: a search engine for large-scale integrated genome analysis.

Ryan M Layer1,2, Brent S Pedersen1,2, Tonya DiSera1,2, Gabor T Marth1,2, Jason Gertz3, Aaron R Quinlan1,2,4.   

Abstract

GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation.

Entities:  

Mesh：

Year:  2018        PMID： 29309061      PMCID： PMC5872823          DOI： 10.1038/nmeth.4556

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


  22 in total

1.  A novel significance score for gene selection and ranking.

Authors:  Yufei Xiao; Tzu-Hung Hsiao; Uthra Suresh; Hung-I Harry Chen; Xiaowu Wu; Steven E Wolf; Yidong Chen
Journal:  Bioinformatics       Date:  2012-02-09       Impact factor: 6.937

2.  The dilemma of choosing the ideal permutation strategy while estimating statistical significance of genome-wide enrichment.

Authors:  Subhajyoti De; Brent S Pedersen; Katerina Kechris
Journal:  Brief Bioinform       Date:  2013-08-16       Impact factor: 11.622

3.  Binary Interval Search: a scalable algorithm for counting interval intersections.

Authors:  Ryan M Layer; Kevin Skadron; Gabriel Robins; Ira M Hall; Aaron R Quinlan
Journal:  Bioinformatics       Date:  2012-11-04       Impact factor: 6.937

4.  Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.

Authors:  Jason S Carroll; X Shirley Liu; Alexander S Brodsky; Wei Li; Clifford A Meyer; Anna J Szary; Jerome Eeckhoute; Wenlin Shao; Eli V Hestermann; Timothy R Geistlinger; Edward A Fox; Pamela A Silver; Myles Brown
Journal:  Cell       Date:  2005-07-15       Impact factor: 41.582

5.  Condensin I and II Complexes License Full Estrogen Receptor α-Dependent Enhancer Activation.

Authors:  Wenbo Li; Yiren Hu; Soohwan Oh; Qi Ma; Daria Merkurjev; Xiaoyuan Song; Xiang Zhou; Zhijie Liu; Bogdan Tanasa; Xin He; Aaron Yun Chen; Kenny Ohgi; Jie Zhang; Wen Liu; Michael G Rosenfeld
Journal:  Mol Cell       Date:  2015-07-09       Impact factor: 17.970

6.  Gateways to the FANTOM5 promoter level mammalian expression atlas.

Authors:  Marina Lizio; Jayson Harshbarger; Hisashi Shimoji; Jessica Severin; Takeya Kasukawa; Serkan Sahin; Imad Abugessaisa; Shiro Fukuda; Fumi Hori; Sachi Ishikawa-Kato; Christopher J Mungall; Erik Arner; J Kenneth Baillie; Nicolas Bertin; Hidemasa Bono; Michiel de Hoon; Alexander D Diehl; Emmanuel Dimont; Tom C Freeman; Kaori Fujieda; Winston Hide; Rajaram Kaliyaperumal; Toshiaki Katayama; Timo Lassmann; Terrence F Meehan; Koro Nishikata; Hiromasa Ono; Michael Rehli; Albin Sandelin; Erik A Schultes; Peter A C 't Hoen; Zuotian Tatum; Mark Thompson; Tetsuro Toyoda; Derek W Wright; Carsten O Daub; Masayoshi Itoh; Piero Carninci; Yoshihide Hayashizaki; Alistair R R Forrest; Hideya Kawaji
Journal:  Genome Biol       Date:  2015-01-05       Impact factor: 13.583

7.  Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse.

Authors:  Shenglin Mei; Qian Qin; Qiu Wu; Hanfei Sun; Rongbin Zheng; Chongzhi Zang; Muyuan Zhu; Jiaxin Wu; Xiaohui Shi; Len Taing; Tao Liu; Myles Brown; Clifford A Meyer; X Shirley Liu
Journal:  Nucleic Acids Res       Date:  2016-10-26       Impact factor: 16.971

8.  Endogenous purification reveals GREB1 as a key estrogen receptor regulatory factor.

Authors:  Hisham Mohammed; Clive D'Santos; Aurelien A Serandour; H Raza Ali; Gordon D Brown; Alan Atkins; Oscar M Rueda; Kelly A Holmes; Vasiliki Theodorou; Jessica L L Robinson; Wilbert Zwart; Amel Saadi; Caryn S Ross-Innes; Suet-Feung Chin; Suraj Menon; John Stingl; Carlo Palmieri; Carlos Caldas; Jason S Carroll
Journal:  Cell Rep       Date:  2013-02-09       Impact factor: 9.423

9.  GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility.

Authors:  Vasiliki Theodorou; Rory Stark; Suraj Menon; Jason S Carroll
Journal:  Genome Res       Date:  2012-11-21       Impact factor: 9.043

10.  Progesterone receptor modulates ERα action in breast cancer.

Authors:  Hisham Mohammed; I Alasdair Russell; Rory Stark; Oscar M Rueda; Theresa E Hickey; Gerard A Tarulli; Aurelien A Serandour; Aurelien A A Serandour; Stephen N Birrell; Alejandra Bruna; Amel Saadi; Suraj Menon; James Hadfield; Michelle Pugh; Ganesh V Raj; Gordon D Brown; Clive D'Santos; Jessica L L Robinson; Grace Silva; Rosalind Launchbury; Charles M Perou; John Stingl; Carlos Caldas; Wayne D Tilley; Jason S Carroll
Journal:  Nature       Date:  2015-07-08       Impact factor: 49.962
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  47 in total

1.  MendelVar: gene prioritisation at GWAS loci using phenotypic enrichment of mendelian disease genes.

Authors:  Sobczyk M K; Gaunt T R; Paternoster L
Journal:  Bioinformatics       Date:  2021-01-16       Impact factor: 6.937

2.  MUC1-C Dictates JUN and BAF-Mediated Chromatin Remodeling at Enhancer Signatures in Cancer Stem Cells.

Authors:  Atrayee Bhattacharya; Atsushi Fushimi; Nami Yamashita; Masayuki Hagiwara; Yoshihiro Morimoto; Hasan Rajabi; Mark D Long; Maha Abdulla; Rehan Ahmad; Kelly Street; Song Liu; Tao Liu; Donald Kufe
Journal:  Mol Cancer Res       Date:  2022-04-01       Impact factor: 5.852

3.  Analysis of Enhancers and Transcriptional Networks in Thermogenic Adipocytes.

Authors:  Anne Loft; Maja Worm Andersen; Jesper Grud Skat Madsen; Susanne Mandrup
Journal:  Methods Mol Biol       Date:  2022

4.  Drug-Induced Epigenomic Plasticity Reprograms Circadian Rhythm Regulation to Drive Prostate Cancer toward Androgen Independence.

Authors:  Simon Linder; Marlous Hoogstraat; Suzan Stelloo; Nils Eickhoff; Karianne Schuurman; Hilda de Barros; Maartje Alkemade; Elise M Bekers; Tesa M Severson; Joyce Sanders; Chia-Chi Flora Huang; Tunc Morova; Umut Berkay Altintas; Liesbeth Hoekman; Yongsoo Kim; Sylvan C Baca; Martin Sjöström; Anniek Zaalberg; Dorine C Hintzen; Jeroen de Jong; Roelof J C Kluin; Iris de Rink; Claudia Giambartolomei; Ji-Heui Seo; Bogdan Pasaniuc; Maarten Altelaar; René H Medema; Felix Y Feng; Amina Zoubeidi; Matthew L Freedman; Lodewyk F A Wessels; Lisa M Butler; Nathan A Lack; Henk van der Poel; Andries M Bergman; Wilbert Zwart
Journal:  Cancer Discov       Date:  2022-09-02       Impact factor: 38.272

5.  Genome-wide alterations of uracil distribution patterns in human DNA upon chemotherapeutic treatments.

Authors:  Hajnalka L Pálinkás; Angéla Békési; Gergely Róna; Lőrinc Pongor; Gábor Papp; Gergely Tihanyi; Eszter Holub; Ádám Póti; Carolina Gemma; Simak Ali; Michael J Morten; Eli Rothenberg; Michele Pagano; Dávid Szűts; Balázs Győrffy; Beáta G Vértessy
Journal:  Elife       Date:  2020-09-21       Impact factor: 8.140

6.  Analytical Approaches for ATAC-seq Data Analysis.

Authors:  Jason P Smith; Nathan C Sheffield
Journal:  Curr Protoc Hum Genet       Date:  2020-06

7.  MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes.

Authors:  M K Sobczyk; T R Gaunt; L Paternoster
Journal:  Bioinformatics       Date:  2021-04-09       Impact factor: 6.937

8.  Reprogramming of the FOXA1 cistrome in treatment-emergent neuroendocrine prostate cancer.

Authors:  Sylvan C Baca; David Y Takeda; Ji-Heui Seo; Justin Hwang; Sheng Yu Ku; Rand Arafeh; Taylor Arnoff; Supreet Agarwal; Connor Bell; Edward O'Connor; Xintao Qiu; Sarah Abou Alaiwi; Rosario I Corona; Marcos A S Fonseca; Claudia Giambartolomei; Paloma Cejas; Klothilda Lim; Monica He; Anjali Sheahan; Amin Nassar; Jacob E Berchuck; Lisha Brown; Holly M Nguyen; Ilsa M Coleman; Arja Kaipainen; Navonil De Sarkar; Peter S Nelson; Colm Morrissey; Keegan Korthauer; Mark M Pomerantz; Leigh Ellis; Bogdan Pasaniuc; Kate Lawrenson; Kathleen Kelly; Amina Zoubeidi; William C Hahn; Himisha Beltran; Henry W Long; Myles Brown; Eva Corey; Matthew L Freedman
Journal:  Nat Commun       Date:  2021-03-30       Impact factor: 14.919

9.  Dynamics of replication origin over-activation.

Authors:  Haiqing Fu; Christophe E Redon; Bhushan L Thakur; Koichi Utani; Robin Sebastian; Sang-Min Jang; Jacob M Gross; Sara Mosavarpour; Anna B Marks; Sophie Z Zhuang; Sarah B Lazar; Mishal Rao; Shira T Mencer; Adrian M Baris; Lorinc S Pongor; Mirit I Aladjem
Journal:  Nat Commun       Date:  2021-06-08       Impact factor: 14.919

10.  FILER: a framework for harmonizing and querying large-scale functional genomics knowledge.

Authors:  Pavel P Kuksa; Yuk Yee Leung; Prabhakaran Gangadharan; Zivadin Katanic; Lauren Kleidermacher; Alexandre Amlie-Wolf; Chien-Yueh Lee; Liming Qu; Emily Greenfest-Allen; Otto Valladares; Li-San Wang
Journal:  NAR Genom Bioinform       Date:  2022-01-14
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