Literature DB >> 30962623

cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data.

Carmen Bravo González-Blas1,2, Liesbeth Minnoye1,2, Dafni Papasokrati1,2, Sara Aibar1,2, Gert Hulselmans1,2, Valerie Christiaens1,2, Kristofer Davie1,2, Jasper Wouters1,2, Stein Aerts3,4.   

Abstract

We present cisTopic, a probabilistic framework used to simultaneously discover coaccessible enhancers and stable cell states from sparse single-cell epigenomics data ( http://github.com/aertslab/cistopic ). Using a compendium of single-cell ATAC-seq datasets from differentiating hematopoietic cells, brain and transcription factor perturbations, we demonstrate that topic modeling can be exploited for robust identification of cell types, enhancers and relevant transcription factors. cisTopic provides insight into the mechanisms underlying regulatory heterogeneity in cell populations.

Entities:  

Mesh：

Year:  2019        PMID： 30962623      PMCID： PMC6517279          DOI： 10.1038/s41592-019-0367-1

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


  50 in total

1.  Finding scientific topics.

Authors:  Thomas L Griffiths; Mark Steyvers
Journal:  Proc Natl Acad Sci U S A       Date:  2004-02-10       Impact factor: 11.205

2.  Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation.

Authors:  Jason D Buenrostro; M Ryan Corces; Caleb A Lareau; Beijing Wu; Alicia N Schep; Martin J Aryee; Ravindra Majeti; Howard Y Chang; William J Greenleaf
Journal:  Cell       Date:  2018-04-26       Impact factor: 41.582

3.  Editorial: NIH and the support of biomedical research.

Authors:  R S Stone
Journal:  Hum Pathol       Date:  1974-07       Impact factor: 3.466

4.  A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility.

Authors:  Darren A Cusanovich; Andrew J Hill; Delasa Aghamirzaie; Riza M Daza; Hannah A Pliner; Joel B Berletch; Galina N Filippova; Xingfan Huang; Lena Christiansen; William S DeWitt; Choli Lee; Samuel G Regalado; David F Read; Frank J Steemers; Christine M Disteche; Cole Trapnell; Jay Shendure
Journal:  Cell       Date:  2018-08-02       Impact factor: 41.582

5.  Essential role of EBF1 in the generation and function of distinct mature B cell types.

Authors:  Bojan Vilagos; Mareike Hoffmann; Abdallah Souabni; Qiong Sun; Barbara Werner; Jasna Medvedovic; Ivan Bilic; Martina Minnich; Elin Axelsson; Markus Jaritz; Meinrad Busslinger
Journal:  J Exp Med       Date:  2012-04-02       Impact factor: 14.307

6.  Single-cell regulome data analysis by SCRAT.

Authors:  Zhicheng Ji; Weiqiang Zhou; Hongkai Ji
Journal:  Bioinformatics       Date:  2017-09-15       Impact factor: 6.937

7.  Unsupervised clustering and epigenetic classification of single cells.

Authors:  Mahdi Zamanighomi; Zhixiang Lin; Timothy Daley; Xi Chen; Zhana Duren; Alicia Schep; William J Greenleaf; Wing Hung Wong
Journal:  Nat Commun       Date:  2018-06-20       Impact factor: 14.919

8.  chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data.

Authors:  Alicia N Schep; Beijing Wu; Jason D Buenrostro; William J Greenleaf
Journal:  Nat Methods       Date:  2017-08-21       Impact factor: 28.547

9.  BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization.

Authors:  Carl G de Boer; Aviv Regev
Journal:  BMC Bioinformatics       Date:  2018-07-03       Impact factor: 3.169

Review 10.  Mapping gene regulatory networks from single-cell omics data.

Authors:  Mark W E J Fiers; Liesbeth Minnoye; Sara Aibar; Carmen Bravo González-Blas; Zeynep Kalender Atak; Stein Aerts
Journal:  Brief Funct Genomics       Date:  2018-07-01       Impact factor: 4.241
View more
  87 in total

1.  Single-cell joint detection of chromatin occupancy and transcriptome enables higher-dimensional epigenomic reconstructions.

Authors:  Haiqing Xiong; Yingjie Luo; Qianhao Wang; Xianhong Yu; Aibin He
Journal:  Nat Methods       Date:  2021-05-06       Impact factor: 28.547

2.  Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells.

Authors:  Vijay Ramani; Xinxian Deng; Ruolan Qiu; Choli Lee; Christine M Disteche; William S Noble; Jay Shendure; Zhijun Duan
Journal:  Methods       Date:  2019-09-16       Impact factor: 3.608

3.  Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements.

Authors:  Gi Bum Kim; David Rincon Fernandez Pacheco; David Saxon; Amy Yang; Sara Sabet; Marina Dutra-Clarke; Rachelle Levy; Ashley Watkins; Hannah Park; Aslam Abbasi Akhtar; Paul W Linesch; Naomi Kobritz; Swasty S Chandra; Katie Grausam; Alberto Ayala-Sarmiento; Jessica Molina; Kristyna Sedivakova; Kendy Hoang; Jeremiah Tsyporin; Daniel S Gareau; Mariella G Filbin; Serguei Bannykh; Chintda Santiskulvong; Yizhou Wang; Jie Tang; Mario L Suva; Bin Chen; Moise Danielpour; Joshua J Breunig
Journal:  Cell       Date:  2019-09-19       Impact factor: 41.582

4.  Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin.

Authors:  Sai Ma; Bing Zhang; Lindsay M LaFave; Andrew S Earl; Zachary Chiang; Yan Hu; Jiarui Ding; Alison Brack; Vinay K Kartha; Tristan Tay; Travis Law; Caleb Lareau; Ya-Chieh Hsu; Aviv Regev; Jason D Buenrostro
Journal:  Cell       Date:  2020-10-23       Impact factor: 41.582

5.  OpenAnnotate: a web server to annotate the chromatin accessibility of genomic regions.

Authors:  Shengquan Chen; Qiao Liu; Xuejian Cui; Zhanying Feng; Chunquan Li; Xiaowo Wang; Xuegong Zhang; Yong Wang; Rui Jiang
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

6.  A human cell atlas of fetal chromatin accessibility.

Authors:  Silvia Domcke; Andrew J Hill; Riza M Daza; Junyue Cao; Diana R O'Day; Hannah A Pliner; Kimberly A Aldinger; Dmitry Pokholok; Fan Zhang; Jennifer H Milbank; Michael A Zager; Ian A Glass; Frank J Steemers; Dan Doherty; Cole Trapnell; Darren A Cusanovich; Jay Shendure
Journal:  Science       Date:  2020-11-13       Impact factor: 47.728

7.  Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics.

Authors:  Carmen Bravo González-Blas; Xiao-Jiang Quan; Ramon Duran-Romaña; Ibrahim Ihsan Taskiran; Duygu Koldere; Kristofer Davie; Valerie Christiaens; Samira Makhzami; Gert Hulselmans; Maxime de Waegeneer; David Mauduit; Suresh Poovathingal; Sara Aibar; Stein Aerts
Journal:  Mol Syst Biol       Date:  2020-05       Impact factor: 11.429

8.  The intersectional genetics landscape for humans.

Authors:  Andre Macedo; Alisson M Gontijo
Journal:  Gigascience       Date:  2020-08-01       Impact factor: 6.524

9.  APEC: an accesson-based method for single-cell chromatin accessibility analysis.

Authors:  Bin Li; Young Li; Kun Li; Lianbang Zhu; Qiaoni Yu; Pengfei Cai; Jingwen Fang; Wen Zhang; Pengcheng Du; Chen Jiang; Jun Lin; Kun Qu
Journal:  Genome Biol       Date:  2020-05-12       Impact factor: 13.583

10.  Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets.

Authors:  Rossin Erbe; Michael D Kessler; Alexander V Favorov; Hariharan Easwaran; Daria A Gaykalova; Elana J Fertig
Journal:  Nucleic Acids Res       Date:  2020-07-09       Impact factor: 16.971
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.