Literature DB >> 28983521

Topological methods for genomics: present and future directions.

Pablo G Cámara1.   

Abstract

Topological methods are emerging as a new set of tools for the analysis of large genomic datasets. They are mathematically grounded methods that extract information from the geometric structure of data. In the last few years, applications to evolutionary biology, cancer genomics, and the analysis of complex diseases have uncovered significant biological results, highlighting their utility for fulfilling some of the current analytic needs of genomics. In this review, the state of the art in the application of topological methods to genomics is summarized, and some of the present limitations and possible future developments are reviewed.

Entities:  

Year:  2016        PMID： 28983521      PMCID： PMC5624534          DOI： 10.1016/j.coisb.2016.12.007

Source DB:  PubMed          Journal:  Curr Opin Syst Biol        ISSN： 2452-3100


  25 in total

Review 1.  Lateral gene transfer and the nature of bacterial innovation.

Authors:  H Ochman; J G Lawrence; E A Groisman
Journal:  Nature       Date:  2000-05-18       Impact factor: 49.962

Review 2.  Sequencing technologies - the next generation.

Authors:  Michael L Metzker
Journal:  Nat Rev Genet       Date:  2009-12-08       Impact factor: 53.242

3.  Identification of type 2 diabetes subgroups through topological analysis of patient similarity.

Authors:  Li Li; Wei-Yi Cheng; Benjamin S Glicksberg; Omri Gottesman; Ronald Tamler; Rong Chen; Erwin P Bottinger; Joel T Dudley
Journal:  Sci Transl Med       Date:  2015-10-28       Impact factor: 17.956

Review 4.  Coming of age: ten years of next-generation sequencing technologies.

Authors:  Sara Goodwin; John D McPherson; W Richard McCombie
Journal:  Nat Rev Genet       Date:  2016-05-17       Impact factor: 53.242

5.  Human infection with a novel avian-origin influenza A (H7N9) virus.

Authors:  Rongbao Gao; Bin Cao; Yunwen Hu; Zijian Feng; Dayan Wang; Wanfu Hu; Jian Chen; Zhijun Jie; Haibo Qiu; Ke Xu; Xuewei Xu; Hongzhou Lu; Wenfei Zhu; Zhancheng Gao; Nijuan Xiang; Yinzhong Shen; Zebao He; Yong Gu; Zhiyong Zhang; Yi Yang; Xiang Zhao; Lei Zhou; Xiaodan Li; Shumei Zou; Ye Zhang; Xiyan Li; Lei Yang; Junfeng Guo; Jie Dong; Qun Li; Libo Dong; Yun Zhu; Tian Bai; Shiwen Wang; Pei Hao; Weizhong Yang; Yanping Zhang; Jun Han; Hongjie Yu; Dexin Li; George F Gao; Guizhen Wu; Yu Wang; Zhenghong Yuan; Yuelong Shu
Journal:  N Engl J Med       Date:  2013-04-11       Impact factor: 91.245

Review 6.  Reassortment in segmented RNA viruses: mechanisms and outcomes.

Authors:  Sarah M McDonald; Martha I Nelson; Paul E Turner; John T Patton
Journal:  Nat Rev Microbiol       Date:  2016-05-23       Impact factor: 60.633

7.  SW1PerS: Sliding windows and 1-persistence scoring; discovering periodicity in gene expression time series data.

Authors:  Jose A Perea; Anastasia Deckard; Steve B Haase; John Harer
Journal:  BMC Bioinformatics       Date:  2015-08-16       Impact factor: 3.169

8.  An integrated map of genetic variation from 1,092 human genomes.

Authors:  Goncalo R Abecasis; Adam Auton; Lisa D Brooks; Mark A DePristo; Richard M Durbin; Robert E Handsaker; Hyun Min Kang; Gabor T Marth; Gil A McVean
Journal:  Nature       Date:  2012-11-01       Impact factor: 49.962

9.  Comparison of pattern detection methods in microarray time series of the segmentation clock.

Authors:  Mary-Lee Dequéant; Sebastian Ahnert; Herbert Edelsbrunner; Thomas M A Fink; Earl F Glynn; Gaye Hattem; Andrzej Kudlicki; Yuriy Mileyko; Jason Morton; Arcady R Mushegian; Lior Pachter; Maga Rowicka; Anne Shiu; Bernd Sturmfels; Olivier Pourquié
Journal:  PLoS One       Date:  2008-08-06       Impact factor: 3.240

Review 10.  Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity.

Authors:  Stephen J Clark; Heather J Lee; Sébastien A Smallwood; Gavin Kelsey; Wolf Reik
Journal:  Genome Biol       Date:  2016-04-18       Impact factor: 13.583
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  8 in total

Review 1.  Precision Medicine for Acute Kidney Injury (AKI): Redefining AKI by Agnostic Kidney Tissue Interrogation and Genetics.

Authors:  Krzysztof Kiryluk; Andrew S Bomback; Yim-Ling Cheng; Katherine Xu; Pablo G Camara; Raul Rabadan; Peter A Sims; Jonathan Barasch
Journal:  Semin Nephrol       Date:  2018-01       Impact factor: 5.299

Review 2.  Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.

Authors:  Anja Spang; Tara A Mahendrarajah; Pierre Offre; Courtney W Stairs
Journal:  Genome Biol Evol       Date:  2022-05-31       Impact factor: 4.065

3.  Identification of stem cells from large cell populations with topological scoring.

Authors:  Mihaela E Sardiu; Andrew C Box; Jeffrey S Haug; Michael P Washburn
Journal:  Mol Omics       Date:  2020-09-14

Review 4.  The 2019 mathematical oncology roadmap.

Authors:  Russell C Rockne; Andrea Hawkins-Daarud; Kristin R Swanson; James P Sluka; James A Glazier; Paul Macklin; David A Hormuth; Angela M Jarrett; Ernesto A B F Lima; J Tinsley Oden; George Biros; Thomas E Yankeelov; Kit Curtius; Ibrahim Al Bakir; Dominik Wodarz; Natalia Komarova; Luis Aparicio; Mykola Bordyuh; Raul Rabadan; Stacey D Finley; Heiko Enderling; Jimmy Caudell; Eduardo G Moros; Alexander R A Anderson; Robert A Gatenby; Artem Kaznatcheev; Peter Jeavons; Nikhil Krishnan; Julia Pelesko; Raoul R Wadhwa; Nara Yoon; Daniel Nichol; Andriy Marusyk; Michael Hinczewski; Jacob G Scott
Journal:  Phys Biol       Date:  2019-06-19       Impact factor: 2.959

5.  Topological gene expression networks recapitulate brain anatomy and function.

Authors:  Alice Patania; Pierluigi Selvaggi; Mattia Veronese; Ottavia Dipasquale; Paul Expert; Giovanni Petri
Journal:  Netw Neurosci       Date:  2019-07-01

6.  An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis.

Authors:  Ko Abe; Shimpei I Kubota; Noriaki Fukatsu; Kei Takahashi; Yasuyuki Morishita; Yasuhiro Yoshimatsu; Satoshi Hirakawa; Yoshiaki Kubota; Tetsuro Watabe; Shogo Ehata; Hiroki R Ueda; Teppei Shimamura; Kohei Miyazono
Journal:  Nat Commun       Date:  2022-09-12       Impact factor: 17.694

7.  Identification of relevant genetic alterations in cancer using topological data analysis.

Authors:  Raúl Rabadán; Yamina Mohamedi; Udi Rubin; Tim Chu; Adam N Alghalith; Oliver Elliott; Luis Arnés; Santiago Cal; Álvaro J Obaya; Arnold J Levine; Pablo G Cámara
Journal:  Nat Commun       Date:  2020-07-30       Impact factor: 14.919

8.  Classification of apatite structures via topological data analysis: a framework for a 'Materials Barcode' representation of structure maps.

Authors:  Scott Broderick; Ruhil Dongol; Tianmu Zhang; Krishna Rajan
Journal:  Sci Rep       Date:  2021-06-02       Impact factor: 4.379
  8 in total

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