Literature DB >> 28966343

Computational Biology in the 21st Century: Scaling with Compressive Algorithms.

Bonnie Berger1, Noah M Daniels2, Y William Yu2.   

Abstract

Entities:  

Year:  2016        PMID： 28966343      PMCID： PMC5615407          DOI： 10.1145/2957324

Source DB:  PubMed          Journal:  Commun ACM        ISSN： 0001-0782            Impact factor:   4.654


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  33 in total

Review 1.  16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls.

Authors:  J Michael Janda; Sharon L Abbott
Journal:  J Clin Microbiol       Date:  2007-07-11       Impact factor: 5.948

2.  Compressive mapping for next-generation sequencing.

Authors:  Deniz Yorukoglu; Yun William Yu; Jian Peng; Bonnie Berger
Journal:  Nat Biotechnol       Date:  2016-04       Impact factor: 54.908

3.  Recovering key biological constituents through sparse representation of gene expression.

Authors:  Yosef Prat; Menachem Fromer; Nathan Linial; Michal Linial
Journal:  Bioinformatics       Date:  2011-01-21       Impact factor: 6.937

4.  Entropy-scaling search of massive biological data.

Authors:  Y William Yu; Noah M Daniels; David Christian Danko; Bonnie Berger
Journal:  Cell Syst       Date:  2015-08-26       Impact factor: 10.304

5.  Small Molecule Subgraph Detector (SMSD) toolkit.

Authors:  Syed Asad Rahman; Matthew Bashton; Gemma L Holliday; Rainer Schrader; Janet M Thornton
Journal:  J Cheminform       Date:  2009-08-10       Impact factor: 5.514

6.  Cloud computing and the DNA data race.

Authors:  Michael C Schatz; Ben Langmead; Steven L Salzberg
Journal:  Nat Biotechnol       Date:  2010-07       Impact factor: 54.908

7.  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

8.  Fast and accurate read mapping with approximate seeds and multiple backtracking.

Authors:  Enrico Siragusa; David Weese; Knut Reinert
Journal:  Nucleic Acids Res       Date:  2013-01-28       Impact factor: 16.971

9.  Compressive genomics for protein databases.

Authors:  Noah M Daniels; Andrew Gallant; Jian Peng; Lenore J Cowen; Michael Baym; Bonnie Berger
Journal:  Bioinformatics       Date:  2013-07-01       Impact factor: 6.937

10.  Going the distance for protein function prediction: a new distance metric for protein interaction networks.

Authors:  Mengfei Cao; Hao Zhang; Jisoo Park; Noah M Daniels; Mark E Crovella; Lenore J Cowen; Benjamin Hescott
Journal:  PLoS One       Date:  2013-10-23       Impact factor: 3.240
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  5 in total

1.  To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics.

Authors:  R A Leo Elworth; Qi Wang; Pavan K Kota; C J Barberan; Benjamin Coleman; Advait Balaji; Gaurav Gupta; Richard G Baraniuk; Anshumali Shrivastava; Todd J Treangen
Journal:  Nucleic Acids Res       Date:  2020-06-04       Impact factor: 16.971

2.  XSI - A genotype compression tool for compressive genomics in large biobanks.

Authors:  Rick Wertenbroek; Simone Rubinacci; Ioannis Xenarios; Yann Thoma; Olivier Delaneau
Journal:  Bioinformatics       Date:  2022-06-24       Impact factor: 6.931

3.  Theory of local k-mer selection with applications to long-read alignment.

Authors:  Jim Shaw; Yun William Yu
Journal:  Bioinformatics       Date:  2022-10-14       Impact factor: 6.931

4.  Levenshtein Distance, Sequence Comparison and Biological Database Search.

Authors:  Bonnie Berger; Michael S Waterman; Yun William Yu
Journal:  IEEE Trans Inf Theory       Date:  2020-05-21       Impact factor: 2.501

5.  Reflections on a journey: a retrospective of the ISCB Student Council symposium series.

Authors:  Mehedi Hassan; Aishwarya Alex Namasivayam; Dan DeBlasio; Nazeefa Fatima; Benjamin Siranosian; R Gonzalo Parra; Bart Cuypers; Sayane Shome; Alexander Miguel Monzon; Julien Fumey; Farzana Rahman
Journal:  BMC Bioinformatics       Date:  2018-10-09       Impact factor: 3.169
  5 in total

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