Literature DB >> 31409480

Biophysics and the Genomic Sciences.

David C Schwartz1.   

Abstract

It is now rare to find biological, or genetic investigations that do not rely on the tools, data, and thinking drawn from the genomic sciences. Much of this revolution is powered by contemporary sequencing approaches that readily deliver large, genome-wide data sets that not only provide genetic insights but also uniquely report molecular outcomes from experiments that biophysicists are increasingly using for potentiating structural and mechanistic investigations. In this perspective, I describe a path of how biophysical thinking greatly contributed to this revolution in ways that parallel advancements in computer science through discussion of several key inventions, described as "foundational devices." These discussions also point at the future of how biophysics and the genomic sciences may become more finely integrated for empowering new measurement paradigms for biological investigations.
Copyright © 2019 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mesh:

Year:  2019        PMID: 31409480      PMCID: PMC6895736          DOI: 10.1016/j.bpj.2019.07.038

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  51 in total

1.  Interaction of the noncovalent molecular adapter, beta-cyclodextrin, with the staphylococcal alpha-hemolysin pore.

Authors:  L Q Gu; H Bayley
Journal:  Biophys J       Date:  2000-10       Impact factor: 4.033

2.  Structural variation analysis with strobe reads.

Authors:  Anna Ritz; Ali Bashir; Benjamin J Raphael
Journal:  Bioinformatics       Date:  2010-04-08       Impact factor: 6.937

3.  Monodisperse double emulsions generated from a microcapillary device.

Authors:  A S Utada; E Lorenceau; D R Link; P D Kaplan; H A Stone; D A Weitz
Journal:  Science       Date:  2005-04-22       Impact factor: 47.728

Review 4.  The challenges of sequencing by synthesis.

Authors:  Carl W Fuller; Lyle R Middendorf; Steven A Benner; George M Church; Timothy Harris; Xiaohua Huang; Stevan B Jovanovich; John R Nelson; Jeffery A Schloss; David C Schwartz; Dmitri V Vezenov
Journal:  Nat Biotechnol       Date:  2009-11-06       Impact factor: 54.908

5.  Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Authors:  Evan Z Macosko; Anindita Basu; Rahul Satija; James Nemesh; Karthik Shekhar; Melissa Goldman; Itay Tirosh; Allison R Bialas; Nolan Kamitaki; Emily M Martersteck; John J Trombetta; David A Weitz; Joshua R Sanes; Alex K Shalek; Aviv Regev; Steven A McCarroll
Journal:  Cell       Date:  2015-05-21       Impact factor: 41.582

6.  Reading the primary structure of a protein with 0.07 nm3 resolution using a subnanometre-diameter pore.

Authors:  Eamonn Kennedy; Zhuxin Dong; Clare Tennant; Gregory Timp
Journal:  Nat Nanotechnol       Date:  2016-07-25       Impact factor: 39.213

7.  Molecular propulsion: chemical sensing and chemotaxis of DNA driven by RNA polymerase.

Authors:  Hua Yu; Kyubong Jo; Kristy L Kounovsky; Juan J de Pablo; David C Schwartz
Journal:  J Am Chem Soc       Date:  2009-04-29       Impact factor: 15.419

8.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

Review 9.  A primer on deep learning in genomics.

Authors:  James Zou; Mikael Huss; Abubakar Abid; Pejman Mohammadi; Ali Torkamani; Amalio Telenti
Journal:  Nat Genet       Date:  2018-11-26       Impact factor: 38.330

10.  Single-molecule protein identification by sub-nanopore sensors.

Authors:  Mikhail Kolmogorov; Eamonn Kennedy; Zhuxin Dong; Gregory Timp; Pavel A Pevzner
Journal:  PLoS Comput Biol       Date:  2017-05-09       Impact factor: 4.475

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