The real cost of sequencing: scaling computation to keep pace with data generation.
Paul Muir,Shantao Li,Shaoke Lou,Daifeng Wang,Daniel Spakowicz,Leonidas Salichos,Jing Zhang,George M. Weinstock,Farren J. Isaacs,Joel Rozowsky,Mark Gerstein +10 more
TLDR
As the cost of sequencing continues to decrease and the amount of sequence data generated grows, new paradigms for data storage and analysis are increasingly important.Abstract:
As the cost of sequencing continues to decrease and the amount of sequence data generated grows, new paradigms for data storage and analysis are increasingly important. The relative scaling behavior of these evolving technologies will impact genomics research moving forward.read more
Citations
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Opportunities and obstacles for deep learning in biology and medicine.
Travers Ching,Daniel Himmelstein,Brett K. Beaulieu-Jones,Alexandr A. Kalinin,Brian T. Do,Gregory P. Way,Enrico Ferrero,Paul-Michael Agapow,Michael Zietz,Michael M. Hoffman,Michael M. Hoffman,Wei Xie,Gail L. Rosen,Benjamin J. Lengerich,Johnny Israeli,Jack Lanchantin,Stephen Woloszynek,Anne E. Carpenter,Avanti Shrikumar,Jinbo Xu,Evan M. Cofer,Evan M. Cofer,Christopher A. Lavender,Srinivas C. Turaga,Amr Alexandari,Zhiyong Lu,David J. Harris,Dave DeCaprio,Yanjun Qi,Anshul Kundaje,Yifan Peng,Laura K. Wiley,Marwin H. S. Segler,Simina M. Boca,S. Joshua Swamidass,Austin Huang,Anthony Gitter,Anthony Gitter,Casey S. Greene +38 more
TL;DR: It is found that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art.
Journal ArticleDOI
Benefits and limitations of genome-wide association studies.
Vivian W.Y. Tam,Nikunj Patel,Michelle Turcotte,Yohan Bossé,Guillaume Paré,David Meyre,David Meyre +6 more
TL;DR: This Review comprehensively assess the benefits and limitations of GWAS in human populations and discusses the relevance of performing more GWAS, with a focus on the cardiometabolic field.
Journal ArticleDOI
MAFFT-DASH: integrated protein sequence and structural alignment.
TL;DR: MAFFT-DASH showed 10–20% improvement over standard MAFFT for MSA problems with weak similarity, in terms of Sum-of-Pairs (SP), a measure of how well a program succeeds at aligning input sequences in comparison to a reference alignment.
Journal ArticleDOI
A novel community driven software for functional enrichment analysis of extracellular vesicles data
Mohashin Pathan,Shivakumar Keerthikumar,David Chisanga,Riccardo Alessandro,Ching-Seng Ang,Philip W. Askenase,Arsen O. Batagov,Alberto Benito-Martin,Giovanni Camussi,Aled Clayton,Federica Collino,Dolores Di Vizio,Juan M. Falcón-Pérez,Pedro Fonseca,Pamali Fonseka,Simona Fontana,Yong Song Gho,An Hendrix,Esther N. M. Nolte-‘t Hoen,Nunzio Iraci,Kenneth Kastaniegaard,Thomas Kislinger,Joanna Kowal,Igor V. Kurochkin,Tommaso Leonardi,Yaxuan Liang,Alicia Llorente,Taral R. Lunavat,Sayantan Maji,Francesca Monteleone,Anders Øverbye,Theocharis Panaretakis,Tushar Patel,Héctor Peinado,Stefano Pluchino,Simona Principe,Göran Ronquist,Felix Royo,Susmita Sahoo,Cristiana Spinelli,Allan Stensballe,Clotilde Théry,Martijn J. C. van Herwijnen,Marca H. M. Wauben,Joanne L. Welton,Kening Zhao,Suresh Mathivanan +46 more
TL;DR: A novel community-driven approach to build a comprehensive functional enrichment analysis tool using the existing FunRich tool as a template and inviting researchers to request additional features and/or changes was able to implement 90% of the requested features.
Journal ArticleDOI
Recent Advances in SELEX Technology and Aptamer Applications in Biomedicine
Zhenjian Zhuo,Yuanyuan Yu,Maolin Wang,Jie Li,Zong-Kang Zhang,Jin Liu,Xiaohao Wu,Aiping Lu,Ge Zhang,Bao-Ting Zhang +9 more
TL;DR: The limitations and notable advances of aptamer selection are presented, and the different methods used in the kinetic characterization of aptamers are compared, to comprehensively review the current shortage and achievement ofaptamer-related technology.
References
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Basic Local Alignment Search Tool
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Alexander Dobin,Carrie A. Davis,Felix Schlesinger,Jorg Drenkow,Chris Zaleski,Sonali Jha,Philippe Batut,Mark Chaisson,Thomas R. Gingeras +8 more
TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
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