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Adam M. Novak
Researcher at University of California, Santa Cruz
Publications - 56
Citations - 3548
Adam M. Novak is an academic researcher from University of California, Santa Cruz. The author has contributed to research in topics: Genome & Reference genome. The author has an hindex of 21, co-authored 51 publications receiving 2166 citations. Previous affiliations of Adam M. Novak include University of Oxford & Harvey Mudd College.
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Journal ArticleDOI
Toil enables reproducible, open source, big biomedical data analyses
John Vivian,Arjun A. Rao,Frank Austin Nothaft,Christopher Ketchum,Joel Armstrong,Adam M. Novak,Jacob Pfeil,Jake Narkizian,Alden Deran,Audrey Musselman-Brown,Hannes Schmidt,Peter Amstutz,Brian Craft,Mary Goldman,Kate R. Rosenbloom,Melissa S. Cline,Brian O'Connor,Megan Hanna,Chet Birger,W. James Kent,David A. Patterson,Anthony D. Joseph,Jingchun Zhu,Sasha Zaranek,Gad Getz,David Haussler,Benedict Paten +26 more
TL;DR: It is envisage that in future individual research laboratories, or clusters of colocated laboratories, will have in-house, low-cost automation work cells but will access DNA foundries via the cloud to carry out complex experimental workflows and accelerate the development and sharing of standardized protocols and metrology standards.
Journal ArticleDOI
Variation graph toolkit improves read mapping by representing genetic variation in the reference.
Erik Garrison,Jouni Sirén,Adam M. Novak,Glenn Hickey,Jordan M. Eizenga,Eric T. Dawson,Eric T. Dawson,William J. Jones,Shilpa Garg,Charles Markello,Michael F. Lin,Benedict Paten,Richard Durbin,Richard Durbin +13 more
TL;DR: Vg as discussed by the authors is a toolkit of computational methods for creating, manipulating, and using these structures as references at the scale of the human genome, which provides an efficient approach to mapping reads onto arbitrary variation graphs using generalized compressed suffix arrays, with improved accuracy over alignment to a linear reference.
Journal ArticleDOI
Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis
Ian T. Fiddes,Gerrald A Lodewijk,Meghan Mooring,Colleen M. Bosworth,Adam D. Ewing,Gary L. Mantalas,Adam M. Novak,Anouk van den Bout,Alex Bishara,Jimi L. Rosenkrantz,Jimi L. Rosenkrantz,Ryan Lorig-Roach,Andrew R. Field,Maximilian Haeussler,Lotte Russo,Aparna Bhaduri,Tomasz J. Nowakowski,Alex A. Pollen,Max L. Dougherty,Xander Nuttle,Xander Nuttle,Marie-Claude Addor,Simon Zwolinski,Sol Katzman,Arnold R. Kriegstein,Evan E. Eichler,Sofie R. Salama,Sofie R. Salama,Frank M. J. Jacobs,Frank M. J. Jacobs,David Haussler,David Haussler +31 more
TL;DR: The emergence of human-specific NOTCH2NL genes may have contributed to the rapid evolution of the larger human neocortex, accompanied by loss of genomic stability at the 1q21.1 locus and resulting recurrent neurodevelopmental disorders.
Journal ArticleDOI
Genome graphs and the evolution of genome inference
TL;DR: This work surveys various projects underway to build and apply graph-based structures-which it is referred to as genome graphs-and discusses the improvements in read mapping, variant calling, and haplotype determination that genome graphs are expected to produce.
Journal ArticleDOI
Computational pan-genomics: status, promises and challenges.
Tobias Marschall,Manja Marz,Manja Marz,Thomas Abeel,Louis Dijkstra,Bas E. Dutilh,Ali Ghaffaari,Ali Ghaffaari,Paul Kersey,Wigard P. Kloosterman,Veli Mäkinen,Adam M. Novak,Benedict Paten,David Porubsky,Eric Rivals,Can Alkan,Jasmijn A. Baaijens,Paul I.W. de Bakker,Valentina Boeva,Raoul J. P. Bonnal,Francesca Chiaromonte,Rayan Chikhi,Francesca D. Ciccarelli,Robin Cijvat,Erwin Datema,Cornelia M. van Duijn,Evan E. Eichler,Evan E. Eichler,Corinna Ernst,Eleazar Eskin,Erik Garrison,Mohammed El-Kebir,Gunnar W. Klau,Jan O. Korbel,Eric-Wubbo Lameijer,Benjamin Langmead,Marcel Martin,Paul Medvedev,John C. Mu,Pieter B. Neerincx,Klaasjan G. Ouwens,Pierre Peterlongo,Nadia Pisanti,Sven Rahmann,Ben Raphael,Knut Reinert,Dick de Ridder,Jeroen de Ridder,Matthias Schlesner,Ole Schulz-Trieglaff,Ashley D. Sanders,Siavash Sheikhizadeh,Carl Shneider,Sandra Smit,Daniel Valenzuela,Jiayin Wang,Lodewyk F. A. Wessels,Y. Zhang,Victor Guryev,Fabio Vandin,Kai Ye,Alexander Schönhuth +61 more
TL;DR: Already available approaches to construct and use pan-genomes are examined, the potential benefits of future technologies and methodologies are discussed, and open challenges from the vantage point of the above-mentioned biological disciplines are reviewed.