B
Bud Mishra
Researcher at New York University
Publications - 225
Citations - 4424
Bud Mishra is an academic researcher from New York University. The author has contributed to research in topics: Temporal logic & Model checking. The author has an hindex of 32, co-authored 222 publications receiving 4079 citations. Previous affiliations of Bud Mishra include University of Wisconsin-Madison & Watson School of Biological Sciences.
Papers
More filters
Journal ArticleDOI
Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules
Junping Jing,Jason Reed,John Huang,John Huang,Xinghua Hu,Virginia Clarke,Joanne Edington,Dan Housman,Thomas Anantharaman,Edward J. Huff,Bud Mishra,Brett Porter,Alexander Shenker,Estarose Wolfson,Catharina Hiort,Ron Kantor,Christopher Aston,David C. Schwartz +17 more
TL;DR: The aggregate significance of this work is the development of an integrated system for mapping small insert clones allowing biochemical data obtained from engineered ensembles of individual molecules to be automatically accumulated and analyzed for map construction.
Journal ArticleDOI
Whole-genome shotgun optical mapping of Deinococcus radiodurans.
Jieyi Lin,Rong Qi,Christopher Aston,Junping Jing,Thomas Anantharaman,Bud Mishra,Owen White,Michael J. Daly,Kenneth W. Minton,J. Craig Venter,David C. Schwartz,David C. Schwartz +11 more
TL;DR: A whole-genome restriction map of Deinococcus radiodurans, a radiation-resistant bacterium able to survive up to 15,000 grays of ionizing radiation, was constructed without using DNA libraries, the polymerase chain reaction, or electrophoresis.
Journal ArticleDOI
Comparing de novo genome assembly: the long and short of it.
TL;DR: This paper highlights common anomalies in assembly accuracy through a rigorous study of several assemblers, compared under both standard metrics as well as a more comprehensive metric (Feature-Response Curves, FRC) that is introduced here; FRC transparently captures the trade-offs between contigs' quality against their sizes.
Journal ArticleDOI
Model building and model checking for biochemical processes.
TL;DR: A novel computational tool is described that achieves many of the goals of this new discipline of computational systems biology and involves an automaton-based semantics of the temporal evolution of complex biochemical reactions starting from the representation given as a set of differential equations.
Journal ArticleDOI
Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs.
Kevin Hadi,Xiaotong Yao,Julie M. Behr,Aditya Deshpande,Charalampos Xanthopoulakis,Huasong Tian,Sarah Kudman,Joel Rosiene,Madison Darmofal,Joseph DeRose,Rick Mortensen,Emily M. Adney,Alon Shaiber,Zoran Gajic,Michael Sigouros,Kenneth Eng,Jeremiah Wala,Jeremiah Wala,Jeremiah Wala,Kazimierz O. Wrzeszczynski,Kanika Arora,Minita Shah,Anne-Katrin Emde,Vanessa Felice,Mayu O. Frank,Robert B. Darnell,Mahmoud Ghandi,Franklin W. Huang,Franklin W. Huang,Sally M. Dewhurst,John Maciejowski,Titia de Lange,Jeremy Setton,Nadeem Riaz,Jorge S. Reis-Filho,Simon N. Powell,David A. Knowles,Ed Reznik,Bud Mishra,Rameen Beroukhim,Rameen Beroukhim,Michael C. Zody,Nicolas Robine,Kenji Oman,Carissa A. Sanchez,Mary K. Kuhner,Lucian P. Smith,Patricia C. Galipeau,Thomas G. Paulson,Brian J. Reid,Brian J. Reid,Xiaohong Li,David Wilkes,Andrea Sboner,Juan Miguel Mosquera,Olivier Elemento,Marcin Imielinski +56 more
TL;DR: Clustering of tumors according to genome graph-derived features identified subgroups associated with DNA repair defects and poor prognosis and uncovered three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas.