A
Angel Pizarro
Researcher at University of Pennsylvania
Publications - 41
Citations - 3275
Angel Pizarro is an academic researcher from University of Pennsylvania. The author has contributed to research in topics: Proteomics Standards Initiative & Mass spectrometry data format. The author has an hindex of 21, co-authored 39 publications receiving 2997 citations. Previous affiliations of Angel Pizarro include Amazon.com & Genomics Institute of the Novartis Research Foundation.
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Journal ArticleDOI
mzML - a Community Standard for Mass Spectrometry Data
Lennart Martens,Matthew C. Chambers,Marc Sturm,Darren Kessner,Fredrik Levander,Jim Shofstahl,Wilfred H. Tang,Andreas Römpp,Steffen Neumann,Angel Pizarro,Luisa Montecchi-Palazzi,Natalie Tasman,Michael K. Coleman,Florian Reisinger,Puneet Souda,Henning Hermjakob,Pierre-Alain Binz,Eric W. Deutsch +17 more
TL;DR: The resulting standard data format, mzML, is a well tested open-source format formass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology.
Journal ArticleDOI
Design and implementation of microarray gene expression markup language (MAGE-ML)
Paul T. Spellman,Michael W. Miller,Jason E. Stewart,Charles Troup,Ugis Sarkans,Steve Chervitz,Derek Bernhart,Gavin Sherlock,Catherine A. Ball,Marc Lepage,Marcin Swiatek,WL Marks,Jason Goncalves,Scott Markel,Daniel Iordan,Mohammadreza Shojatalab,Angel Pizarro,Joseph White,Robert Hubley,Eric W. Deutsch,Martin Senger,Bruce J. Aronow,Alan J. Robinson,Doug Bassett,Christian J. Stoeckert,Alvis Brazma +25 more
TL;DR: MAGE will help microarray data producers and users to exchange information by providing a common platform for data exchange, and MAGE-STK will make the adoption of MAGE easier.
Journal ArticleDOI
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM)
Gregory R. Grant,Michael H. Farkas,Angel Pizarro,Nicholas F. Lahens,Jonathan Schug,Brian P. Brunk,Christian J. Stoeckert,John B. Hogenesch,Eric A. Pierce +8 more
TL;DR: An RNA-Seq simulator is developed that models the main impediments to RNA alignment, including alternative splicing, insertions, deletions, substitutions, sequencing errors and intron signal, and a pipeline based on BLAT is developed to explore the performance of established tools for this problem, and to compare it to the recently developed methods.
Journal ArticleDOI
CircaDB: a database of mammalian circadian gene expression profiles
TL;DR: A new database of circadian transcriptional profiles from time course expression experiments from mice and humans, where each transcript’s expression was evaluated by three separate algorithms, JTK_Cycle, Lomb Scargle and DeLichtenberg.
Journal ArticleDOI
The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results
Andrew R. Jones,Martin Eisenacher,Gerhard Mayer,Oliver Kohlbacher,Jennifer A. Siepen,Simon J. Hubbard,Julian N. Selley,Brian C. Searle,James Shofstahl,Sean L. Seymour,Randall K. Julian,Pierre-Alain Binz,Eric W. Deutsch,Henning Hermjakob,Florian Reisinger,Johannes Griss,Juan Antonio Vizcaíno,Matthew C. Chambers,Angel Pizarro,David M. Creasy +19 more
TL;DR: The release of mzIdentML enables proteomics scientists to start working with the standard for exchanging and publishing data sets in support of publications and they provide a stable platform for bioinformatics groups and commercial software vendors to work with a single file format for identification data.