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Tanja Magoc
Researcher at Johns Hopkins University School of Medicine
Publications - 16
Citations - 11368
Tanja Magoc is an academic researcher from Johns Hopkins University School of Medicine. The author has contributed to research in topics: Computer science & Medicine. The author has an hindex of 7, co-authored 7 publications receiving 8056 citations. Previous affiliations of Tanja Magoc include Johns Hopkins University.
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Journal ArticleDOI
FLASH: Fast Length Adjustment of Short Reads to Improve Genome Assemblies
Tanja Magoc,Steven L. Salzberg +1 more
TL;DR: FLASH is a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short and when FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds.
Journal ArticleDOI
GAGE: A critical evaluation of genome assemblies and assembly algorithms
Steven L. Salzberg,Adam M. Phillippy,Aleksey V. Zimin,Daniela Puiu,Tanja Magoc,Sergey Koren,Sergey Koren,Todd J. Treangen,Michael C. Schatz,Arthur L. Delcher,Michael Roberts,Guillaume Marçais,Mihai Pop,James A. Yorke +13 more
TL;DR: Evaluating several of the leading de novo assembly algorithms on four different short-read data sets generated by Illumina sequencers concludes that data quality, rather than the assembler itself, has a dramatic effect on the quality of an assembled genome.
Journal ArticleDOI
Genomic signatures of evolutionary transitions from solitary to group living
Karen M. Kapheim,Karen M. Kapheim,Hailin Pan,Cai Li,Steven L. Salzberg,Steven L. Salzberg,Daniela Puiu,Tanja Magoc,Hugh M. Robertson,Matthew E. Hudson,Aarti Venkat,Aarti Venkat,Brielle J. Fischman,Brielle J. Fischman,Alvaro G. Hernandez,Mark Yandell,Daniel D. Ence,Carson Holt,George D. Yocum,William P. Kemp,Jordi Bosch,Robert M. Waterhouse,Evgeny M. Zdobnov,Evgeny M. Zdobnov,Eckart Stolle,Eckart Stolle,F. Bernhard Kraus,Sophie Helbing,Robin F. A. Moritz,Karl M. Glastad,Brendan G. Hunt,Michael A. D. Goodisman,Frank Hauser,Cornelis J. P. Grimmelikhuijzen,Daniel Guariz Pinheiro,Daniel Guariz Pinheiro,Francis M. F. Nunes,Michelle P.M. Soares,E. D. Tanaka,Zilá Luz Paulino Simões,Klaus Hartfelder,Jay D. Evans,Seth M. Barribeau,Reed M. Johnson,Jonathan Massey,Jonathan Massey,Bruce R. Southey,Martin Hasselmann,Daniel Hamacher,Matthias Biewer,Clement F. Kent,Clement F. Kent,Amro Zayed,Charles Blatti,Saurabh Sinha,J. Spencer Johnston,Shawn J. Hanrahan,Sarah D. Kocher,Jun Wang,Gene E. Robinson,Guojie Zhang +60 more
TL;DR: There is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings and these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements.
Journal ArticleDOI
GAGE-B: an evaluation of genome assemblers for bacterial organisms
Tanja Magoc,Stephan Pabinger,Stefan Canzar,Xinyue Liu,Qi Su,Daniela Puiu,Luke J. Tallon,Steven L. Salzberg +7 more
TL;DR: In this article, the authors evaluated the ability of multiple genome assembly programs to assemble bacterial genomes from a single, deep-coverage library and compared the assembly produced by this very high coverage, one-library strategy to the best assemblies created by two-library sequencing, and found that remarkably good bacterial assemblies are possible with just one library.
Journal ArticleDOI
EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes.
TL;DR: EDGE-pro (Estimated Degree of Gene Expression in PROkaryotes) processes the raw data from an RNA-seq experiment on a bacterial or archaeal species and produces estimates of the expression levels for each gene in these gene-dense genomes.