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Daniela Puiu
Researcher at Johns Hopkins University
Publications - 75
Citations - 10939
Daniela Puiu is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Genome & Sequence assembly. The author has an hindex of 38, co-authored 68 publications receiving 9207 citations. Previous affiliations of Daniela Puiu include Johns Hopkins University School of Medicine & Virginia Commonwealth University.
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Journal ArticleDOI
A whole-genome assembly of the domestic cow, Bos taurus
Aleksey V. Zimin,Arthur L. Delcher,Liliana Florea,David R. Kelley,Michael C. Schatz,Daniela Puiu,Finnian Hanrahan,Geo Pertea,Curtis P. Van Tassell,Tad S. Sonstegard,Guillaume Marçais,Michael Roberts,Poorani Subramanian,James A. Yorke,Steven L. Salzberg +14 more
TL;DR: By using independent mapping data and conserved synteny between the cow and human genomes, this work was able to construct an assembly with excellent large-scale contiguity in which a large majority (approximately 91%) of the genome has been placed onto the 30 B. taurus chromosomes.
Journal ArticleDOI
The MaSuRCA genome assembler
Aleksey V. Zimin,Guillaume Marçais,Daniela Puiu,Michael Roberts,Steven L. Salzberg,James A. Yorke +5 more
TL;DR: A new hybrid approach that has the computational efficiency of de Bruijn graph methods and the flexibility of overlap-based assembly strategies, and which allows variable read lengths while tolerating a significant level of sequencing error is described.
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
The genome of Cryptosporidium hominis
Ping Xu,Giovanni Widmer,Yingping Wang,Luiz S. Ozaki,João M. P. Alves,Myrna G. Serrano,Daniela Puiu,Patricio Manque,Donna E. Akiyoshi,Aaron J. Mackey,Aaron J. Mackey,William R. Pearson,Paul H. Dear,Alan T. Bankier,Darrell L. Peterson,Mitchell S. Abrahamsen,Vivek Kapur,Saul Tzipori,Gregory A. Buck +18 more
TL;DR: The eight-chromosome ∼9.2-million-base genome of C. hominis shows a striking concordance with the requirements imposed by the environmental niches the parasite inhabits, and phenotypic differences between these parasites must be due to subtle sequence divergence.
Journal ArticleDOI
Draft genome sequence of the oilseed species Ricinus communis
Agnes P. Chan,Jonathan Crabtree,Qi Zhao,Hernan Lorenzi,Joshua Orvis,Daniela Puiu,Admasu Melake-Berhan,Kristine M Jones,Julia C. Redman,Grace Q. Chen,Edgar B. Cahoon,Melaku Gedil,Mario Stanke,Brian J. Haas,Jennifer R. Wortman,Claire M. Fraser-Liggett,Jacques Ravel,Pablo D. Rabinowicz,Pablo D. Rabinowicz +18 more
TL;DR: Comparative genomics analysis suggests the presence of an ancient hexaploidization event that is conserved across the dicotyledonous lineage and the number of members of the ricin gene family is larger than previously thought.