D
Daniel P. Depledge
Researcher at New York University
Publications - 81
Citations - 4676
Daniel P. Depledge is an academic researcher from New York University. The author has contributed to research in topics: Varicella zoster virus & Virus. The author has an hindex of 25, co-authored 72 publications receiving 3695 citations. Previous affiliations of Daniel P. Depledge include University of York & University College London.
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Journal ArticleDOI
TriTrypDB: a functional genomic resource for the Trypanosomatidae
Martin Aslett,Cristina Aurrecoechea,Matthew Berriman,John Brestelli,Brian P. Brunk,Mark Carrington,Daniel P. Depledge,Steve Fischer,Bindu Gajria,Xin Gao,Malcolm J. Gardner,Alan R. Gingle,Gregory R. Grant,Omar S. Harb,Mark Heiges,Christiane Hertz-Fowler,Robin Houston,Frank Innamorato,John Iodice,Jessica C. Kissinger,Eileen Kraemer,Wei Li,Flora J. Logan,John A. Miller,Siddhartha Mitra,Peter J. Myler,Vishal Nayak,Cary Pennington,Isabelle Phan,Deborah F. Pinney,Gowthaman Ramasamy,Matthew B. Rogers,David S. Roos,Christopher A. Ross,Dhileep Sivam,Deborah F. Smith,Ganesh Srinivasamoorthy,Christian J. Stoeckert,Sandhya Subramanian,Ryan Thibodeau,Adrian Tivey,Charles Treatman,Giles S. Velarde,Haiming Wang +43 more
TL;DR: TriTrypDB is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs, utilizing a sophisticated search strategy system.
Journal ArticleDOI
Comparative genomic analysis of three Leishmania species that cause diverse human disease
Christopher S. Peacock,Kathy Seeger,David Harris,Lee Murphy,Jeronimo C. Ruiz,Michael A. Quail,Nicholas S. Peters,Ellen Adlem,Adrian Tivey,Martin Aslett,Arnaud Kerhornou,Alasdair Ivens,Audrey Fraser,Marie-Adèle Rajandream,Tim Carver,Halina Norbertczak,Tracey Chillingworth,Zahra Hance,Kay Jagels,Sharon Moule,Doug Ormond,Simon Rutter,Rob Squares,Sally Whitehead,Ester Rabbinowitsch,Claire Arrowsmith,Brian White,Scott Thurston,Frédéric Bringaud,Sandra L. Baldauf,Adam Faulconbridge,Daniel C. Jeffares,Daniel P. Depledge,Samuel O. Oyola,James D. Hilley,Loislene O. Brito,Luiz R. O. Tosi,Barclay G. Barrell,Angela K. Cruz,Jeremy C. Mottram,Deborah F. Smith,Matthew Berriman +41 more
TL;DR: It is shown that pseudogene formation and gene loss are the principal forces shaping the different genomes of Leishmania, and genes that are differentially distributed between the species encode proteins implicated in host-pathogen interactions and parasite survival in the macrophage.
Journal ArticleDOI
Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
Matthew B. Rogers,James D. Hilley,Nicholas J. Dickens,Jon Wilkes,Paul A. Bates,Daniel P. Depledge,David A. Harris,Yerim Her,Pawel Herzyk,Hideo Imamura,Thomas D. Otto,Mandy Sanders,Kathy Seeger,Jean-Claude Dujardin,Matthew Berriman,Deborah F. Smith,Christiane Hertz-Fowler,Jeremy C. Mottram +17 more
TL;DR: It is demonstrated that there is little variation in unique gene content across Leishmania species, but large-scale genetic heterogeneity can result through gene amplification on disomic chromosomes and variation in chromosome number.
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Rapid Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates Directly from Clinical Samples
Amanda C. Brown,Josephine M. Bryant,Katja Einer-Jensen,Jolyon Holdstock,Darren T. Houniet,Jacqueline Z.-M. Chan,Daniel P. Depledge,Vladyslav Nikolayevskyy,Agnieszka Broda,Madeline J. Stone,Mette T. Christiansen,Rachel Williams,Michael B. McAndrew,Helena J. Tutill,Julianne R Brown,Mark Melzer,Caryn Rosmarin,Timothy D. McHugh,R.J. Shorten,Francis Drobniewski,Graham Speight,Judith Breuer +21 more
TL;DR: This study demonstrated for the first time the successful and accurate sequencing of M. tuberculosis genomes directly from uncultured sputa, allowing whole-genome sequencing without the requirement of culture.
Journal ArticleDOI
Specific Capture and Whole-Genome Sequencing of Viruses from Clinical Samples
Daniel P. Depledge,Anne L. Palser,Simon J. Watson,Imogen Yi-Chun Lai,Imogen Yi-Chun Lai,Eleanor R. Gray,Paul R. Grant,Ravinder K. Kanda,Emily M LeProust,Paul Kellam,Paul Kellam,Judith Breuer +11 more
TL;DR: The use of sample sparing target enrichment (by hybridisation) for viral nucleic acid separation and deep-sequencing of herpesvirus genomes directly from a range of clinical samples including saliva, blood, virus vesicles, cerebrospinal fluid, and tumour cell lines are reported.