D
David Koslicki
Researcher at Pennsylvania State University
Publications - 74
Citations - 1784
David Koslicki is an academic researcher from Pennsylvania State University. The author has contributed to research in topics: Computer science & Metagenomics. The author has an hindex of 14, co-authored 60 publications receiving 1186 citations. Previous affiliations of David Koslicki include Royal Institute of Technology & Drexel University.
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Journal ArticleDOI
Critical Assessment of Metagenome Interpretation - A benchmark of metagenomics software
Alexander Sczyrba,Peter Hofmann,Peter Hofmann,Peter Belmann,David Koslicki,Stefan Janssen,Johannes Dröge,Johannes Dröge,Ivan Gregor,Ivan Gregor,Stephan Majda,Jessika Fiedler,Eik Dahms,Eik Dahms,Andreas Bremges,Adrian Fritz,Ruben Garrido-Oter,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Tue Sparholt Jørgensen,Nicole Shapiro,Philip D. Blood,Alexey Gurevich,Yang Bai,Dmitrij Turaev,Matthew Z. DeMaere,Rayan Chikhi,Niranjan Nagarajan,Christopher Quince,Fernando Meyer,Monika Balvočiūtė,Lars Hestbjerg Hansen,Søren J. Sørensen,Burton Kuan Hui Chia,Bertrand Denis,Jeff Froula,Zhong Wang,Robert Egan,Dongwan Don Kang,Jeffrey J. Cook,Charles Deltel,Michael Beckstette,Claire Lemaitre,Pierre Peterlongo,Guillaume Rizk,Dominique Lavenier,Yu Wei Wu,Yu Wei Wu,Steven W. Singer,Steven W. Singer,Chirag Jain,Marc Strous,Heiner Klingenberg,Peter Meinicke,Michael D. Barton,Thomas Lingner,Hsin-Hung Lin,Yu-Chieh Liao,Genivaldo G. Z. Silva,Daniel A. Cuevas,Robert Edwards,Surya Saha,Vitor C. Piro,Vitor C. Piro,Bernhard Y. Renard,Mihai Pop,Hans-Peter Klenk,Markus Göker,Nikos C. Kyrpides,Tanja Woyke,Julia A. Vorholt,Paul Schulze-Lefert,Edward M. Rubin,Aaron E. Darling,Thomas Rattei,Alice C. McHardy +75 more
TL;DR: The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on highly complex and realistic data sets, generated from ∼700 newly sequenced microorganisms and ∼600 novel viruses and plasmids and representing common experimental setups as discussed by the authors.
Journal ArticleDOI
Sparse Recovery by Means of Nonnegative Least Squares
Simon Foucart,David Koslicki +1 more
TL;DR: It is demonstrated that sparse recovery can be achieved by an L1-minimization ersatz easily implemented using a conventional nonnegative least squares algorithm.
Journal ArticleDOI
Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia
Loes M. Olde Loohuis,Serghei Mangul,Anil P.S. Ori,Guillaume Jospin,David Koslicki,Harry Taegyun Yang,Timothy Wu,Marco P. Boks,Catherine Lomen-Hoerth,Martina Wiedau-Pazos,Rita M. Cantor,Willem M. de Vos,Willem M. de Vos,René S. Kahn,René S. Kahn,Eleazar Eskin,Roel A. Ophoff,Roel A. Ophoff,Roel A. Ophoff +18 more
TL;DR: Interestingly, there is an increased microbial diversity in schizophrenia patients compared to the three other groups, supporting a link between microbial products found in blood, immunity and schizophrenia.
Journal ArticleDOI
MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation.
David Koslicki,Daniel Falush +1 more
TL;DR: The algorithm MetaPalette is presented, which uses long k-mer sizes to fit a k-Mer “palette” of a given sample to the k-MER palette of reference organisms, and returns a traditional, fixed-rank taxonomic profile which is shown on independently simulated data to be one of the most accurate to date.
Journal ArticleDOI
Striped UniFrac: enabling microbiome analysis at unprecedented scale
Daniel McDonald,Yoshiki Vázquez-Baeza,David Koslicki,Jason McClelland,Nicolai Reeve,Zhenjiang Xu,Antonio Gonzalez,Rob Knight +7 more
TL;DR: Joshua T. Vogelstein1*, Eric Perlman1, Benjamin Falk1, Alex Baden1, William Gray Roncal2, Vikram Chandrashekhar1, Forrest Collman3, Sharmishtaa Seshamani3, Jesse L. Patsolic1, Kunal Lillaney1, Michael Kazhdan1, Robert Hider Jr.