Philip Hugenholtz

17 papers C 1Journal 15Unranked 1
YearRankTypeTitle / Venue / Authors
2022 J jnl
GTDB-Tk v2: memory friendly classification with the genome taxonomy database.
Bioinform.
Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks
2022 J jnl
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy.
Nucleic Acids Res.
Donovan H. Parks, Maria Chuvochina, Christian Rinke, Aaron J. Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz
2020 J jnl
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.
Bioinform.
Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks
2014 J jnl
STAMP: statistical analysis of taxonomic and functional profiles.
Bioinform.
Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz, Robert G. Beiko
2013 J jnl
Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data.
PLoS Comput. Biol.
Lauren M. Bragg, Glenn Stone, Margaret K. Butler, Philip Hugenholtz, Gene W. Tyson
2010 J jnl
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.
Nucleic Acids Res.
Konstantinos Liolios, I-Min A. Chen, Konstantinos Mavrommatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M. Markowitz, Nikos Kyrpides
2009 J jnl
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes.
Bioinform.
Erik Kristiansson, Philip Hugenholtz, Daniel Dalevi
2008 C conf
Annotation of metagenome short reads using proxygenes.
ECCB
Daniel Dalevi, Natalia Ivanova, Konstantinos Mavrommatis, Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos Kyrpides, Victor M. Markowitz
2008 J jnl
IMG/M: a data management and analysis system for metagenomes.
Nucleic Acids Res.
Victor M. Markowitz, Natalia Ivanova, Ernest Szeto, Krishna Palaniappan, Ken Chu, Daniel Dalevi, I-Min A. Chen, Yuri Grechkin, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Philip Hugenholtz, Nikos Kyrpides
2007 J jnl
Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool.
BMC Bioinform.
Daniel Dalevi, Todd Z. DeSantis, Jakob Fredslund, Gary L. Andersen, Victor M. Markowitz, Philip Hugenholtz
2007 J jnl
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.
BMC Bioinform.
Charles Bland, Teresa L. Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos Kyrpides, Philip Hugenholtz
2006 — conf
An experimental metagenome data management and analysis system.
ISMB (Supplement of Bioinformatics)
Victor M. Markowitz, Natalia Ivanova, Krishna Palaniappan, Ernest Szeto, Frank Korzeniewski, Athanasios Lykidis, Iain Anderson, Konstantinos Mavrommatis, Victor Kunin, Héctor García Martín, Inna Dubchak, Philip Hugenholtz, Nikos Kyrpides
2006 J jnl
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes.
Nucleic Acids Res.
Todd Z. DeSantis, Philip Hugenholtz, Keith Keller, Eoin L. Brodie, Niels Larsen, Yvette M. Piceno, Richard Phan, Gary L. Andersen
2006 J jnl
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.
Nucleic Acids Res.
Konstantinos Liolios, Nektarios Tavernarakis, Philip Hugenholtz, Nikos Kyrpides
2006 J jnl
The integrated microbial genomes (IMG) system.
Nucleic Acids Res.
Victor M. Markowitz, Frank Korzeniewski, Krishna Palaniappan, Ernest Szeto, Greg Werner, Anu Padki, Xueling Zhao, Inna Dubchak, Philip Hugenholtz, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides
2005 J jnl
SNP-VISTA: An interactive SNP visualization tool.
BMC Bioinform.
Nameeta Y. Shah, Michael V. Teplitsky, Simon Minovitsky, Len A. Pennacchio, Philip Hugenholtz, Bernd Hamann, Inna Dubchak
2004 J jnl
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.
Bioinform.
Thomas Huber, Geoffrey J. Faulkner, Philip Hugenholtz