Philip Hugenholtz

Publication Activity (10 Years)

Years Active: 2004-2022
Publications (10 Years): 3

Top Topics

Escherichia Coli

Generalized Association Rules

Statistical Analysis

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Donovan H. Parks, Maria Chuvochina, Christian Rinke, Aaron J. Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res. 50 (D1) (2022)
Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks
GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinform. 38 (23) (2022)
Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinform. 36 (6) (2020)
Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz, Robert G. Beiko
STAMP: statistical analysis of taxonomic and functional profiles. Bioinform. 30 (21) (2014)
Lauren M. Bragg, Glenn Stone, Margaret K. Butler, Philip Hugenholtz, Gene W. Tyson
Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data. PLoS Comput. Biol. 9 (4) (2013)
Konstantinos Liolios, I-Min A. Chen, Konstantinos Mavrommatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M. Markowitz, Nikos Kyrpides
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 38 (Database-Issue) (2010)
Erik Kristiansson, Philip Hugenholtz, Daniel Dalevi
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinform. 25 (20) (2009)
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
IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 36 (Database-Issue) (2008)
Daniel Dalevi, Natalia Ivanova, Konstantinos Mavrommatis, Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos Kyrpides, Victor M. Markowitz
Annotation of metagenome short reads using proxygenes. ECCB (2008)
Charles Bland, Teresa L. Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos Kyrpides, Philip Hugenholtz
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinform. 8 (2007)
Daniel Dalevi, Todd Z. DeSantis, Jakob Fredslund, Gary L. Andersen, Victor M. Markowitz, Philip Hugenholtz
Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool. BMC Bioinform. 8 (2007)
Konstantinos Liolios, Nektarios Tavernarakis, Philip Hugenholtz, Nikos Kyrpides
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res. 34 (Database-Issue) (2006)
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
An experimental metagenome data management and analysis system. ISMB (Supplement of Bioinformatics) (2006)
Todd Z. DeSantis, Philip Hugenholtz, Keith Keller, Eoin L. Brodie, Niels Larsen, Yvette M. Piceno, Richard Phan, Gary L. Andersen
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
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
The integrated microbial genomes (IMG) system. Nucleic Acids Res. 34 (Database-Issue) (2006)
Nameeta Y. Shah, Michael V. Teplitsky, Simon Minovitsky, Len A. Pennacchio, Philip Hugenholtz, Bernd Hamann, Inna Dubchak
SNP-VISTA: An interactive SNP visualization tool. BMC Bioinform. 6 (2005)
Thomas Huber, Geoffrey Faulkner, Philip Hugenholtz
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinform. 20 (14) (2004)