Philip Hugenholtz

According to our database, Philip Hugenholtz authored at least 17 papers between 2004 and 2022.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2022

GTDB-Tk v2: memory friendly classification with the genome taxonomy database.

Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks

Bioinform., November, 2022

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy.

Donovan H. Parks, Maria Chuvochina, Christian Rinke, Aaron J. Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz

Nucleic Acids Res., 2022

2020

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database.

Pierre-Alain Chaumeil, Aaron J. Mussig, Philip Hugenholtz, Donovan H. Parks

Bioinform., 2020

2014

STAMP: statistical analysis of taxonomic and functional profiles.

Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz, Robert G. Beiko

Bioinform., 2014

2013

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data.

Lauren M. Bragg, Glenn Stone, Margaret K. Butler, Philip Hugenholtz, Gene W. Tyson

PLoS Comput. Biol., 2013

2010

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata.

Konstantinos Liolios, I-Min A. Chen, Konstantinos Mavrommatis, Nektarios Tavernarakis, Philip Hugenholtz, Victor M. Markowitz, Nikos Kyrpides

Nucleic Acids Res., 2010

2009

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes.

Erik Kristiansson, Philip Hugenholtz, Daniel Dalevi

Bioinform., 2009

2008

IMG/M: a data management and analysis system for metagenomes.

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

Nucleic Acids Res., 2008

Annotation of metagenome short reads using proxygenes.

Daniel Dalevi, Natalia Ivanova, Konstantinos Mavrommatis, Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos Kyrpides, Victor M. Markowitz

Proceedings of the ECCB'08 Proceedings, 2008

2007

Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool.

Daniel Dalevi, Todd Z. DeSantis, Jakob Fredslund, Gary L. Andersen, Victor M. Markowitz, Philip Hugenholtz

BMC Bioinform., 2007

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats.

Charles Bland, Teresa L. Ramsey, Fareedah Sabree, Micheal Lowe, Kyndall Brown, Nikos Kyrpides, Philip Hugenholtz

BMC Bioinform., 2007

2006

The integrated microbial genomes (IMG) system.

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

Nucleic Acids Res., 2006

The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.

Konstantinos Liolios, Nektarios Tavernarakis, Philip Hugenholtz, Nikos Kyrpides

Nucleic Acids Res., 2006

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes.

Todd Z. DeSantis, Philip Hugenholtz, Keith Keller, Eoin L. Brodie, Niels Larsen, Yvette M. Piceno, Richard Phan, Gary L. Andersen

Nucleic Acids Res., 2006

An experimental metagenome data management and analysis system.

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

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

SNP-VISTA: An interactive SNP visualization tool.

Nameeta Y. Shah, Michael V. Teplitsky, Simon Minovitsky, Len A. Pennacchio, Philip Hugenholtz, Bernd Hamann, Inna Dubchak

BMC Bioinform., 2005

2004

Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.

Thomas Huber, Geoffrey J. Faulkner, Philip Hugenholtz

Bioinform., 2004