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2020 – today
- 2022
[j15]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): 5315-5316 (2022)- [j14]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): 785-794 (2022) - 2020
- [j13]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): 1925-1927 (2020)
2010 – 2019
- 2014
- [j12]Donovan H. Parks, Gene W. Tyson, Philip Hugenholtz, Robert G. Beiko:
STAMP: statistical analysis of taxonomic and functional profiles. Bioinform. 30(21): 3123-3124 (2014) - 2013
- [j11]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) - 2010
- [j10]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): 346-354 (2010)
2000 – 2009
- 2009
- [j9]Erik Kristiansson, Philip Hugenholtz, Daniel Dalevi:
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. Bioinform. 25(20): 2737-2738 (2009) - 2008
- [j8]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): 534-538 (2008) - [c2]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: 7-13 - 2007
- [j7]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) - [j6]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) - 2006
- [j5]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): 332-334 (2006) - [j4]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): 344-348 (2006) - [j3]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): 394-399 (2006) - [c1]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: 359-367 - 2005
- [j2]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: 292 (2005) - 2004
- [j1]Thomas Huber, Geoffrey J. Faulkner, Philip Hugenholtz:
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinform. 20(14): 2317-2319 (2004)
Coauthor Index
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