Bland, Charles, Ramsey, Teresa L., Sabree, Fareedah, Lowe, Micheal, Brown, Kyndall, Kyrpides, Nikos C., ...
Metagenomic analysis of phosphorus removing sludge communities (2008)
Garcia Martin, Hector, Ivanova, Natalia, Kunin, Victor, Warnecke, Falk, Barry, Kerrie, McHardy, Alice C., ...
Enhanced Biological Phosphorus Removal (EBPR) is not well understood at the metabolic level despite being one of the best-studied microbially-mediated industrial processes due to its ecological and...
Building on basic metagenomics with complementary technologies (2007)
Warnecke, Falk, Hugenholtz, Philip
Abstract Metagenomics, the application of random shotgun sequencing to environmental samples, is a powerful approach for characterizing microbial communities. However, this method only represents the...
Dalevi, Daniel, DeSantis, Todd Z, Fredslund, Jakob, Andersen, Gary L, Markowitz, Victor M, Hugenholtz, Philip
Abstract Background Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a...
Bland, Charles, Ramsey, Teresa L, Sabree, Fareedah, Lowe, Micheal, Brown, Kyndall, Kyrpides, Nikos C, ...
Abstract Background Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract...
Evolutionary conservation of sequence and secondary structures in CRISPR repeats (2007)
Kunin, Victor, Sorek, Rotem, Hugenholtz, Philip
Abstract Background Clustered regularly interspaced short palindromic repeats (CRISPRs) are a novel class of direct repeats, separated by unique spacer sequences of similar length, that are present...
Use of simulated data sets to evaluate the fidelity of Metagenomic processing methods (2006)
Mavromatis, Konstantinos, Ivanova, Natalia, Barry, Kerri, Shapiro, Harris, Goltsman, Eugene, McHardy, Alice C., ...
Accurate phylogenetic classification of DNA fragments based on sequence composition (2006)
McHardy, Alice C., Garcia Martin, Hector, Tsirigos, Aristotelis, Hugenholtz, Philip, Rigoutsos, Isidore
Metagenome studies have retrieved vast amounts of sequence out of a variety of environments, leading to novel discoveries and great insights into the uncultured microbial world. Except for very...
An Experimental Metagenome Data Management and Analysis System (2006)
Markowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Ivanova, Natalia N., Kyrpides, Nikos C., ...
SNP-VISTA: An interactive SNP visualization tool (2005)
Shah, Nameeta, Teplitsky, Michael V, Minovitsky, Simon, Pennacchio, Len A, Hugenholtz, Philip, Hamann, Bernd, ...
Abstract Background Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single...
SNP-VISTA: An interactive SNP visualization tool (2005)
Shah, Nameeta, Teplitsky, Michael V, Minovitsky, Simon, Pennacchio, Len A, Hugenholtz, Philip, Hamann, Bernd, ...
Background: Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide...
SNP-VISTA: An Interactive SNPs Visualization Tool (2005)
Shah, Nameeta, Teplitsky, Michael V., Pennacchio, Len A., Hugenholtz, Philip, Hamann, Bernd, Dubchak, Inna L.
Recent advances in sequencing technologies promise better diagnostics for many diseases as well as better understanding of evolution of microbial populations. Single Nucleotide Polymorphisms (SNPs)...
Comparative metagenomics of microbial communities (2004)
Tringe, Susannah Green, Von Mering, Christian, Kobayashi, Arthur, Salamov, Asaf A., Chen, Kevin, Chang, Hwai W., ...
The predicted proteins encoded in DNA isolated from environmental microbial community samples reveal habitat-specific metabolic demands.
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments (2004)
Thomas Huber, Geoffrey Faulkner, Philip Hugenholtz
Chimeras are problematic in surveys of microbial communities. They suggest the presence of non-existing organisms and, as we demonstrated earlier, currently accumulate in databases (Hugenholtz and...
Bellerophon; a program to detect chimeric sequences in multiple sequence alignments (2004)
Huber, Thomas, Faulkner, Geoffrey, Hugenholtz, Philip
Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene...
Bellerophon; a program to detect chimeric sequences in multiple sequence alignments (2004)
Huber, Thomas, Faulkner, Geoffrey, Hugenholtz, Philip
Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene...
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments (2004)
Thomas Huber, Geoffrey Faulkner, Philip Hugenholtz
Chimeras are problematic in surveys of microbial communities. They suggest the presence of non-existing organisms and, as we demonstrated earlier, currently accumulate in databases (Hugenholtz and...
Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases (2003)
Hugenholtz, Philip, Huber, Thomas
A significant number of chimeric 16S rDNA sequences of diverse origin were identified in the public databases by partial treeing analysis. This suggests that chimeric sequences, representing...
Christopher A. McDevitt, Philip Hugenholtz, Graeme Hanson, Alastair McEwan
This paper describes the molecular properties of an important enzyme from the DMSO reductase family of molybdenum enzymes. The first phylogenetic analysis of this large family of enzymes is presented...
Exploring prokaryotic diversity in the genomic era (2002)
Abstract Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced sampling bias towards four bacterial phyla - Proteobacteria,...
Christopher A. McDevitt, Philip Hugenholtz, Graeme Hanson, Alastair McEwan
This paper describes the molecular properties of an important enzyme from the DMSO reductase family of molybdenum enzymes. The first phylogenetic analysis of this large family of enzymes is presented...
Spine title: Investigation of bacterial biofilm in an air-handling system.
Spine title: Investigation of bacterial biofilm in an air-handling system. Includes bibliography.
Crocetti, Gregory R., Hugenholtz, Philip, Bond, Philip L., Schuler, Andrew, Keller, Jürg, Jenkins, David, ...
Laboratory-scale sequencing batch reactors (SBRs) as models for activated sludge processes were used to study enhanced biological phosphorus removal (EBPR) from wastewater. Enrichment for...
Hugenholtz, Philip, Tyson, Gene W., Webb, Richard I., Wagner, Ankia M., Blackall, Linda L.
A molecular approach was used to investigate a recently described candidate division of the domain Bacteria, TM7, currently known only from environmental 16S ribosomal DNA sequence data. A number of...
Sandler, Steven J., Hugenholtz, Philip, Schleper, Christa, DeLong, Edward F., Pace, Norman R., Clark, Alvin J.
Archaea-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal...
Klein, Michael, Friedrich, Michael, Roger, Andrew J., Hugenholtz, Philip, Fishbain, Susan, Abicht, Heike, ...
A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing...
Dojka, Michael A., Hugenholtz, Philip, Haack, Sheridan K., Pace, Norman R.
A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and...
Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring
Hugenholtz, Philip, Pitulle, Christian, Hershberger, Karen L., Pace, Norman R.
A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), a Yellowstone National Park hot spring previously shown to contain remarkable...
Exploring prokaryotic diversity in the genomic era
Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced sampling bias towards four bacterial phyla - Proteobacteria, Firmicutes,...
Baker, Brett J., Hugenholtz, Philip, Dawson, Scott C., Banfield, Jillian F.
During a molecular phylogenetic survey of extremely acidic (pH < 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a...
Laboratory Cultivation of Widespread and Previously Uncultured Soil Bacteria
Joseph, Shayne J., Hugenholtz, Philip, Sangwan, Parveen, Osborne, Catherine A., Janssen, Peter H.
Most soil bacteria belong to family-level phylogenetic groups with few or no known cultivated representatives. We cultured a collection of 350 isolates from soil by using simple solid media in petri...
Ginige, Maneesha P., Hugenholtz, Philip, Daims, Holger, Wagner, Michael, Keller, Jürg, Blackall, Linda L.
A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source...
Schoenborn, Liesbeth, Yates, Penelope S., Grinton, Bronwyn E., Hugenholtz, Philip, Janssen, Peter H.
Representatives of only four well-characterized bacterial phyla were isolated from a pasture soil by using liquid serial dilution culture. In contrast, members of Acidobacteria, Verrucomicrobia, and...
Sangwan, Parveen, Chen, Xiaolei, Hugenholtz, Philip, Janssen, Peter H.
The phylum Verrucomicrobia is increasingly recognized as an environmentally significant group of bacteria, particularly in soil habitats. At least six subdivisions of the Verrucomicrobia are resolved...
Tyson, Gene W., Lo, Ian, Baker, Brett J., Allen, Eric E., Hugenholtz, Philip, Banfield, Jillian F.
Analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. This was found on a genome fragment belonging to a...
SNP-VISTA: An interactive SNP visualization tool
Shah, Nameeta, Teplitsky, Michael V, Minovitsky, Simon, Pennacchio, Len A, Hugenholtz, Philip, Hamann, Bernd, ...
The integrated microbial genomes (IMG) system
Markowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Werner, Greg, Padki, Anu, ...
The integrated microbial genomes (IMG) system is a new data management and analysis platform for microbial genomes provided by the Joint Genome Institute (JGI). IMG contains both draft and complete...
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
Liolios, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip, Kyrpides, Nikos C.
The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates...
Imachi, Hiroyuki, Sekiguchi, Yuji, Kamagata, Yoichi, Loy, Alexander, Qiu, Yan-Ling, Hugenholtz, Philip, ...
The classical perception of members of the gram-positive Desulfotomaculum cluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability...
Crocetti, Gregory R., Hugenholtz, Philip, Bond, Philip L., Schuler, Andrew, Keller, Jürg, Jenkins, David, ...
Laboratory-scale sequencing batch reactors (SBRs) as models for activated sludge processes were used to study enhanced biological phosphorus removal (EBPR) from wastewater. Enrichment for...
Hugenholtz, Philip, Tyson, Gene W., Webb, Richard I., Wagner, Ankia M., Blackall, Linda L.
A molecular approach was used to investigate a recently described candidate division of the domain Bacteria, TM7, currently known only from environmental 16S ribosomal DNA sequence data. A number of...
Sandler, Steven J., Hugenholtz, Philip, Schleper, Christa, DeLong, Edward F., Pace, Norman R., Clark, Alvin J.
Archaea-specific radA primers were used with PCR to amplify fragments of radA genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal...
Klein, Michael, Friedrich, Michael, Roger, Andrew J., Hugenholtz, Philip, Fishbain, Susan, Abicht, Heike, ...
A large fragment of the dissimilatory sulfite reductase genes (dsrAB) was PCR amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing...
Dojka, Michael A., Hugenholtz, Philip, Haack, Sheridan K., Pace, Norman R.
A culture-independent molecular phylogenetic approach was used to survey constituents of microbial communities associated with an aquifer contaminated with hydrocarbons (mainly jet fuel) and...
Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring
Hugenholtz, Philip, Pitulle, Christian, Hershberger, Karen L., Pace, Norman R.
A culture-independent molecular phylogenetic survey was carried out for the bacterial community in Obsidian Pool (OP), a Yellowstone National Park hot spring previously shown to contain remarkable...
Exploring prokaryotic diversity in the genomic era
Our understanding of prokaryote biology from study of pure cultures and genome sequencing has been limited by a pronounced sampling bias towards four bacterial phyla - Proteobacteria, Firmicutes,...
Baker, Brett J., Hugenholtz, Philip, Dawson, Scott C., Banfield, Jillian F.
During a molecular phylogenetic survey of extremely acidic (pH < 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a...
Laboratory Cultivation of Widespread and Previously Uncultured Soil Bacteria
Joseph, Shayne J., Hugenholtz, Philip, Sangwan, Parveen, Osborne, Catherine A., Janssen, Peter H.
Most soil bacteria belong to family-level phylogenetic groups with few or no known cultivated representatives. We cultured a collection of 350 isolates from soil by using simple solid media in petri...
Ginige, Maneesha P., Hugenholtz, Philip, Daims, Holger, Wagner, Michael, Keller, Jürg, Blackall, Linda L.
A denitrifying microbial consortium was enriched in an anoxically operated, methanol-fed sequencing batch reactor (SBR) fed with a mineral salts medium containing methanol as the sole carbon source...
Schoenborn, Liesbeth, Yates, Penelope S., Grinton, Bronwyn E., Hugenholtz, Philip, Janssen, Peter H.
Representatives of only four well-characterized bacterial phyla were isolated from a pasture soil by using liquid serial dilution culture. In contrast, members of Acidobacteria, Verrucomicrobia, and...
Sangwan, Parveen, Chen, Xiaolei, Hugenholtz, Philip, Janssen, Peter H.
The phylum Verrucomicrobia is increasingly recognized as an environmentally significant group of bacteria, particularly in soil habitats. At least six subdivisions of the Verrucomicrobia are resolved...
Tyson, Gene W., Lo, Ian, Baker, Brett J., Allen, Eric E., Hugenholtz, Philip, Banfield, Jillian F.
Analysis of assembled random shotgun sequence data from a low-diversity, subsurface acid mine drainage (AMD) biofilm revealed a single nif operon. This was found on a genome fragment belonging to a...
SNP-VISTA: An interactive SNP visualization tool
Shah, Nameeta, Teplitsky, Michael V, Minovitsky, Simon, Pennacchio, Len A, Hugenholtz, Philip, Hamann, Bernd, ...
The integrated microbial genomes (IMG) system
Markowitz, Victor M., Korzeniewski, Frank, Palaniappan, Krishna, Szeto, Ernest, Werner, Greg, Padki, Anu, ...
The integrated microbial genomes (IMG) system is a new data management and analysis platform for microbial genomes provided by the Joint Genome Institute (JGI). IMG contains both draft and complete...
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
Liolios, Konstantinos, Tavernarakis, Nektarios, Hugenholtz, Philip, Kyrpides, Nikos C.
The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates...
Imachi, Hiroyuki, Sekiguchi, Yuji, Kamagata, Yoichi, Loy, Alexander, Qiu, Yan-Ling, Hugenholtz, Philip, ...
The classical perception of members of the gram-positive Desulfotomaculum cluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability...
Evolutionary conservation of sequence and secondary structures in CRISPR repeats
Kunin, Victor, Sorek, Rotem, Hugenholtz, Philip
The categorisation and structural analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) sequences from 195 microbial genomes show that repeats from diverse organisms can be...
Bland, Charles, Ramsey, Teresa L, Sabree, Fareedah, Lowe, Micheal, Brown, Kyndall, Kyrpides, Nikos C, ...
Dalevi, Daniel, DeSantis, Todd Z, Fredslund, Jakob, Andersen, Gary L, Markowitz, Victor M, Hugenholtz, Philip
Marcy, Yann, Ouverney, Cleber, Bik, Elisabeth M., Lösekann, Tina, Ivanova, Natalia, Martin, Hector Garcia, ...
We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial...
IMG/M: a data management and analysis system for metagenomes
Markowitz, Victor M., Ivanova, Natalia N., Szeto, Ernest, Palaniappan, Krishna, Chu, Ken, Dalevi, Daniel, ...
IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Department of Energy's (DOE) Joint Genome Institute (JGI). IMG/M consists of metagenome data...