pypi: MetaPathways | Projects | Ecosyste.ms: Papers

10.1038/sdata.2017.35

A geographically-diverse collection of 418 human gut microbiome pathway genome databases
Cited by: 6
Author(s): Aria S. Hahn, Tomer Altman, Kishori M. Konwar, Niels W. Hanson, Dongjae Kim, David A. Relman, David L. Dill, Steven J. Hallam
Software Mentions: 6
Published: over 7 years ago

10.3389/fmicb.2018.01914

Diverse Bacteria Utilize Alginate Within the Microbiome of the Giant Kelp Macrocystis pyrifera
Cited by: 30
Author(s): Jordan D. Lin, Matthew A. Lemay, Laura Wegener Parfrey
Software Mentions: 4
Published: over 6 years ago

10.3389/fmicb.2015.00966

Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential
Cited by: 39
Author(s): Richard Allen White, Ian M. Power, Gregory M. Dipple, Gordon Southam, Curtis A. Suttle
Software Mentions: 4
Published: about 9 years ago

10.3389/fmicb.2015.01531

Metagenomic Analysis Suggests Modern Freshwater Microbialites Harbor a Distinct Core Microbial Community
Cited by: 43
Author(s): Richard Allen White, Amy M. Chan, Gregory S. Gavelis, Brian S. Leander, A. L. Brady, G. F. Slater, D. S. S. Lim, Curtis A. Suttle
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41396-018-0215-9

Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome
Cited by: 28
Author(s): Zachary Armstrong, Keith Mewis, Feng Liu, Connor Morgan-Lang, Melanie Scofield, Evan W Durno, Hong Ming Chen, Kevin Mehr, Stephen G. Withers, Steven J. Hallam
Software Mentions: 3
Published: over 6 years ago

10.1128/mSystems.00061-19

Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations
Cited by: 36
Author(s): Taniya Roy Chowdhury, Joon‐Yong Lee, Eric Bottos, Colin Brislawn, Richard Allen White, Lisa Bramer, Joseph Brown, Jeremy Zucker, Young Mo Kim, Ari Jumpponen, Charles W. Rice, Sarah Fansler, Thomas O. Metz, Lee Ann McCue, Stephen Callister, Hyun‐Seob Song, Janet K. Jansson
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-14-202

MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information
Cited by: 94
Author(s): Kishori M. Konwar, Niels W. Hanson, Antoine Pagé, Steven J. Hallam
Software Mentions: 3
Published: over 11 years ago

10.1093/gigascience/gix096

MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle
Cited by: 24
Author(s): Valerie De Anda, Icoquih Zapata‐Peñasco, Augusto César Poot-Hernández, Luis E. Eguiarte, Bruno Contreras‐Moreira, Valeria Souza
Software Mentions: 3
Published: about 7 years ago

10.1128/mSystems.00193-18

Integrated Omic Analyses Provide Evidence that a “ Candidatus Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions
Cited by: 38
Author(s): Pamela Y. Camejo, Ben O. Oyserman, Katherine D. McMahon, Daniel R. Noguera
Software Mentions: 3
Published: almost 6 years ago

10.1128/AEM.02242-19

Medium-Chain Fatty Acid Synthesis by “ Candidatus Weimeria bifida” gen. nov., sp. nov., and “ Candidatus Pseudoramibacter fermentans” sp. nov
Cited by: 42
Author(s): Matthew Scarborough, Kevin S. Myers, Timothy J. Donohue, Daniel R. Noguera
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2164-15-619

Metabolic pathways for the whole community
Cited by: 51
Author(s): Niels W. Hanson, Kishori M. Konwar, Alyse K. Hawley, Tomer Altman, Peter D. Karp, Steven J. Hallam
Software Mentions: 2
Published: over 10 years ago

10.1186/s13068-018-1044-9

Genomic comparison of Clostridium species with the potential of utilizing red algal biomass for biobutanol production
Cited by: 41
Author(s): Chongran Sun, Shuangfei Zhang, Fengxue Xin, Sabarathinam Shanmugam, Yi-Rui Wu
Software Mentions: 2
Published: almost 7 years ago

10.1128/mSystems.00221-18

Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome
Cited by: 58
Author(s): Matthew Scarborough, Christopher E. Lawson, Joshua J. Hamilton, Timothy J. Donohue, Daniel R. Noguera
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.03125

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics
Cited by: 173
Author(s): Simon Roux, Alyse K. Hawley, Mónica Torres Beltrán, Melanie Scofield, Patrick Schwientek, Ramunas Stepanauskas, Tanja Woyke, Steven J. Hallam, Matthew B. Sullivan
Software Mentions: 2
Published: over 10 years ago

10.1128/genomeA.01584-16

Draft Genome Sequence of the Pelagic Photoferrotroph Chlorobium phaeoferrooxidans
Cited by: 26
Author(s): Sean A. Crowe, Aria S. Hahn, Connor Morgan-Lang, Katherine Jenny Thompson, Rachel L. Simister, Marc Llirós, Martin Hirst, Steven J. Hallam
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2017.01212

Nutrient Acquisition and the Metabolic Potential of Photoferrotrophic Chlorobi
Cited by: 26
Author(s): Katherine Jenny Thompson, Rachel L. Simister, Aria S. Hahn, Steven J. Hallam, Sean A. Crowe
Software Mentions: 1
Published: over 7 years ago

10.1128/MRA.00271-19

Draft Genome Sequence from a Putative New Genus and Species in the Family Methanoregulaceae Isolated from the Anoxic Basin of Lake Untersee in East Antarctica
Cited by: 3
Author(s): Nicole Yasmin Wagner, Aria S. Hahn, Dale T. Andersen, Mary Beth Wilhelm, Connor Morgan-Lang, M. Vanderwilt, S. S. Johnson
Software Mentions: 1
Published: over 5 years ago

10.1038/sdata.2017.160

A compendium of multi-omic sequence information from the Saanich Inlet water column
Cited by: 34
Author(s): Alyse K. Hawley, Mónica Torres-Beltrán, Elena Zaikova, David A. Walsh, A. Mueller, Melanie Scofield, Sam Kheirandish, Chris Payne, Larysa Pakhomova, Maya P. Bhatia, Olena O Shevchuk, Esther A. Gies, Diane Fairley, Stephanie Malfatti, Angela D. Norbeck, Heather M. Brewer, Ljiljana Paša‐Tolić, Tijana Glavina del Rio, Curtis A. Suttle, Susannah G. Tringe, Steven J. Hallam
Software Mentions: 1
Published: about 7 years ago

10.1128/mSystems.00059-17

Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “ Candidatus Nitrospira nitrosa”
Cited by: 100
Author(s): Pamela Y. Camejo, Jorge Santo Domingo, Katherine D. McMahon, Daniel R. Noguera
Software Mentions: 1
Published: about 7 years ago

10.1186/s12915-015-0195-4

MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes
Cited by: 31
Author(s): Pavel Petrenko, Briallen Lobb, Daniel Kurtz, Josh D. Neufeld, Andrew C. Doxey
Software Mentions: 1
Published: about 9 years ago

10.1093/bioinformatics/btv361

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements
Cited by: 44
Author(s): Kishori M. Konwar, Niels W. Hanson, Maya P. Bhatia, Dongjae Kim, Shang‐Ju Wu, Aria S. Hahn, Connor Morgan-Lang, Hiu Kan Cheung, Steven J. Hallam
Software Mentions: 1
Published: over 9 years ago

10.1128/mSystems.00082-19

High-Throughput Recovery and Characterization of Metagenome-Derived Glycoside Hydrolase-Containing Clones as a Resource for Biocatalyst Development
Cited by: 11
Author(s): Zachary Armstrong, Feng Liu, Sam Kheirandish, Hongming Chen, Keith Mewis, Tianmeng Duo, Connor Morgan-Lang, Steven J. Hallam, Stephen G. Withers
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-016-2823-y

Inferring metabolic pathway activity levels from RNA-Seq data
Cited by: 9
Author(s): Yvette Temate‐Tiagueu, Sahar Al Seesi, Meril Mathew, Igor Mandric, Álex Rodríguez, Kayla Bean, Qiong Cheng, Olga Glebova, Ion Măndoiu, Nicole B. Lopanik, Alexander Zelikovsky
Software Mentions: 1
Published: over 8 years ago

10.3389/fmicb.2018.02180

The Complete Genome and Physiological Analysis of the Microbialite-Dwelling Agrococcus pavilionensis sp. nov; Reveals Genetic Promiscuity and Predicted Adaptations to Environmental Stress
Cited by: 10
Author(s): Richard Allen White, Greg S. Gavelis, Sarah A. Soles, Emma Gosselin, G. F. Slater, D. S. S. Lim, Brian S. Leander, Curtis A. Suttle
Software Mentions: 1
Published: about 6 years ago

10.3389/fmicb.2018.03189

The Complete Genome and Physiological Analysis of the Eurythermal Firmicute Exiguobacterium chiriqhucha Strain RW2 Isolated From a Freshwater Microbialite, Widely Adaptable to Broad Thermal, pH, and Salinity Ranges
Cited by: 21
Author(s): Richard Allen White, Sarah A. Soles, Greg S. Gavelis, Emma Gosselin, G. F. Slater, D. S. S. Lim, Brian S. Leander, Curtis A. Suttle
Software Mentions: 1
Published: almost 6 years ago

Ecosyste.ms: Papers

Projects: pypi: MetaPathways

Papers Mentioning MetaPathways 25