Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: biom-format
https://packages.ecosyste.ms/registries/pypi.org/packages/biom-format
Biological Observation Matrix (BIOM) format
20 versions
Latest release: over 1 year ago
14 dependent packages
5,130 downloads last month
Papers Mentioning biom-format 11
10.7717/peerj.4395
COREMIC: a web-tool to search for a niche associated CORE MICrobiomeCited by: 17
Author(s): Richard R. Rodrigues, Nyle C. Rodgers, Xiaowei Wu, Mark A. Williams
Software Mentions: 11
Published: almost 7 years ago
10.1128/mSystems.00541-20
Evidence for Succession and Putative Metabolic Roles of Fungi and Bacteria in the Farming Mutualism of the Ambrosia Beetle Xyleborus affinisCited by: 17
Author(s): Luis A. Ibarra-Juárez, Maureen Burton, Peter H. W. Biedermann, Luisa F. Cruz, Damaris Desgarennes, Enrique Ibarra-Laclette, Amparo Latorre, Alexandro Alonso-Sánchez, Emanuel Villafán, Greta Hanako-Rosas, Loredana Lopez, Mirna Vázquez-Rosas-Landa, Gloria Carrión, Daniel Carrillo, Andrés Moya, Araceli Lamelas
Software Mentions: 10
Published: about 4 years ago
10.3389/fmicb.2020.01536
Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane ConcentrationsCited by: 13
Author(s): Elias Broman, Xiaole Sun, Christian Stranne, Marco Salgado, Stefano Bonaglia, M. C. Geibel, Martin Jakobsson, Alf Norkko, Christoph Humborg, Francisco J. A. Nascimento
Software Mentions: 9
Published: over 4 years ago
10.7717/peerj.4925
Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome dataCited by: 166
Author(s): Jonathan M. Palmer, Michelle A. Jusino, Mark T. Banik, Daniel L. Lindner
Software Mentions: 8
Published: over 6 years ago
10.12688/f1000research.9618.2
biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) formatCited by: 2
Author(s): Markus J. Ankenbrand, Niklas Terhoeven, Sonja Hohlfeld, Frank Förster, Alexander Keller
Software Mentions: 7
Published: almost 8 years ago
10.3390/life8040063
Impact of Rearing Conditions on the Ambrosia Beetle’s MicrobiomeCited by: 17
Author(s): Luis A. Ibarra-Juárez, Damaris Desgarennes, Mirna Vázquez-Rosas-Landa, Emanuel Villafán, Alexandro Alonso-Sánchez, Ofelia Ferrera-Rodríguez, Andrés Moya, Daniel Carrillo, Luisa F. Cruz, Gloria Carrión, Abel López-Buenfil, Clemente de Jesús García-Ávila, Enrique Ibarra-Laclette, Araceli Lamelas
Software Mentions: 4
Published: almost 6 years ago
10.1038/s42003-020-0822-7
Uncovering diversity and metabolic spectrum of animals in dead zone sedimentsCited by: 16
Author(s): Elias Broman, Stefano Bonaglia, Oleksandr Holovachov, Ugo Marzocchi, Per Hall, Francisco J. A. Nascimento
Software Mentions: 3
Published: over 4 years ago
10.1038/s41598-020-62183-9
Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen speciesCited by: 55
Author(s): Viswanathan Baskaran, Prasanna Kumar Patil, M. Leo Antony, Satheesha Avunje, Vinay Tharabenahalli Nagaraju, Sudeep D. Ghate, Suganya Nathamuni, N. Dineshkumar, S.V. Alavandi, K. Vijayan
Software Mentions: 2
Published: over 4 years ago
10.1186/s40168-018-0549-6
Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantationCited by: 70
Author(s): Christopher Staley, Thomas Kaiser, Byron P. Vaughn, Carolyn Graiziger, Matthew J. Hamilton, Tauseef Ur Rehman, Kevin Song, Alexander Khoruts, Michael J. Sadowsky
Software Mentions: 2
Published: about 6 years ago
10.3389/fmicb.2014.00414
Core functional traits of bacterial communities in the Upper Mississippi River show limited variation in response to land coverCited by: 76
Author(s): Christopher Staley, Trevor Gould, Ping Wang, Jane Phillips, James B. Cotner, Michael J. Sadowsky
Software Mentions: 1
Published: over 10 years ago
10.1186/2047-217X-1-7
The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-omeCited by: 626
Author(s): Daniel McDonald, José C. Clemente, Justin Kuczynski, Jai Ram Rideout, Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan M. Huse, John Hufnagle, Patrick Meyer, Rob Knight, J. Gregory Caporaso
Software Mentions: 1
Published: over 12 years ago