pypi: o | Projects | Ecosyste.ms: Papers

10.1186/s12859-020-03703-2

SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o
Cited by: 25
Author(s): Fernando Puente-Sánchez, Natalia García-García, Javier Tamames
Software Mentions: 9
Published: about 4 years ago

10.1186/s13059-020-02195-w

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
Cited by: 107
Author(s): Alon Shaiber, Amy Willis, Tom O. Delmont, Simon Roux, Lin-Xing Chen, Abigail C. Schmid, Mahmoud Yousef, Andrea R. Watson, Karen Lolans, Özcan C. Esen, Sonny T. M. Lee, Nora Downey, Hilary G. Morrison, Floyd E. Dewhirst, Jessica L. Mark Welch, A. Murat Eren
Software Mentions: 8
Published: almost 4 years ago

10.1186/s40168-020-00813-0

Disinfection exhibits systematic impacts on the drinking water microbiome
Cited by: 37
Author(s): Zihan Dai, Maria C. Sevillano-Rivera, Szymon T. Calus, Quyen Melina Bautista-de los Santos, A. Murat Eren, P.W.J.J. van der Wielen, Umer Zeeshan Ijaz, Ameet J. Pinto
Software Mentions: 7
Published: over 4 years ago

10.7717/peerj.4320

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome
Cited by: 272
Author(s): Tom O. Delmont, A. Murat Eren
Software Mentions: 6
Published: over 6 years ago

10.1128/mSystems.00145-20

Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens
Cited by: 14
Author(s): Briallen Lobb, Rhiannon Hodgson, Michael D. J. Lynch, Michael J. Mansfield, Jiujun Cheng, Trevor C. Charles, Josh D. Neufeld, Paul M. Craig, Andrew C. Doxey
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-019-39576-6

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia
Cited by: 57
Author(s): Laetitia G. E. Wilkins, Cassandra L. Ettinger, Guillaume Jospin, Jonathan A. Eisen
Software Mentions: 6
Published: over 5 years ago

10.3389/fmicb.2019.00993

The Water Microbiome Through a Pilot Scale Advanced Treatment Facility for Direct Potable Reuse
Cited by: 33
Author(s): Rose Kantor, Scott Miller, Kara L. Nelson
Software Mentions: 5
Published: over 5 years ago

10.7717/peerj.3035

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation
Cited by: 132
Author(s): Elaina D. Graham, John F. Heidelberg, Benjamin J. Tully
Software Mentions: 5
Published: over 7 years ago

10.7717/peerj.1319

Anvi’o: an advanced analysis and visualization platform for ‘omics data
Cited by: 1,274
Author(s): A. Murat Eren, Özcan C. Esen, Christopher Quince, Joseph H. Vineis, Hilary G. Morrison, Mitchell L. Sogin, Tom O. Delmont
Software Mentions: 5
Published: almost 9 years ago

10.7717/peerj.7548

Genome-resolved insights into a novelSpiroplasmasymbiont of the Wheat Stem Sawfly (Cephus cinctus)
Cited by: 11
Author(s): Carl J. Yeoman, Laura M. Brutscher, Özcan C. Esen, Furkan Ibaoglu, Curtis Fowler, A. Murat Eren, Kevin W. Wanner, David K. Weaver
Software Mentions: 4
Published: about 5 years ago

10.3389/fninf.2016.00023

A General Procedure to Study Subcellular Models of Transsynaptic Signaling at Inhibitory Synapses
Cited by: 3
Author(s): Carmen Alina Lupaşcu, Annunziato Morabito, Elisabetta Merenda, Silvia Marinelli, Cristina Marchetti, Rosanna Migliore, Enrico Cherubini, Michele Migliore
Software Mentions: 4
Published: about 8 years ago

10.1111/1462-2920.14806

Genome‐resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep‐sea hydrothermal vents
Cited by: 49
Author(s): David Galambos, R. Anderson, Julie Réveillaud, Julie A. Huber
Software Mentions: 4
Published: almost 5 years ago

10.1186/s40168-018-0550-0

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Cited by: 67
Author(s): Johannes Alneberg, Christofer M. G. Karlsson, Anna-Maria Divne, Claudia Bergin, Félix Homa, Markus V. Lindh, Luisa W. Hugerth, Thijs J. G. Ettema, Stefan Bertilsson, Anders F. Andersson, Jarone Pinhassi
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0089456

A Semi-Automated Pipeline for the Segmentation of Rhesus Macaque Hippocampus: Validation across a Wide Age Range
Cited by: 8
Author(s): Michael R. Hunsaker, David G. Amaral
Software Mentions: 4
Published: over 10 years ago

10.3390/antibiotics10020191

Gentamicin Adsorption onto Soil Particles Prevents Overall Short-Term Effects on the Soil Microbiome and Resistome
Cited by: 3
Author(s): Concepcion Sanchez-Cid, Alexandre Guironnet, Laure Wiest, Emmanuelle Vulliet, Timothy M. Vogel
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.1839

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies
Cited by: 86
Author(s): Tom O. Delmont, A. Murat Eren
Software Mentions: 3
Published: over 8 years ago

10.1186/s13059-020-02200-2

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
Cited by: 36
Author(s): Daniel R. Utter, Gary G. Borisy, A. Murat Eren, Colleen M. Cavanaugh, Jessica L. Mark Welch
Software Mentions: 3
Published: almost 4 years ago

10.1155/2016/1562041

Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of Glycine max
Cited by: 2
Author(s): Kevin Lambirth, Adam M. Whaley, Jessica A. Schlueter, Kenneth J. Piller, Kenneth L. Bost
Software Mentions: 3
Published: almost 8 years ago

10.1080/20002297.2020.1773067

A case study of salivary microbiome in smokers and non-smokers in Hungary: analysis by shotgun metagenome sequencing
Cited by: 14
Author(s): Roland Wirth, Gergely Maróti, Róbert Mihók, Donát Simon-Fiala, Márk Antal, Bernadett Pap, Anett Demcsák, János Minárovits, Kornél L. Kovács
Software Mentions: 3
Published: over 4 years ago

10.1186/s40168-020-0790-7

A pipeline for targeted metagenomics of environmental bacteria
Cited by: 33
Author(s): Anissa Grieb, Robert M. Bowers, Monike Oggerin, Danielle Goudeau, Janey Lee, Rex R. Malmstrom, Tanja Woyke, Bernhard M. Fuchs
Software Mentions: 2
Published: over 4 years ago

10.1038/s42003-021-02105-1

Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts
Cited by: 42
Author(s): Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, David A. Duchêne, Lara Puetz, Tom O. Delmont, Harald Sveier, Louise von Gersdorff Jørgensen, Kim Præbel, Michael D. Martin, Anders Miki Bojesen, M. Thomas P. Gilbert, Karsten Kristiansen, Morten T. Limborg
Software Mentions: 2
Published: over 3 years ago

10.1186/s40168-018-0411-x

Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity
Cited by: 31
Author(s): Julie Réveillaud, R. Anderson, Sintra Reves-Sohn, Colleen M. Cavanaugh, J. A. Huber
Software Mentions: 2
Published: over 6 years ago

10.3389/fbioe.2020.557572

Chlorella vulgaris and Its Phycosphere in Wastewater: Microalgae-Bacteria Interactions During Nutrient Removal
Cited by: 25
Author(s): Roland Wirth, Bernadett Pap, Tamás Böjti, Prateek Shetty, Gergely Lakatos, Zoltán Bagi, Kornél L. Kovács, Gergely Maróti
Software Mentions: 2
Published: almost 4 years ago

10.3389/fmicb.2021.680620

An Ecological Basis for Dual Genetic Code Expansion in Marine Deltaproteobacteria
Cited by: 2
Author(s): Veronika Kivenson, Blair G. Paul, David L. Valentine
Software Mentions: 2
Published: about 3 years ago

10.1080/20002297.2020.1814666

Isolation and cultivation of candidate phyla radiation Saccharibacteria (TM7) bacteria in coculture with bacterial hosts
Cited by: 34
Author(s): Pallavi Murugkar, Andrew J. Collins, Tsute Chen, Floyd E. Dewhirst
Software Mentions: 2
Published: over 4 years ago

10.1038/srep32689

A HTML5 open source tool to conduct studies based on Libet’s clock paradigm
Cited by: 10
Author(s): Pablo Garaizar, Carmelo P. Cubillas, Helena Matute
Software Mentions: 2
Published: about 8 years ago

10.1186/s12859-018-2189-z

SAMSA2: a standalone metatranscriptome analysis pipeline
Cited by: 91
Author(s): Samuel T. Westreich, Michelle L. Treiber, David A. Mills, Ian F Korf, Danielle G. Lemay
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms9010186

Comparative Genomics of Marine Bacteria from a Historically Defined Plastic Biodegradation Consortium with the Capacity to Biodegrade Polyhydroxyalkanoates
Cited by: 8
Author(s): Fons A. de Vogel, Cathleen Schlundt, Robert Stote, Jo Ann Ratto, Linda Amaral‐Zettler
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms9010191

Core and Accessory Genome Analysis of Vibrio mimicus
Cited by: 5
Author(s): Iliana Guardiola-Avila, Leonor Sánchez-Busó, Evelia Acedo-Félix, Bruno Gómez‐Gil, Manuel Zúñiga, Fernando Gónzález-Candelas, Lorena Noriega-Orozco
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-018-5381-7

Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing
Cited by: 99
Author(s): Sarah Goldstein, Lidia Beka, Joerg Graf, Jonathan L. Klassen
Software Mentions: 1
Published: over 5 years ago

10.1038/sdata.2017.37

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids
Cited by: 60
Author(s): Sean P. Jungbluth, Jan P. Amend, Michael S. Rappé
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pgen.1006810

Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes
Cited by: 128
Author(s): Violette Da Cunha, Morgan Gaïa, Danièle Gadelle, Arshan Nasir, Patrick Forterre
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2020.593915

Putative Novel Effector Genes Revealed by the Genomic Analysis of the Phytopathogenic Fungus Fusarium oxysporum f. sp. physali (Foph) That Infects Cape Gooseberry Plants
Cited by: 8
Author(s): Jaime Simbaqueba, Edwin A. Rodríguez, Diana Burbano‐David, Carolina González, Alejandro Caro‐Quintero
Software Mentions: 1
Published: over 3 years ago

10.1002/cam4.2787

Loss of skeletal muscle index and survival in patients with metastatic colorectal cancer: Secondary analysis of the phase 3 CAIRO3 trial
Cited by: 22
Author(s): Sophie A Kurk, Petra H.M. Peeters, Bram Dorresteijn, Pim A. de Jong, Marion Jourdan, Geert-Jan Creemers, Frans Erdkamp, Felix E. de Jongh, Peter A. M. Kint, Boelo Jan Poppema, Sandra A. Radema, Lieke H.J. Simkens, Bea C. Tanis, M.L.R. Tjin-A-Ton, A. van der Velden, Cornelis J.A. Punt, Miriam Koopman, Anne M. May
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2019.01902

Shifts in the Human Gut Microbiota Structure Caused by Quadruple Helicobacter pylori Eradication Therapy
Cited by: 35
Author(s): Evgenii I. Olekhnovich, Alexander I. Manolov, Andrei E. Samoilov, Nikita Prianichnikov, Maja V. Malakhova, Alexander V. Tyakht, Alexander V. Pavlenko, Vlad V. Babenko, Andrey K. Larin, Boris A. Kovarsky, Elizaveta V. Starikova, Oksana E. Glushchenko, Dilyara Safina, Maria Markelova, Eugenia A. Boulygina, Dilyara Khusnutdinova, Sergey Malanin, С. Р. Абдулхаков, Р. А. Абдулхаков, Tatiana V. Grigoryeva, Elena S. Kostryukova, Vadim M. Govorun, Elena N. Ilina
Software Mentions: 1
Published: about 5 years ago

10.1111/bph.15022

The antiarrhythmic compound efsevin directly modulates voltage‐dependent anion channel 2 by binding to its inner wall and enhancing mitochondrial Ca 2+ uptake
Cited by: 15
Author(s): Fabiola Wilting, R. Kopp, Philip A. Gurnev, Anna Schedel, Nathan J. Dupper, Ohyun Kwon, Annette Nicke, Thomas Gudermann, Johann Schredelseker
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2105-5-171

Cited by: 9
Author(s): Chunlin Wang, Elliot J. Lefkowitz
Software Mentions: 1
Published: over 20 years ago

Ecosyste.ms: Papers

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