pypi: EMIRGE | Projects | Ecosyste.ms: Papers

10.1093/bioinformatics/btaa177

Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Cited by: 11
Author(s): Yaxin Xue, Anders Lanzén, Inge Jonassen
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2015.00277

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust
Cited by: 44
Author(s): Ulisses Nunes da Rocha, Hinsby Cadillo‐Quiroz, Ulaş Karaöz, Lara Rajeev, Niels Klitgord, Sean Dunn, Viet Truong, Mayra Buenrostro, Benjamin P. Bowen, Ferrán García-Pichel, Aindrila Mukhopadhyay, Trent Northen, Eoin L. Brodie
Software Mentions: 6
Published: over 9 years ago

10.3389/fmicb.2019.01347

Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture
Cited by: 194
Author(s): Chrats Melkonian, Willi Gottstein, Sonja Blasche, Yongkyu Kim, Martin Abel-Kistrup, Hentie Swiegers, Sofie Saerens, Nathalia Edwards, Kiran R. Patil, Bas Teusink, Douwe Molenaar
Software Mentions: 6
Published: about 5 years ago

10.7717/peerj.6174

Kelpie: generating full-length ‘amplicons’ from whole-metagenome datasets
Cited by: 9
Author(s): Paul Greenfield, Nai Tran‐Dinh, David J. Midgley
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-017-16375-5

Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico
Cited by: 45
Author(s): Adrien Vigneron, Eric Alsop, Perrine Cruaud, Gwenaelle Philibert, Benjamin L. King, Leslie Baksmaty, D. A. Lavallée, Bart P. Lomans, Nikos C. Kyrpides, Ian M. Head, Nicolas Tsesmetzis
Software Mentions: 5
Published: almost 7 years ago

10.1093/femsec/fiaa016

Total RNA sequencing reveals multilevel microbial community changes and functional responses to wood ash application in agricultural and forest soil
Cited by: 25
Author(s): Toke Bang‐Andreasen, Muhammad Zohaib Anwar, Anders Lanzén, Rasmus Kjøller, Regin Rønn, Flemming Ekelund, Carsten Suhr Jacobsen
Software Mentions: 5
Published: over 4 years ago

10.1128/mBio.00201-16

Status of the Archaeal and Bacterial Census: an Update
Cited by: 117
Author(s): Patrick D. Schloss, R. Girard, Thomas Martin, Joshua Edwards, J. Cameron Thrash
Software Mentions: 5
Published: about 8 years ago

10.1038/s41396-018-0263-1

In situ development of a methanotrophic microbiome in deep-sea sediments
Cited by: 56
Author(s): S. Emil Ruff, Janine Felden, Harald R. Gruber‐Vodicka, Yann Marcon, Katrin Knittel, Alban Ramette, Antje Boetius
Software Mentions: 5
Published: about 6 years ago

10.1186/s40168-017-0392-1

Metabolic capability and in situ activity of microorganisms in an oil reservoir
Cited by: 61
Author(s): Yi Fan Liu, Daniela Domingos Galzerani, Serge Maurice Mbadinga, Livia S. Zaramela, Ji Dong Gu, Bo Zhong Mu, Karsten Zengler
Software Mentions: 5
Published: over 6 years ago

10.1186/s40168-021-01090-1

Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs
Cited by: 16
Author(s): Chanenath Sriaporn, Kathleen A. Campbell, Martin J. Van Kranendonk, Kim M. Handley
Software Mentions: 5
Published: over 3 years ago

10.1038/s41396-020-0676-5

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium
Cited by: 27
Author(s): Hwee Sze Tee, David W. Waite, Leo S. Payne, Martin Middleditch, Susie Wood, Kim M. Handley
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0174930

Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater
Cited by: 24
Author(s): William B. Ludington, Thaddeus D. Seher, Olin Applegate, Xunde Li, J.I. Kliegman, Charles Langelier, Edward R. Atwill, Thomas Harter, Joseph L. DeRisi
Software Mentions: 4
Published: over 7 years ago

10.1128/mBio.00815-18

Members of the Genus Methylobacter Are Inferred To Account for the Majority of Aerobic Methane Oxidation in Oxic Soils from a Freshwater Wetland
Cited by: 48
Author(s): Garrett J. Smith, Jordan C. Angle, Lindsey Solden, Mikayla A. Borton, Timothy H. Morin, Rebecca A. Daly, Michael D. Johnston, Kay C. Stefanik, Richard A. Wolfe, Gil Bohrer, Kelly Wrighton
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-20414-0

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies
Cited by: 53
Author(s): Stefano Campanaro, Laura Treu, Panagiotis Kougias, Xinyu Zhu, Irini Angelidaki
Software Mentions: 4
Published: over 6 years ago

10.3390/microorganisms8091350

Metagenomic and Metatranscriptomic Study of Microbial Metal Resistance in an Acidic Pit Lake
Cited by: 14
Author(s): Diana E. Ayala, William D. Burgos, Javier Sánchez España, Estelle Couradeau, Carmen Falagán, Jennifer L. Macalady
Software Mentions: 4
Published: about 4 years ago

10.3390/v11060484

Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
Cited by: 24
Author(s): René Kallies, Martin Hölzer, Rodolfo Brizola Toscan, Ulisses Nunes da Rocha, John C. Anders, Antonis Chatzinotas
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2016.00603

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity
Cited by: 22
Author(s): Beverly E. Flood, Palmer Fliss, Daniel S. Jones, Gregory J. Dick, Sunit Jain, Anne‐Kristin Kaster, Matthias Winkel, Marc Mußmann, Jake V. Bailey
Software Mentions: 4
Published: over 8 years ago

10.1186/s12866-021-02230-1

A synbiotic intervention modulates meta-omics signatures of gut redox potential and acidity in elective caesarean born infants
Cited by: 12
Author(s): Christophe Lay, Collins Wenhan Chu, Rikky W. Purbojati, Enzo Acerbi, Daniela I. Drautz–Moses, Paola Flórez de Sessions, Jié Song, Eliza Xin Pei Ho, Yee Jiun Kok, Xinyan Bi, Shuwen Chen, Shi Ya Mak, Mei Chien Chua, Angela Goh, Wen Chin Chiang, Rajeshwar Rao, Surasith Chaithongwongwatthana, Nipon Khemapech, Voranush Chongsrisawat, Rocı́o Martı́n, Yanqing Koh, Sachin R. Lohar, Ivan Chin Hin Tan, Wong Anng Anng, Jie Chen, Nana Bartke, Kaouther Ben-Amor, Ingrid B. Renes, Fiona Wong, Guus Roeselers, Ying Swan Ho, Martin L. Hibberd, Stephan C. Schuster, Jan Knol
Software Mentions: 4
Published: about 3 years ago

10.1186/2049-2618-2-1

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants
Cited by: 314
Author(s): Brandon Brooks, Brian Firek, Christopher S. Miller, Itai Sharon, Brian C. Thomas, Robyn Baker, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 4
Published: over 10 years ago

10.1186/s40168-021-01145-3

Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling
Cited by: 19
Author(s): Hwee Sze Tee, David W. Waite, Gavin Lear, Kim M. Handley
Software Mentions: 4
Published: almost 3 years ago

10.1371/journal.pone.0157046

Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules
Cited by: 29
Author(s): James E. McDonald, Niels Larsen, Andrea Pennington, John Connolly, Corrin Wallis, David J. Rooks, Neil Hall, Alan J. McCarthy, Heather E. Allison
Software Mentions: 3
Published: over 8 years ago

10.1111/1462-2920.14788

Metatranscriptomic and metabolite profiling reveals vertical heterogeneity within a Zygnema green algal mat from Svalbard (High Arctic)
Cited by: 25
Author(s): Martin Rippin, Martina Pichrtová, Erwann Arc, Ilse Kranner, Burkhard Becker, Andreas Holzinger
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0216330

Microbiome in the hair follicle of androgenetic alopecia patients
Cited by: 34
Author(s): Brian Ho, Eliza Xin Pei Ho, Collins Wenhan Chu, Srinivas Ramasamy, Mei Bigliardi-Qi, Paola Flórez de Sessions, Paul L. Bigliardi
Software Mentions: 3
Published: over 5 years ago

10.7717/peerj.3134

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
Cited by: 44
Author(s): Sean P. Jungbluth, Tijana Glavina del Rio, Susannah G. Tringe, Ramunas Stepanauskas, Michael S. Rappé
Software Mentions: 3
Published: over 7 years ago

10.1128/mSphereDirect.00011-19

Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions
Cited by: 27
Author(s): Ruben Props, Pieter Monsieurs, Peter Vandamme, Natalie Leys, Vincent J. Denef, Nico Boon
Software Mentions: 3
Published: over 5 years ago

10.3390/biom11070999

Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization
Cited by: 3
Author(s): Helena Torrell, Adrià Ceretó-Massagué, Polina Kazakova, Lorena García, Hector H. Palacios, Núria Canela
Software Mentions: 3
Published: about 3 years ago

10.1186/gb-2011-12-5-r44

EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data
Cited by: 309
Author(s): Christopher S. Miller, Brett J. Baker, Brian C. Thomas, Steven W. Singer, Jillian F. Banfield
Software Mentions: 3
Published: over 13 years ago

10.3389/fmicb.2020.622824

Genomic Insights Into the Lifestyles of Thaumarchaeota Inside Sponges
Cited by: 11
Author(s): Markus Haber, Ilia Burgsdorf, Kim M. Handley, Maxim Rubin‐Blum, Laura Steindler
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2017.00472

Untangling Genomes of Novel Planctomycetal and Verrucomicrobial Species from Monterey Bay Kelp Forest Metagenomes by Refined Binning
Cited by: 47
Author(s): John Vollmers, Martinique Frentrup, Patrick Rast, Christian Jogler, Anne‐Kristin Kaster
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-1107

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms
Cited by: 60
Author(s): Nicholas B. Justice, Anders Norman, Christopher T. Brown, Anil K. Singh, Brian C. Thomas, Jillian F. Banfield
Software Mentions: 3
Published: over 10 years ago

10.1128/mSphereDirect.00257-17

Sulfide Generation by Dominant Halanaerobium Microorganisms in Hydraulically Fractured Shales
Cited by: 52
Author(s): Anne E. Booker, Mikayla A. Borton, Rebecca A. Daly, Susan A. Welch, Carrie Nicora, David Hoyt, Tom Wilson, Samuel O. Purvine, Richard A. Wolfe, Shikha Sharma, Paula J. Mouser, David R. Cole, Mary Lipton, Kelly Wrighton, Michael J. Wilkins
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0201768

Human pharyngeal microbiota in age-related macular degeneration
Cited by: 23
Author(s): Eliza Xin Pei Ho, Chui Ming Gemmy Cheung, Shuzhen Sim, Collins Wenhan Chu, Andreas Wilm, Clarabelle Bitong Lin, Ranjana Mathur, Doric Wong, Choi Mun Chan, Mayuri Bhagarva, Augustinus Laude, Tock Han Lim, Tien Yin Wong, Ching‐Yu Cheng, Sonia Dávila, Martin L. Hibberd
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2017.02036

Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems
Cited by: 13
Author(s): Ya Ping Zhang, Masaaki Kitajima, Andrew J. Whittle, Wen Tso Liu
Software Mentions: 2
Published: almost 7 years ago

10.1186/1471-2180-13-259

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains
Cited by: 10
Author(s): Hannah M. Doll, David Armitage, Rebecca A. Daly, Joanne B. Emerson, Daniela S. Aliaga Goltsman, Alexis P Yelton, Jennifer Kerekes, Mary K. Firestone, Matthew D. Potts
Software Mentions: 2
Published: over 11 years ago

10.1186/s12866-015-0615-1

Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads
Cited by: 21
Author(s): Vímac Nolla-Ardèvol, Miriam Peces, Marc Strous, Halina E. Tegetmeyer
Software Mentions: 2
Published: almost 9 years ago

10.1186/s40168-018-0546-9

Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil
Cited by: 34
Author(s): Jingjing Peng, Carl‐Eric Wegner, Qicheng Bei, Pengfei Liu, Werner Liesack
Software Mentions: 2
Published: about 6 years ago

10.1186/s40168-020-00851-8

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys
Cited by: 53
Author(s): Jialin Hou, Stefan M. Sievert, Yinzhao Wang, Jeffrey S. Seewald, Vengadesh Perumal Natarajan, Fengping Wang, Xiang Xiao
Software Mentions: 2
Published: about 4 years ago

10.1186/2049-2618-1-30

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life
Cited by: 52
Author(s): Christopher T. Brown, Itai Sharon, Brian C. Thomas, Cindy J. Castelle, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 2
Published: almost 11 years ago

10.1186/s40168-016-0162-5

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains
Cited by: 54
Author(s): Yemin Lan, Gail Rosen, Ruth Hershberg
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0151214

Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome
Cited by: 20
Author(s): Daniel E. Ross, C. W. Marshall, Harold D. May, R. Sean Norman
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0060811

Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences
Cited by: 88
Author(s): Swee Hoe Ong, Vinutha Uppoor Kukkillaya, Andreas Wilm, Christophe Lay, Eliza Xin Pei Ho, Louie Low, Martin L. Hibberd, Niranjan Nagarajan
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0174609

MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool
Cited by: 7
Author(s): Bin Zou, JieFu Li, Quan Zhou, Zhe‐Xue Quan
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0056018

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments
Cited by: 115
Author(s): Christopher S. Miller, Kim M. Handley, Kelly Wrighton, Kyle R. Frischkorn, Brian C. Thomas, Jillian F. Banfield
Software Mentions: 2
Published: over 11 years ago

10.1016/j.ebiom.2016.04.034

Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma
Cited by: 87
Author(s): Kern Rei Chng, Sock Hoai Chan, Amanda Hui Qi Ng, Chenhao Li, Apinya Jusakul, Denis Bertrand, Andreas Wilm, Su Pin Choo, Damien Meng Yew Tan, Kiat Hon Lim, Roy Soetinko, Choon Kiat Ong, Dan G. Duda, Simona Dima, Irinel Popescu, Chaisiri Wongkham, Feng Zhu, Khay Guan Yeoh, Bin Tean Teh, Puangrat Yongvanit, Sopit Wongkham, Vajaraphongsa Bhudhisawasdi, Narong Khuntikeo, Patrick Tan, Chawalit Pairojkul, Joanne Ngeow, Niranjan Nagarajan
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2015.00329

riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics
Cited by: 15
Author(s): Matteo Ramazzotti, Luisa Berná, Claudio Donati, Duccio Cavalieri
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2016.00301

Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments
Cited by: 45
Author(s): Alexander Crits-Christoph, Courtney K. Robinson, Bing Ma, Jacques Ravel, Jacek Wierzchos, Carmen Ascaso, Octavio Artieda, Virginia Souza-Egipsy, María Cristina Casero, Jocelyne DiRuggiero
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2016.00598

Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria
Cited by: 35
Author(s): Trinity L. Hamilton, Roderick J. Bovee, Sarah R. Sattin, Wiebke Mohr, William P. Gilhooly, Timothy W. Lyons, Ann Pearson, Jennifer L. Macalady
Software Mentions: 2
Published: over 8 years ago

10.3389/fmicb.2018.02646

Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin
Cited by: 26
Author(s): Morgan V. Evans, Jenny Panescu, Andrea Hanson, Susan A. Welch, J. Sheets, Nicholas Nastasi, Rebecca A. Daly, David R. Cole, Thomas H. Darrah, Michael J. Wilkins, Kelly Wrighton, Paula J. Mouser
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2017.00099

Metabolomic and Metagenomic Analysis of Two Crude Oil Production Pipelines Experiencing Differential Rates of Corrosion
Cited by: 34
Author(s): Vincent Bonifay, Boris Wawrik, Jan Sunner, Emily C. Snodgrass, Egemen Aydın, Kathleen E. Duncan, Amy V. Callaghan, Athenia L. Oldham, Turid Liengen, Iwona B. Beech
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2018.01235

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies
Cited by: 13
Author(s): Maggie C. Y. Lau, Rachel L. Harris, Youmi Oh, Min Joo Yi, Aida Behmard, Tullis C. Onstott
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2017.00791

Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin
Cited by: 28
Author(s): Allison Sharrar, Beverly E. Flood, Jake V. Bailey, Daniel S. Jones, Bopaiah A. Biddanda, Steven A. Ruberg, Daniel N. Marcus, Gregory J. Dick
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2016.01521

Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes
Cited by: 79
Author(s): María-Eugenia DeCastro, Esther Rodrı́guez-Belmonte, María-Isabel González-Siso
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2015.00364

Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange
Cited by: 104
Author(s): Cara L. Fiore, Micheline S. Labrie, Jessica K. Jarett, Michael P. Lesser
Software Mentions: 2
Published: over 9 years ago

10.1038/srep32165

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon
Cited by: 67
Author(s): Riccardo Rosselli, Ottavia Romoli, Nicola Vitulo, Alessandro Vezzi, Stefano Campanaro, Fabio De Pascale, Riccardo Schiavon, Maurizio Tiarca, Fabio Poletto, Giuseppe Concheri, Giorgio Valle, Andrea Squartini
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-019-39699-w

New ecosystems in the deep subsurface follow the flow of water driven by geological activity
Cited by: 13
Author(s): Gaëtan Borgonie, Cara Magnabosco, Antonio García-Moyano, Borja Linage-Alvarez, Abidemi Oluranti Ojo, Lee Freese, C. Van Jaarsveld, Carina van Rooyen, Olukayode Kuloyo, Errol D. Cason, Jan‐G Vermeulen, Colette Pienaar, Esta van Heerden, Barbara Sherwood Lollar, Tullis C. Onstott, Scott O. C. Mundle
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-020-64904-6

Novel clostridial lineages recovered from metagenomes of a hot oil reservoir
Cited by: 12
Author(s): Glenn D. Christman, Rosa León‐Zayas, Rui Zhao, Zarath M. Summers, Jennifer F. Biddle
Software Mentions: 2
Published: over 4 years ago

10.1128/mSphere.00613-19

Genome-Resolved Metagenomics Extends the Environmental Distribution of the Verrucomicrobia Phylum to the Deep Terrestrial Subsurface
Cited by: 33
Author(s): Sophie L. Nixon, Rebecca A. Daly, Mikayla A. Borton, Lindsey Solden, Susan A. Welch, David R. Cole, Paula J. Mouser, Michael J. Wilkins, Kelly Wrighton
Software Mentions: 2
Published: almost 5 years ago

10.1128/mSystems.00169-19

Time Series Genome-Centric Analysis Unveils Bacterial Response to Operational Disturbance in Activated Sludge
Cited by: 22
Author(s): Maidelyn Díaz Pérez, Leandro D. Guerrero, Esteban Orellana, Eva Lucía Margarita Figuerola, Leonardo Erijman
Software Mentions: 2
Published: about 5 years ago

10.3389/fmicb.2014.00756

Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem
Cited by: 56
Author(s): Trinity L. Hamilton, Daniel S. Jones, Irene Schaperdoth, Jennifer L. Macalady
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0057819

Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface
Cited by: 19
Author(s): Michael J. Wilkins, Kelly Wrighton, Carrie Nicora, Kenneth H. Williams, Lee Ann McCue, Kim M. Handley, Christopher S. Miller, Ludovic Giloteaux, Alison P. Montgomery, Derek R. Lovley, Jillian F. Banfield, Philip E. Long, Mary Lipton
Software Mentions: 1
Published: over 11 years ago

10.3389/fmicb.2014.00231

Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat
Cited by: 37
Author(s): Anna Hanke, Emmo Hamann, Ritin Sharma, Jeanine S. Geelhoed, Theresa Hargesheimer, Beate Kraft, Volker Meyer, Sabine Lenk, Harald Osmers, Rong Yang Wu, Kofi A. A. Makinwa, Robert L. Hettich, Jillian F. Banfield, Halina E. Tegetmeyer, Marc Strous
Software Mentions: 1
Published: over 10 years ago

10.1186/s40168-015-0093-6

Xander: employing a novel method for efficient gene-targeted metagenomic assembly
Cited by: 80
Author(s): Qiong Wang, Jordan A. Fish, Mariah Gilman, Yanni Sun, C. Titus Brown, James M. Tiedje, James R. Cole
Software Mentions: 1
Published: about 9 years ago

10.1264/jsme2.ME20016

Viral RNA Genomes Identified from Marine Macroalgae and a Diatom
Cited by: 14
Author(s): Yuto Chiba, Yuji Tomaru, Hiromori Shimabukuro, Kei Kimura, Miho Hirai, Yoshihiro Takaki, Daisuke Hagiwara, Takuro Nunoura, Syun-ichi Urayama
Software Mentions: 1
Published: over 4 years ago

10.1186/s40168-018-0442-3

Hybridization capture reveals microbial diversity missed using current profiling methods
Cited by: 28
Author(s): Cyrielle Gasc, Pierre Peyret
Software Mentions: 1
Published: over 6 years ago

10.1128/mBio.01792-18

Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere
Cited by: 31
Author(s): Margarita López-Fernández, Domenico Simone, Xiaofen Wu, Lucile Soler, Emelie Nilsson, Karin Holmfeldt, Henrik Lantz, Stefan Bertilsson, Mark Dopson
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2020.570714

Methanogens Within a High Salinity Oil Reservoir From the Gulf of Mexico
Cited by: 5
Author(s): Glenn D. Christman, Rosa León‐Zayas, Zarath M. Summers, Jennifer F. Biddle
Software Mentions: 1
Published: about 4 years ago

10.1186/s13068-016-0524-z

Cellular adhesiveness and cellulolytic capacity in Anaerolineae revealed by omics-based genome interpretation
Cited by: 172
Author(s): Yu Xia, Yübo Wang, Yi Wang, Francis Y. L. Chin, Tong Zhang
Software Mentions: 1
Published: over 8 years ago

10.1128/mSphere.00529-18

Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing
Cited by: 13
Author(s): Andre Mu, Jason C Kwong, Nicole Isles, Anders Gonçalves da Silva, Mark B. Schultz, Susan A Ballard, Courtney R Lane, Glen P. Carter, Deborah A. Williamson, Torsten Seemann, Timothy P. Stinear, Benjamin P Howden
Software Mentions: 1
Published: over 5 years ago

10.3390/genes10030220

Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome
Cited by: 19
Author(s): Gherman Uritskiy, Jocelyne DiRuggiero
Software Mentions: 1
Published: over 5 years ago

10.1128/genomeA.01183-13

Genome Sequence of Youngiibacter fragilis, the Type Strain of the Genus Youngiibacter
Cited by: 4
Author(s): Colin B. Wawrik, Amy V. Callaghan, Blake W. Stamps, Boris Wawrik
Software Mentions: 1
Published: over 10 years ago

10.1128/genomeA.00291-15

Draft Genomes of Two Sordariomycete Fungi That Produce Novel Secondary Metabolites
Cited by: 5
Author(s): Blake W. Stamps, Lin Du, Carter A. Mitchell, Robert H. Cichecwicz, Bradley S. Stevenson
Software Mentions: 1
Published: over 9 years ago

10.1186/2049-2618-1-22

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling
Cited by: 423
Author(s): Laura Hug, Cindy J. Castelle, Kelly Wrighton, Brian C. Thomas, Itai Sharon, Kyle R. Frischkorn, Kenneth H. Williams, Susannah G. Tringe, Jillian F. Banfield
Software Mentions: 1
Published: about 11 years ago

10.1098/rspb.2017.0764

Specificity in diversity: single origin of a widespread ciliate-bacteria symbiosis
Cited by: 33
Author(s): Brandon K. B. Seah, Thomas Schwaha, Jean-Marie Volland, Bruno Huettel, Nicole Dubilier, Harald R. Gruber‐Vodicka
Software Mentions: 1
Published: about 7 years ago

10.1038/srep22541

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge
Cited by: 55
Author(s): Julie Meyer, Ulrike Jaekel, Benjamin J. Tully, Brian T. Glazer, C. G. Wheat, Hsiang Ju Lin, Chia Chien Hsieh, James P. Cowen, S. Hulme, Peter R. Girguis, Julie A. Huber
Software Mentions: 1
Published: over 8 years ago

10.1186/s13068-018-1136-6

Bioreactor microbial ecosystems with differentiated methanogenic phenol biodegradation and competitive metabolic pathways unraveled with genome-resolved metagenomics
Cited by: 15
Author(s): Feng Ju, Yübo Wang, Tong Zhang
Software Mentions: 1
Published: over 6 years ago

10.1038/srep34362

Single sample resolution of rare microbial dark matter in a marine invertebrate metagenome
Cited by: 33
Author(s): Ian Miller, T Weyna, Stephen S. Fong, Grace Lim-Fong, Jason C. Kwan
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-017-08877-z

Metabolic Reconstruction and Modeling Microbial Electrosynthesis
Cited by: 85
Author(s): C. W. Marshall, Daniel E. Ross, Kim M. Handley, Pamela Weisenhorn, Janaka N. Edirisinghe, Christopher S. Henry, Jack A. Gilbert, Harold D. May, R. Sean Norman
Software Mentions: 1
Published: about 7 years ago

10.1186/s40168-019-0663-0

Mobile antibiotic resistome in wastewater treatment plants revealed by Nanopore metagenomic sequencing
Cited by: 211
Author(s): Ying Che, Yu Xia, Lei Liu, An Dong Li, Yu Yang, Tong Zhang
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-017-17351-9

Analysis of the cervical microbiome and potential biomarkers from postpartum HIV-positive women displaying cervical intraepithelial lesions
Cited by: 30
Author(s): Gislaine Curty, Raquel L. Costa, Juliana D. Siqueira, Angela I. Meyrelles, Elizabeth S. Machado, Esmeralda A. Soares, Marcelo A. Soares
Software Mentions: 1
Published: almost 7 years ago

10.1264/jsme2.ME15171

FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance
Cited by: 62
Author(s): Syun-ichi Urayama, Yoshihiro Takaki, Takuro Nunoura
Software Mentions: 1
Published: over 8 years ago

10.1093/dnares/dst044

Diet Alters Both the Structure and Taxonomy of the Ovine Gut Microbial Ecosystem
Cited by: 35
Author(s): Melinda J Ellison, Gavin C. Conant, Rebecca Cockrum, Kathy J. Austin, Huan Truong, Michela Becchi, W. R. Lamberson, K. M. Cammack
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0161506

Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal
Cited by: 9
Author(s): Yanping Mao, Zhiping Wang, Liguan Li, Xiaotao Jiang, Xuxiang Zhang, Hongqiang Ren, Tong Zhang
Software Mentions: 1
Published: about 8 years ago

10.1186/s12864-016-3293-y

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis
Cited by: 37
Author(s): Juliane Wippler, Manuel Kleiner, Christian Lott, Alexander Gruhl, Paul E. Abraham, Richard J. Giannone, J. C. Young, Robert L. Hettich, Nicole Dubilier
Software Mentions: 1
Published: almost 8 years ago

10.1155/2013/370871

Virus-Host and CRISPR Dynamics in Archaea-Dominated Hypersaline Lake Tyrrell, Victoria, Australia
Cited by: 65
Author(s): Joanne B. Emerson, Karen Andrade, Brian C. Thomas, Anders Norman, Eric E. Allen, Karla B. Heidelberg, Jillian F. Banfield
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-019-46663-1

Paired RNA Radiocarbon and Sequencing Analyses Indicate the Importance of Autotrophy in a Shallow Alluvial Aquifer
Cited by: 1
Author(s): Brian J. Mailloux, Carol H. Kim, Tess Kichuk, Khue Nguyen, Chandler Precht, Wang Shi, Talia Jewell, Ulaş Karaöz, Eoin L. Brodie, Kenneth H. Williams, Harry R. Beller, Bruce A. Buchholz
Software Mentions: 1
Published: about 5 years ago

10.1186/s12859-017-1825-3

MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs
Cited by: 9
Author(s): Dinghua Li, Yukun Huang, Chi-Ming Leung, Ruibang Luo, Hing-Fung Ting, Tak Wah Lam
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0068465

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass
Cited by: 55
Author(s): Patrik D’haeseleer, John M. Gladden, Martin Allgaier, Patrick Chain, Susannah G. Tringe, Stephanie Malfatti, Joshua T. Aldrich, Carrie Nicora, Eric Robinson, Ljiljana Paša‐Tolić, Philip Hugenholtz, Blake A. Simmons, Steven W. Singer
Software Mentions: 1
Published: about 11 years ago

10.3389/fmicb.2020.561344

Diverged and Active Partitiviruses in Lichen
Cited by: 8
Author(s): Syun-ichi Urayama, Nobutaka Doi, Fumie Kondo, Yuto Chiba, Yoshihiro Takaki, Miho Hirai, Yasutaka Minegishi, Daisuke Hagiwara, Takuro Nunoura
Software Mentions: 1
Published: almost 4 years ago

10.1038/s41598-021-83416-5

Transition from unclassified Ktedonobacterales to Actinobacteria during amorphous silica precipitation in a quartzite cave environment
Cited by: 10
Author(s): Daniele Ghezzi, Francesco Sauro, Andrea Columbu, Cristina Carbone, Pei‐Ying Hong, Freddy Vergara, Jo De Waele, Martina Cappelletti
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2017.01023

Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags
Cited by: 28
Author(s): Carl‐Eric Wegner, Werner Liesack
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2015.01461

Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities
Cited by: 13
Author(s): Anna Hanke, Jasmine S. Berg, Theresa Hargesheimer, Halina E. Tegetmeyer, Christine E. Sharp, Marc Strous
Software Mentions: 1
Published: over 8 years ago

10.1264/jsme2.ME19132

dsRNA-seq Reveals Novel RNA Virus and Virus-Like Putative Complete Genome Sequences from Hymeniacidon sp. Sponge
Cited by: 17
Author(s): Syun-ichi Urayama, Yoshihiro Takaki, Daisuke Hagiwara, Takuro Nunoura
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pone.0039948

Reconstruction of Ribosomal RNA Genes from Metagenomic Data
Cited by: 52
Author(s): Lu Fan, Kerensa McElroy, Torsten Thomas
Software Mentions: 1
Published: about 12 years ago

10.3389/fmicb.2019.00426

An Ionic Limit to Life in the Deep Subsurface
Cited by: 21
Author(s): Samuel J. Payler, Jennifer F. Biddle, Barbara Sherwood Lollar, Mark Fox-Powell, Thomas W. D. Edwards, Bryne T. Ngwenya, S. M. Paling, Charles S. Cockell
Software Mentions: 1
Published: over 5 years ago

Projects: pypi: EMIRGE

Papers Mentioning EMIRGE 94