pypi: eggnog-mapper | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1009065

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study
Cited by: 49
Author(s): Marco Galardini, Olivier Clermont, Agnès Baron, Bede P. Busby, Sara Dion, Sören Schubert, Pedro Beltrão, Erick Denamur
Software Mentions: 20
Published: about 4 years ago

10.1128/mBio.02275-17

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity
Cited by: 99
Author(s): Benjamin Schwessinger, Jana Sperschneider, William S. Cuddy, Diana Garnica, Marisa E. Miller, Jennifer Taylor, Peter N. Dodds, Melania Figueroa, Robert Park, John P. Rathjen
Software Mentions: 13
Published: over 6 years ago

10.1371/journal.pcbi.1008716

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)
Cited by: 14
Author(s): Renaud Van Damme, Martin Hölzer, Adrian Viehweger, Bettina Müller, Erik Bongcam‐Rudloff, Christian Brandt
Software Mentions: 8
Published: almost 4 years ago

10.3389/fgene.2020.568223

Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria
Cited by: 32
Author(s): Jaime Alcorta, Tomás Alarcón-Schumacher, Óscar Rivero Salgado, Beatriz Dı́ez
Software Mentions: 8
Published: about 4 years ago

10.1186/s40168-019-0684-8

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
Cited by: 38
Author(s): Luís Pedro Coelho, Renato Alves, Paulo P. Monteiro, Jaime Huerta-Cepas, Ana T. Freitas, Peer Bork
Software Mentions: 7
Published: over 5 years ago

10.3389/fmicb.2020.560336

Functional Gene Expression in Shark Bay Hypersaline Microbial Mats: Adaptive Responses
Cited by: 15
Author(s): Matthew A. Campbell, Kliti Grice, Pieter T. Visscher, Therese Morris, Hon Lun Wong, Richard Allen White, Brendan P. Burns, Marco J. L. Coolen
Software Mentions: 7
Published: about 4 years ago

10.1093/gbe/evaa071

Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat
Cited by: 30
Author(s): Benjamin Schwessinger, Yan Jun Chen, Richard Tien, Josef Korbinian Vogt, Jana Sperschneider, Ramawatar Nagar, Mark McMullan, Thomas Sicheritz-Pontén, Chris K. Sørensen, Mogens S. Hovmøller, John P. Rathjen, Annemarie Fejer Justesen
Software Mentions: 6
Published: over 4 years ago

10.3390/microorganisms8081225

Lactobacillus Mucosae Strain Promoted by a High-Fiber Diet in Genetic Obese Child Alleviates Lipid Metabolism and Modifies Gut Microbiota in ApoE-/- Mice on a Western Diet
Cited by: 19
Author(s): Tianyi Jiang, Huan Wu, Xin Yang, Yue Li, Ziyi Zhang, Feng Chen, Liping Zhao, Chenhong Zhang
Software Mentions: 6
Published: over 4 years ago

10.1038/s42003-020-01214-7

Genome sequence of segmented filamentous bacteria present in the human intestine
Cited by: 20
Author(s): Hans Jonsson, Luisa W. Hugerth, John Sundh, E. Lundin, Anders F. Andersson
Software Mentions: 4
Published: about 4 years ago

10.1186/s12864-020-06899-y

The wheat pathogen Zymoseptoria tritici senses and responds to different wavelengths of light
Cited by: 7
Author(s): Cassandra B. McCorison, Stephen B. Goodwin
Software Mentions: 4
Published: over 4 years ago

10.1186/s40168-021-01016-x

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics
Cited by: 27
Author(s): Yuan Lin, Liye Wang, Ke Xu, Kan Li, Hongqiang Ren
Software Mentions: 4
Published: over 3 years ago

10.3390/microorganisms7120635

Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses
Cited by: 12
Author(s): Anoop Alex, Agostinho Antunes
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12864-020-06871-w

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria
Cited by: 29
Author(s): Alice Feurtey, Cécile Lorrain, Daniel Croll, Christoph Eschenbrenner, Michael Freitag, Michael Habig, Janine Haueisen, Mareike Möller, Klaas Schotanus, Eva H. Stukenbrock
Software Mentions: 4
Published: about 4 years ago

10.7717/peerj.9646

Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance
Cited by: 19
Author(s): Tanaporn Uengwetwanit, Umaporn Uawisetwathana, Sopacha Arayamethakorn, Juthatip Khudet, Sage Chaiyapechara, Nitsara Karoonuthaisiri, Wanilada Rungrassamee
Software Mentions: 4
Published: over 4 years ago

10.3389/fmicb.2021.674639

Clostridium cellulovorans Proteomic Responses to Butanol Stress
Cited by: 4
Author(s): Paolo Costa, Giulia Usai, Angela Re, Marcello Manfredi, Giuseppe Mannino, Cinzia M. Bertea, Enrica Pessione, Roberto Mazzoli
Software Mentions: 3
Published: over 3 years ago

10.1099/mgen.0.000558

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)
Cited by: 7
Author(s): Carla Perez-Mon, Weihong Qi, Surendra Vikram, Aline Frossard, Thulani P. Makhalanyane, Don A. Cowan, Beat Frey
Software Mentions: 3
Published: over 3 years ago

10.3389/fmicb.2017.02485

Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors
Cited by: 66
Author(s): Raymond Kiu, Shabhonam Caim, Sarah Alexander, Purnima Pachori, Lindsay J. Hall
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12863-021-00981-4

Transcriptome profiling provides insights into the molecular mechanisms of maize kernel and silk development
Cited by: 0
Author(s): Ting Li, Yapeng Wang, Ying Shi, Xiaonan Gou, Bingpeng Yang, Jianzhou Qu, Xinghua Zhang, Jiquan Xue, Shutu Xu
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-019-54488-1

The green peach aphid gut contains host plant microRNAs identified by comprehensive annotation of Brassica oleracea small RNA data
Cited by: 8
Author(s): Max C. Thompson, Honglin Feng, Stefan Wuchty, Alex C. C. Wilson
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-020-6740-8

Genomic characterization of Lactobacillus fermentum DSM 20052
Cited by: 13
Author(s): Katelyn Brandt, Matthew A. Nethery, Sarah O’Flaherty, Rodolphe Barrangou
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-018-5302-9

Comparative genomic analysis of Parageobacillus thermoglucosidasius strains with distinct hydrogenogenic capacities
Cited by: 18
Author(s): Teresa Mohr, Habibu Aliyu, Raphael Kuchlin, Michaela Zwick, Don A. Cowan, Anke Neumann, Pieter De Maayer
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-020-6735-5

Genomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements
Cited by: 17
Author(s): Cynthia Maria Chibani, Olivia Roth, Heiko Liesegang, Carolin Charlotte Wendling
Software Mentions: 2
Published: over 4 years ago

10.1186/s12866-020-02027-8

Adaptive response to iterative passages of five Lactobacillus species in simulated vaginal fluid
Cited by: 5
Author(s): Katelyn Brandt, Rodolphe Barrangou
Software Mentions: 2
Published: about 4 years ago

10.1186/s40168-021-01138-2

Disease-induced changes in plant microbiome assembly and functional adaptation
Cited by: 116
Author(s): Min Gao, Chao Xiong, Cheng Gao, Clement K. M. Tsui, Mengmeng Wang, Xin Zhou, Aimin Zhang, Lei Cai
Software Mentions: 2
Published: about 3 years ago

10.3390/v11050419

Revisiting the Role of Transcription Factors in Coordinating the Defense Response Against Citrus Bark Cracking Viroid Infection in Commercial Hop (Humulus Lupulus L.)
Cited by: 20
Author(s): Vishnu Sukumari Nath, Ajay Kumar Mishra, Atul Kumar, J. Matoušek, Jernej Jakše
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pntd.0007270

Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics
Cited by: 366
Author(s): Antony T. Vincent, Olivier Schiettekatte, Cyrille Goarant, Vasantha Kumari Neela, Ève Bernet, Roman Thibeaux, Nabilah İsmail, Mohd Khairul Nizam Mohd Khalid, Fairuz Amran, Toshiyuki Masuzawa, Ryo Nakao, Anissa Amara Korba, Pascale Bourhy, Frédéric J. Veyrier, Mathieu Picardeau
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.00747

Identification of Ear Morphology Genes in Maize (Zea mays L.) Using Selective Sweeps and Association Mapping
Cited by: 7
Author(s): Ting Li, Jianzhou Qu, Xiaokang Tian, Yonghui Lao, Ningning Wang, Yahui Wang, Yinchuan Hao, Xinghua Zhang, Jiquan Xue, Shutu Xu
Software Mentions: 2
Published: over 4 years ago

10.3389/fmicb.2020.594524

The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria
Cited by: 26
Author(s): Sofia Esquivel-Elizondo, Caner Bağcı, Monika Temovska, Byoung Seung Jeon, Irina Bessarab, Rohan B. H. Williams, Daniel H. Huson, Largus T. Angenent
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-020-75728-9

Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries
Cited by: 22
Author(s): Phuong T. N. Hoang, Anne Fiebig, Petr Novák, Jiří Macas, Hieu X. Cao, Anton Stepanenko, Guimin Chen, Nikolai Borisjuk, Uwe Scholz, Ingo Schubert
Software Mentions: 2
Published: about 4 years ago

10.1128/mSystems.00083-21

Limited and Strain-Specific Transcriptional and Growth Responses to Acquisition of a Multidrug Resistance Plasmid in Genetically Diverse Escherichia coli Lineages
Cited by: 19
Author(s): Steven Dunn, Laura Carrilero, Michael A. Brockhurst, Alan McNally
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.01866

Whole-Genome Sequencing and Bioinformatics Analysis of Apiotrichum mycotoxinivorans: Predicting Putative Zearalenone-Degradation Enzymes
Cited by: 12
Author(s): Junlin Sun, Xia Yan, Dengming Ming
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2019.02916

Comparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species
Cited by: 29
Author(s): Voula Alexandraki, Μαρία Κάζου, Jochen Blom, Bruno Pot, Konstantinos Papadimitriou, Effie Tsakalidou
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-020-07245-y

Genomic analysis of Helicobacter himalayensis sp. nov. isolated from Marmota himalayana
Cited by: 3
Author(s): Shoukui Hu, Niu L, Lei Wu, Xiaoxue Zhu, Yu Cai, Dong Jin, Linlin Yan, Fan Zhao
Software Mentions: 1
Published: about 4 years ago

10.3389/fmolb.2021.703638

Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing
Cited by: 8
Author(s): Yuanfeng Liu, Xiang Li, Yili Yang, Ye Liu, Shijun Wang, Boyang Ji, Yongjun Wei
Software Mentions: 1
Published: over 3 years ago

10.1016/j.cell.2021.01.029

Massive expansion of human gut bacteriophage diversity
Cited by: 286
Author(s): Luis F. Camarillo-Guerrero, Alexandre Almeida, Guillermo Rangel-Piñeros, Alex Bateman, Trevor D. Lawley
Software Mentions: 1
Published: almost 4 years ago

10.1016/j.bioflm.2021.100054

Current production by non-methanotrophic bacteria enriched from an anaerobic methane-oxidizing microbial community
Cited by: 7
Author(s): Stefanie Berger, Dario Rangel Shaw, Tom Berben, Heleen T. Ouboter, Michiel H. in ’t Zandt, Joshua Frank, Joachim Reimann, Mike S. M. Jetten, Cornelia U. Welte
Software Mentions: 1
Published: almost 3 years ago

10.1038/s41396-018-0074-4

Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre
Cited by: 41
Author(s): Daniel K. Olson, Susumu Yoshizawa, Dominique Le Bœuf, Wataru Iwasaki, Edward F. DeLong
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-021-95085-5

De novo transcriptome characterization of Iris atropurpurea (the Royal Iris) and phylogenetic analysis of MADS-box and R2R3-MYB gene families
Cited by: 5
Author(s): Yamit Bar-Lev, Esther Senden, Metsada Pasmanik‐Chor, Yuval Sapir
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2020.01219

Comparative Genomics Uncovers the Genetic Diversity and Characters of Veillonella atypica and Provides Insights Into Its Potential Applications
Cited by: 10
Author(s): Maozhen Han, Gang Liu, Yajun Chen, Dong Wang, Yan Zhang
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2021.672751

Pseudomonas palmensis sp. nov., a Novel Bacterium Isolated From Nicotiana glauca Microbiome: Draft Genome Analysis and Biological Potential for Agriculture
Cited by: 8
Author(s): Enrique Gutierrez‐Albanchez, Ana García‐Villaraco, Jose Antonio Lucas, Ignacio Horche, Beatriz Ramos‐Solano, Francisco Javier Gutiérrez-Mañero
Software Mentions: 1
Published: over 3 years ago

10.3389/fmicb.2021.698069

Genome Sequencing and Comparative Genomics of Indian Isolates of Brucella melitensis
Cited by: 4
Author(s): Kumaragurubaran Karthik, Subbaiyan Anbazhagan, Prasad Thomas, M. Ananda Chitra, Tuticorin Maragatham Alagesan Senthilkumar, R. Sridhar, Gopal Dhinakar Raj
Software Mentions: 1
Published: over 3 years ago

Projects: pypi: eggnog-mapper

Papers Mentioning eggnog-mapper 41