Ecosyste.ms: Papers

10.1080/19490976.2021.1940792

Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections
Cited by: 13
Author(s): Robert Thänert, Anna Thänert, Jocelyn Ou, Adam Bajinting, Carey Ann D. Burnham, Holly J. Engelstad, Maria E. Tecos, I. Malick Ndao, Carla Hall-Moore, Colleen Rouggly-Nickless, Mike A. Carl, Deborah C. Rubin, Nicholas O. Davidson, Phillip I. Tarr, Barbara B. Warner, Gautam Dantas, Brad W. Warner
Software Mentions: 22
Published: almost 4 years ago

10.3389/fgene.2021.719204

RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization
Cited by: 2
Author(s): Zhaoyuan Wei, Jiahe Sun, Qinhui Li, Ting Yao, Haiyue Zeng, Yi Wang
Software Mentions: 16
Published: over 3 years ago

10.1128/mBio.02275-17

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus <i>Puccinia striiformis</i> f. sp. <i>tritici</i> 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

10.1099/mgen.0.000492

Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes
Cited by: 13
Author(s): Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly Yuen, Nadia Warner, Brigid Betz‐Stablein, Fabio Luciani, Peter Revill, Chris M. Brown
Software Mentions: 13
Published: almost 4 years ago

10.1371/journal.pone.0169662

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!
Cited by: 171
Author(s): John Vollmers, Sandra Wiegand, Anne‐Kristin Kaster
Software Mentions: 11
Published: almost 8 years ago

10.3389/fgene.2020.489357

Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results
Cited by: 13
Author(s): Alejandro Abdala Asbun, Marc Besseling, Sergio Balzano, Judith van Bleijswijk, Harry J. Witte, Laura Villanueva, Julia C. Engelmann
Software Mentions: 11
Published: about 4 years ago

10.1111/1755-0998.13219

Genetic structure and insecticide resistance characteristics of fall armyworm populations invading China
Cited by: 103
Author(s): Lei Zhang, Bo Liu, Wengang Zheng, Conghui Liu, Dandan Zhang, Shengyuan Zhao, Zaiyuan Li, Pengjun Xu, Kenneth Wilson, Amy Withers, Christopher M. Jones, Judith A. Smith, Gilson Chipabika, Donald L. Kachigamba, Kiwoong Nam, Emmanuelle d’Alençon, Bei Liu, Xinyue Liang, Minghui Jin, Chao Wu, Swapan Chakrabarty, Xinming Yang, Yuying Jiang, Jie Liu, Xiaolin Liu, Weipeng Quan, Guirong Wang, Wei Fan, Wanqiang Qian, Kongming Wu, Yutao Xiao
Software Mentions: 10
Published: over 4 years ago

10.1038/s41396-020-00862-1

Fungal sporocarps house diverse and host-specific communities of fungicolous fungi
Cited by: 21
Author(s): Sundy Maurice, Gontran Arnault, Jenni Nordén, Synnøve Smebye Botnen, Otto Miettinen, Håvard Kauserud
Software Mentions: 10
Published: almost 4 years ago

10.1111/1755-0998.13266

Chromosome‐level genome assembly of <i>Paralithodes platypus</i> provides insights into evolution and adaptation of king crabs
Cited by: 11
Author(s): Boping Tang, Zhongkai Wang, Qiu-Ning Liu, Zhengfei Wang, Yandong Ren, Huayun Guo, Tingting Qi, Yue‐Tian Li, Huabin Zhang, Senhao Jiang, Baoming Ge, Fujun Xuan, Yue Sun, Shusheng She, Tin Yam Chan, Zhongli Sha, Hui Jiang, Haorong Li, Wei Jiang, Yanli Qin, Kun Wang, Qiang Qiu, Wen Wang, Xinzheng Li, Ngan Kee Ng, Dai-Zhen Zhang, Yongxin Li
Software Mentions: 9
Published: about 4 years ago

10.1002/aps3.11344

A basic dd <scp>RAD</scp> seq two‐enzyme protocol performs well with herbarium and silica‐dried tissues across four genera
Cited by: 20
Author(s): Ingrid E. Jordon‐Thaden, James B. Beck, Catherine A. Rushworth, Michael D. Windham, Nicolas Diaz, Jason T. Cantley, Christopher T. Martine, Carl J. Rothfels
Software Mentions: 9
Published: over 4 years ago

10.1155/2019/3717239

Primary Production in the Water Column as Major Structuring Element of the Biogeographical Distribution and Function of Archaea in Deep-Sea Sediments of the Central Pacific Ocean
Cited by: 9
Author(s): Franziska Wemheuer, Avril Jean Elisabeth von Hoyningen-Huene, Marion Pohlner, Julius Degenhardt, Bert Engelen, Rolf Daniel, Bernd Wemheuer
Software Mentions: 9
Published: over 5 years ago

10.1186/1471-2164-15-786

A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity
Cited by: 47
Author(s): Matthew Hobbs, Ana Pavasovic, Andrew King, Peter J. Prentis, Mark D. B. Eldridge, Zhiliang Chen, Donald J. Colgan, Adam Polkinghorne, Marc R. Wilkins, Cheyne Flanagan, Amber Gillett, Jon Hanger, Rebecca N. Johnson, Peter Timms
Software Mentions: 8
Published: about 10 years ago

10.1371/journal.pone.0022099

Universally Distributed Single-Copy Genes Indicate a Constant Rate of Horizontal Transfer
Cited by: 81
Author(s): Christopher J. Creevey, Tobias Doerks, David A. Fitzpatrick, Jeroen Raes, Peer Bork
Software Mentions: 8
Published: over 13 years ago

10.1002/ece3.5406

Quaternary climate change and habitat preference shaped the genetic differentiation and phylogeography of<i>Rhodiola</i>sect.<i>Prainia</i>in the southern Qinghai–Tibetan Plateau
Cited by: 8
Author(s): Zi‐Meng Wang, Shi‐Yong Meng, Guang‐Yuan Rao
Software Mentions: 7
Published: over 5 years ago

10.1186/s12870-018-1429-8

Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum
Cited by: 10
Author(s): Yihan Wang, Weimei Jiang, Wenqing Ye, Chengxin Fu, Matthew A. Gitzendanner, Pamela S. Soltis, Douglas E. Soltis, Ying‐Xiong Qiu
Software Mentions: 7
Published: about 6 years ago

10.1038/srep40914

Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes
Cited by: 69
Author(s): Franziska Wemheuer, Kristin Kaiser, Petr Karlovský, Rolf Daniel, Stefan Vidal, Bernd Wemheuer
Software Mentions: 7
Published: almost 8 years ago

10.1111/mec.14931

The evolution of abdominal microbiomes in fungus‐growing ants
Cited by: 23
Author(s): Panagiotis Sapountzis, David R. Nash, Morten Schiøtt, Jacobus J. Boomsma
Software Mentions: 7
Published: almost 6 years ago

10.1099/mgen.0.000585

Comparative genomic insights into the epidemiology and virulence of plant pathogenic pseudomonads from Turkey
Cited by: 2
Author(s): Marcus M. Dillon, Tatiana Ruiz-Bedoya, Cedoljub Bundalovic-Torma, Kevin Guttman, Haejin Angela Kwak, Maggie A. Middleton, Pauline W. Wang, Sümer Horuz, Y. Aysan, David S. Guttman
Software Mentions: 6
Published: over 3 years ago

10.3389/fmicb.2016.00563

Proteomic Stable Isotope Probing Reveals Biosynthesis Dynamics of Slow Growing Methane Based Microbial Communities
Cited by: 21
Author(s): Jeffrey J. Marlow, Connor T. Skennerton, Li Zhou, Karuna Chourey, Robert L. Hettich, Chongle Pan, Victoria J. Orphan
Software Mentions: 6
Published: over 8 years ago

10.1099/mgen.0.000156

Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231
Cited by: 23
Author(s): Rodrigo P. Baptista, João Luís Reis-Cunha, Jeremy D. DeBarry, Égler Chiari, Jessica C. Kissinger, Daniella Castanheira Bartholomeu, Andréa Mara Macedo
Software Mentions: 6
Published: over 6 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

10.1099/mgen.0.000123

Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes
Cited by: 3
Author(s): Nina Luhmann, Daniel Doerr, Cédric Chauve
Software Mentions: 6
Published: about 7 years ago

10.1111/irv.12373

Serotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008
Cited by: 12
Author(s): Sylvia Milanoi, Juliette R. Ongus, George Gachara, Rodney L. Coldren, Wallace Bulimo
Software Mentions: 6
Published: over 8 years ago

10.1186/s12863-021-00983-2

Insights into 6S RNA in lactic acid bacteria (LAB)
Cited by: 1
Author(s): Pablo G. Cataldo, Paul Klemm, Marietta Thüring, Lucila Saavedra, Elvira María Hébert, Roland K. Hartmann, Marcus Lechner
Software Mentions: 6
Published: about 3 years ago

10.1038/srep09549

Difference in microRNA expression and editing profile of lung tissues from different pig breeds related to immune responses to HP-PRRSV
Cited by: 33
Author(s): Jia Li, Zhisheng Chen, Junlong Zhao, Liurong Fang, Rui Fang, Jiang Xiao, Xing Chen, Ao Zhou, Yingyin Zhang, Liming Ren, Xiaoxiang Hu, Yaofeng Zhao, Shujun Zhang, Ning Li
Software Mentions: 6
Published: over 9 years ago

10.1111/mec.13914

Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait
Cited by: 44
Author(s): Jill K. Olofsson, Matheus E Bianconi, Guillaume Besnard, Luke T. Dunning, Marjorie R. Lundgren, Hélène Holota, Maria S. Vorontsova, Oriane Hidalgo, Ilia J. Leitch, Patrik Nosil, Colin P. Osborne, Pascal‐Antoine Christin
Software Mentions: 6
Published: almost 8 years ago

10.1111/1755-0998.13022

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring
Cited by: 64
Author(s): Jérôme Morinière, Michael Balke, Dieter Doczkal, Matthias F. Geiger, Laura A. Hardulak, Gerhard Haszprunar, Axel Hausmann, Lars Hendrich, Ledis Regalado, Björn Rulik, Stefan Schmidt, Johann‐Wolfgang Wägele, Paul D. N. Hebert
Software Mentions: 6
Published: over 5 years ago

10.1186/s12859-016-1420-z

T-RECs: rapid and large-scale detection of recombination events among different evolutionary lineages of viral genomes
Cited by: 9
Author(s): Michail Tsimpidis, Georgios Bachoumis, Kalliopi Mimouli, Zaharoula Kyriakopoulou, David L. Robertson, Panayotis Markoulatos, Grigoris D. Amoutzias
Software Mentions: 6
Published: almost 8 years ago

10.1371/journal.pone.0161476

Evolution of the Exon-Intron Structure in Ciliate Genomes
Cited by: 17
Author(s): Vladyslav Bondarenko, Mikhail S. Gelfand
Software Mentions: 5
Published: about 8 years ago

10.1093/gbe/evaa223

Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair
Cited by: 16
Author(s): Mohak Sharda, Anjana Badrinarayanan, Aswin Sai Narain Seshasayee
Software Mentions: 5
Published: about 4 years ago

10.1002/ece3.5538

Old divergence and restricted gene flow between torrent duck ( Merganetta armata ) subspecies in the Central and Southern Andes
Cited by: 2
Author(s): Luis Alza, Philip Lavretsky, Jeffrey L. Peters, Gerardo Cerón, Matthew J. Smith, Cecilia Kopuchian, Andrea A. Astié, Kevin G. McCracken
Software Mentions: 5
Published: over 5 years ago

10.1186/s12862-017-1064-2

Rapid turnover of effectors in grass powdery mildew (Blumeria graminis)
Cited by: 45
Author(s): Fabrizio Menardo, Coraline R. Praz, Thomas Wicker, Beat Keller
Software Mentions: 5
Published: about 7 years ago

10.1186/1471-2105-8-254

Progressive multiple sequence alignments from triplets
Cited by: 22
Author(s): Matthias Kruspe, Peter F. Stadler
Software Mentions: 5
Published: over 17 years ago

10.1371/journal.pone.0153925

Molecular Characterization and Global Expression Analysis of Lectin Receptor Kinases in Bread Wheat (Triticum aestivum)
Cited by: 66
Author(s): . Shumayla, Shailesh Sharma, Ajay Kumar Pandey, Kashmir Singh, Santosh Kumar Upadhyay
Software Mentions: 5
Published: over 8 years ago

10.1099/mgen.0.000207

Taxonogenomics reveal multiple novel genomospecies associated with clinical isolates of Stenotrophomonas maltophilia
Cited by: 20
Author(s): Prabhu B. Patil, Sanjeet Kumar, Samriti Midha, Vikas Gautam
Software Mentions: 5
Published: over 6 years ago

10.1099/ijsem.0.003956

Genome-based analyses reveal a synonymy among Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996, Halorubrum terrestre Ventosa et al. 2004, Halorubrum arcis Xu et al. 2007 and Halorubrum litoreum Cui et al. 2007. Emended description of Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996
Cited by: 13
Author(s): Carmen Infante-Domínguez, Rafael R. de la Haba, Paulina Corral, Cristina Sánchez‐Porro, David R. Arahal, António Ventosa
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-019-47094-8

Odors from phylogenetically-distant plants to Brassicaceae repel an herbivorous Brassica specialist
Cited by: 11
Author(s): Chase A. Stratton, Elisabeth A. Hodgdon, Cesar Rodriguez‐Saona, Anthony M. Shelton, Yolanda H. Chen
Software Mentions: 5
Published: over 5 years ago

10.1099/vir.0.068429-0

Consensus proposals for classification of the family Hepeviridae
Cited by: 549
Author(s): Donald B. Smith, Peter Simmonds, Shahid Jameel, Suzanne U. Emerson, Tim J. Harrison, Xiang‐Jin Meng, Hiroaki Okamoto, Wim van der Poel, Michael A. Purdy
Software Mentions: 5
Published: about 10 years ago

10.3389/fmicb.2020.01663

Cultivation and Genomics Prove Long-Term Colonization of Donor’s Bifidobacteria in Recurrent Clostridioides difficile Patients Treated With Fecal Microbiota Transplantation
Cited by: 7
Author(s): Hanne Jouhten, Aki Ronkainen, Juhani Aakko, Seppo Salminen, Eero Mattila, Perttu Arkkila, Reetta Satokari
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-021-08015-0

Identification of ABC transporter G subfamily in white lupin and functional characterization of L.albABGC29 in phosphorus use
Cited by: 11
Author(s): Mehtab Muhammad Aslam, Muhammad Waseem, Qian Zhang, Ke Wang, Jianhua Zhang, Weifeng Xu
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.ppat.1002567

Comparative Genomics of the Apicomplexan Parasites Toxoplasma gondii and Neospora caninum: Coccidia Differing in Host Range and Transmission Strategy
Cited by: 197
Author(s): Adam J. Reid, Sarah J. Vermont, James A. Cotton, David J. Harris, Grant A. Hill-Cawthorne, Stephanie Könen‐Waisman, Sophia M. Latham, Tobias Mourier, Rebecca Norton, Michael A. Quail, Mandy Sanders, Dhanasekaran Shanmugam, Amandeep Sohal, James D. Wasmuth, Brian P. Brunk, Michael E. Grigg, Jonathan C. Howard, John Parkinson, David S. Roos, A. J. Trees, Matthew Berriman, Arnab Pain, Jonathan M. Wastling
Software Mentions: 5
Published: over 12 years ago

10.1038/s41598-020-79359-y

Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece
Cited by: 9
Author(s): Panos Bravakos, Manolis Mandalakis, Paraskevi Nomikou, Thekla I. Anastasiou, Jon Bent Kristoffersen, M. Stavroulaki, Stephanos P. Kilias, Georgios Kotoulas, Antoniοs Magoulas, Paraskevi N. Polymenakou
Software Mentions: 5
Published: almost 4 years ago

10.1002/ece3.5428

Loss of a chloroplast encoded function could influence species range in kelp
Cited by: 5
Author(s): Shivani Rana, Klaus Valentin, Inka Bartsch, Gernot Glöckner
Software Mentions: 4
Published: over 5 years ago

10.1186/s13100-018-0144-1

Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification
Cited by: 200
Author(s): Pavel Neumann, Petr Novák, Nina Hoštáková, Jiří Macas
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.ppat.1008984

Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics
Cited by: 13
Author(s): Nicola F. Müller, Daniel Wüthrich, Nina Goldman, Nadine Sailer, Claudia Saalfrank, Myrta Brunner, Noémi Augustin, Helena M. B. Seth-Smith, Yvonne Hollenstein, Mohammedyaseen Syedbasha, Daniela Lang, Richard A. Neher, Olivier Dubuis, Michael Naegele, Andreas Buser, Christian H. Nickel, Nicole Ritz, Andreas Zeller, Brian M. Lang, James Hadfield, Trevor Bedford, Manuel Battegay, Rita Schneider-Sliwa, Adrian Egli, Tanja Stadler
Software Mentions: 4
Published: about 4 years ago

10.3390/genes11060610

The Location of the Pseudoautosomal Boundary in Silene latifolia
Cited by: 8
Author(s): Marc Krasovec, Yu Zhang, Dmitry A. Filatov
Software Mentions: 4
Published: over 4 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: about 5 years ago

10.3389/fpls.2018.00049

Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen
Cited by: 28
Author(s): Coraline R. Praz, Fabrizio Menardo, Mark D. Robinson, Marion Müller, Thomas Wicker, Salim Bourras, Beat Keller
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2017.02550

The Biogeographical Distribution of Benthic Roseobacter Group Members along a Pacific Transect Is Structured by Nutrient Availability within the Sediments and Primary Production in Different Oceanic Provinces
Cited by: 20
Author(s): Marion Pohlner, Julius Degenhardt, Avril Jean Elisabeth von Hoyningen-Huene, Bernd Wemheuer, Nora Erlmann, Bernhard Schnetger, Thomas H. Badewien, Bert Engelen
Software Mentions: 4
Published: almost 7 years ago

10.3389/fmicb.2016.01084

Genome and Transcriptome Sequences Reveal the Specific Parasitism of the Nematophagous Purpureocillium lilacinum 36-1
Cited by: 27
Author(s): Jialian Xie, Shaojun Li, Chenmi Mo, Xiangyu Xiao, Deliang Peng, Gaofeng Wang, Yanan Xiao
Software Mentions: 4
Published: over 8 years ago

10.1111/j.1755-0998.2011.03041.x

DNA barcoding of oomycetes with cytochrome <i>c</i> oxidase subunit I and internal transcribed spacer
Cited by: 459
Author(s): G.P. Robideau, A. W. A. M. de Cock, Michael D. Coffey, Hermann Voglmayr, Henk J. Brouwer, Kanak Bala, David W. Chitty, N. L. Désaulniers, Quinn Eggertson, Claire M. M. Gachon, Chia-Hui Hu, Frithjof C. Küpper, Tara L. Rintoul, Ehab Sarhan, E.C.P. Verstappen, Yonghong Zhang, P.J.M. Bonants, Jean Beagle Ristaino, C. André Lévesque
Software Mentions: 4
Published: over 13 years ago

10.1186/s12864-015-1684-0

Hox cluster characterization of Banna caecilian (Ichthyophis bannanicus) provides hints for slow evolution of its genome
Cited by: 7
Author(s): Riga Wu, Qingfeng Li, Sen Meng, Peng Zhang, Dan Liang
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2020.01826

Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen
Cited by: 19
Author(s): Samson Hailemariam, Shengguo Zhao, Jiaqi Wang
Software Mentions: 4
Published: over 4 years ago

10.1099/vir.0.065219-0

Identification of novel anelloviruses with broad diversity in UK rodents
Cited by: 41
Author(s): Shoko Nishiyama, Bernadette M. Dutia, James P. Stewart, Anna Meredith, Darren Shaw, Peter Simmonds, Colin Sharp
Software Mentions: 4
Published: over 10 years ago

10.1186/s12864-015-2194-9

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling
Cited by: 311
Author(s): R. D'Amore, Umer Zeeshan Ijaz, Melanie Schirmer, John Kenny, Richard I. Gregory, Alistair C. Darby, Migun Shakya, Mircea Podar, Christopher Quince, Neil Hall
Software Mentions: 4
Published: almost 9 years ago

10.1186/1471-2105-11-37

Predicting Bevirimat resistance of HIV-1 from genotype
Cited by: 32
Author(s): Dominik Heider, Jens Verheyen, Daniel Hoffmann
Software Mentions: 4
Published: almost 15 years ago

10.1371/journal.pgen.1007915

Functional lability of RNA-dependent RNA polymerases in animals
Cited by: 27
Author(s): Natalia Pinzón, Stéphanie Bertrand, Lucie Subirana, Isabelle Busseau, Héctor Escrivà, Hervé Seitz
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.49030

Formin-2 drives polymerisation of actin filaments enabling segregation of apicoplasts and cytokinesis in Plasmodium falciparum
Cited by: 31
Author(s): Johannes Felix Stortz, Mario Del Rosario, Mirko Singer, Jonathan M. Wilkes, Markus Meissner, Sujaan Das
Software Mentions: 4
Published: over 5 years ago

10.1099/acmi.0.000015

Phylogenomics insights into order and families of Lysobacterales
Cited by: 19
Author(s): Sanjeet Kumar, Kanika Bansal, Prashant P. Patil, Prabhu B. Patil
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2180-10-65

Comparative genomics of VirR regulons in Clostridium perfringens strains
Cited by: 10
Author(s): Antonio Frandi, Alessio Mengoni, Matteo Brilli
Software Mentions: 4
Published: over 14 years ago

10.1371/journal.pone.0117667

Genetic and Genomic Diversity Studies of Acacia Symbionts in Senegal Reveal New Species of Mesorhizobium with a Putative Geographical Pattern
Cited by: 20
Author(s): Fatou Diouf, Diégane Diouf, Agnieszka Klonowska, Antoine Le Quéré, Niokhor Bakhoum, Dioumacor Fall, Marc Neyra, Hugues Parrinello, M. Diouf, Ibrahima Ndoye, Lionel Moulin
Software Mentions: 4
Published: almost 10 years ago

10.1099/mgen.0.000153

Development and implementation of multilocus sequence typing to study the diversity of the yeast Kluyveromyces marxianus in Italian cheeses
Cited by: 13
Author(s): Fabrizia Tittarelli, Javier A. Varela, Loughlin Gethins, Catherine Stanton, R. Paul Ross, Giovanna Suzzi, L. Grazia, Rosanna Tofalo, John P. Morrissey
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12915-020-00862-9

Genome-enabled insights into the biology of thrips as crop pests
Cited by: 44
Author(s): Dorith Rotenberg, Aaron A. Baumann, Sulley Ben-Mahmoud, Olivier Christiaens, Wannes Dermauw, Panagiotis Ioannidis, Chris G.C. Jacobs, Iris M. Vargas Jentzsch, Jonathan E. Oliver, Monica Poelchau, Swapna Priya Rajarapu, Derek J. Schneweis, Simon Snoeck, Clauvis Nji Tizi Taning, Dong Wei, Shirani M. K. Widana Gamage, Daniel Hughes, Shwetha C. Murali, Samuel T. Bailey, Nicolás Bejerman, Christopher J. Holmes, Emily C. Jennings, Andrew J. Rosendale, Andrew E. Rosselot, Kaylee Hervey, Brandi A. Schneweis, Sammy Cheng, Christopher P. Childers, Felipe A. Simão, Ralf G. Dietzgen, Hsu Chao, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Yi Han, Sandra L. Lee, Donna M. Muzny, Jiaxin Qu, Kim C. Worley, Joshua B. Benoit, Markus Friedrich, Jeffery W. Jones, Kristen A. Panfilio, Yoonseong Park, Hugh M. Robertson, Guy Smagghe, Diane E. Ullman, Maurijn van der Zee, Thomas Van Leeuwen, Jan A. Veenstra, Robert M. Waterhouse, Matthew T. Weirauch, John H. Werren, Anna E. Whitfield, Evgeny M. Zdobnov, Richard A. Gibbs, Stephen Richards
Software Mentions: 4
Published: about 4 years ago

10.1099/mgen.0.000574

Potential syntrophic relationship between coral-associated Prosthecochloris and its companion sulfate-reducing bacterium unveiled by genomic analysis
Cited by: 4
Author(s): Yu-Hsiang Chen, Shan‐Hua Yang, Kshitij Tandon, Chien‐Yu Lu, Hsing‐Ju Chen, Chao-Jen Shih, Sen‐Lin Tang
Software Mentions: 4
Published: over 3 years ago

10.3389/fimmu.2018.02999

Shrimp miR-1000 Functions in Antiviral Immunity by Simultaneously Triggering the Degradation of Two Viral mRNAs
Cited by: 11
Author(s): Yi Gong, Chenyu Ju, Xiaobo Zhang
Software Mentions: 4
Published: almost 6 years ago

10.1099/mgen.0.000498

ActDES – a curated Actinobacterial Database for Evolutionary Studies
Cited by: 2
Author(s): Jana Katharina Schniete, Nelly Sélem-Mójica, Anna Sofia Birke, Pablo Cruz-Morales, Iain S. Hunter, Francisco Barona‐Gómez, Paul A. Hoskisson
Software Mentions: 4
Published: almost 4 years ago

10.1002/ece3.5577

Site‐specific distribution of oak rhizosphere‐associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding
Cited by: 21
Author(s): Melanie Sapp, Nicolas Tyborski, Anja Linstädter, Aida López Sánchez, Tim Mansfeldt, Guido Waldhoff, Georg Bareth, Michael Bonkowski, Laura Rose
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giy101

The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation
Cited by: 56
Author(s): Conghui Liu, Yan Zhang, Yingxue Ren, Hengchao Wang, Shuqu Li, Fan Jiang, Lei Yin, Xi Qiao, Guojie Zhang, Wanqiang Qian, Bo Liu, Wei Fan
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pntd.0000258

On the Extent and Origins of Genic Novelty in the Phylum Nematoda
Cited by: 69
Author(s): James D. Wasmuth, Ralf Schmid, Ann Hedley, Mark Blaxter
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2105-8-441

A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures
Cited by: 8
Author(s): Konstantin Popadin, Leila Mamirova, Fyodor A. Kondrashov
Software Mentions: 3
Published: about 17 years ago

10.3390/genes12040569

Sex-Biased Gene Expression and Evolution in the Cerebrum and Syrinx of Chinese Hwamei (Garrulax canorus)
Cited by: 1
Author(s): Hua Jiang, Jianqing Lin, Li Sun, Yanchun Xu, Sheng‐Guo Fang
Software Mentions: 3
Published: over 3 years ago

10.1186/gb-2007-8-11-r242

Quantification of ortholog losses in insects and vertebrates
Cited by: 60
Author(s): Stefan Wyder, Evgenia V. Kriventseva, Reinhard Schröder, Tatsuhiko Kadowaki, Evgeny M. Zdobnov
Software Mentions: 3
Published: almost 18 years ago

10.3389/fmicb.2020.576738

In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides
Cited by: 8
Author(s): Yasmin Neves Vieira Sabino, Katialaine Corrêa de Araújo, Fábia Giovana do Val de Assis, Sofia Magalhães Moreira, Thaynara da Silva Lopes, Tiago Antônio de Oliveira Mendes, Sharon Huws, Hilário Cuquetto Mantovani
Software Mentions: 3
Published: about 4 years ago

10.1186/s12883-020-02040-4

Mild cognitive impairment in novel SPG11 mutation-related sporadic hereditary spastic paraplegia with thin corpus callosum: case series
Cited by: 4
Author(s): Chuan Li, Qi Yan, Feng-ju Duan, Chao Zhao, Zhuo Zhang, Ying Du, Wei Zhang
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12859-018-2172-8

Comparison of metaheuristics to measure gene effects on phylogenetic supports and topologies
Cited by: 1
Author(s): Régis Garnier, Christophe Guyeux, Jean-François Couchot, Michel Salomon, Bashar Al-Nuaimi, Bassam AlKindy
Software Mentions: 3
Published: over 6 years ago

10.1111/j.1742-4658.2012.08597.x

A <i>S</i> ‐adenosylmethionine methyltransferase‐like domain within the essential, Fe‐S‐containing yeast protein Dre2
Cited by: 25
Author(s): Nicolás Soler, Constantin T. Craescu, Jacques Gallay, Yves-Michel Frapart, Daniel Mansuy, Bertrand Raynal, Giuseppe Baldacci, Annalisa Pastore, Meng‐Er Huang, Laurence Vernis
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-017-16171-1

Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline
Cited by: 31
Author(s): Matthew Hobbs, Andrew King, Ryan Salinas, Zhiliang Chen, Kyriakos Tsangaras, Alex D. Greenwood, Rebecca N. Johnson, Katherine Belov, Marc R. Wilkins, Peter Timms
Software Mentions: 3
Published: about 7 years ago

10.1186/1471-2148-8-180

Evolution of a behavior-linked microsatellite-containing element in the 5' flanking region of the primate AVPR1A gene
Cited by: 56
Author(s): Zoe R. Donaldson, Fyodor A. Kondrashov, Andrea S. Putnam, Yaohui Bai, Tara L Stoinski, Elizabeth A. D. Hammock, Larry J. Young
Software Mentions: 3
Published: almost 17 years ago

10.1186/1472-6807-5-19

Natural history of S-adenosylmethionine-binding proteins
Cited by: 240
Author(s): Piotr Koźbiał, Arcady Mushegian
Software Mentions: 3
Published: about 19 years ago

10.1099/mgen.0.000231

SynerClust: a highly scalable, synteny-aware orthologue clustering tool
Cited by: 12
Author(s): C Georgescu, Abigail L. Manson, Alexander D. Griggs, Christopher A. Desjardins, Alejandro Pironti, Ilan Wapinski, Thomas Abeel, Brian J. Haas, Ashlee M. Earl
Software Mentions: 3
Published: about 6 years ago

10.1038/s41684-021-00831-x

Annelid genomes: Enchytraeus crypticus, a soil model for the innate (and primed) immune system
Cited by: 7
Author(s): Mónica J.B. Amorim, Yannick Gansemans, Susana I. L. Gomes, Filip Van Nieuwerburgh, Janeck J. Scott-Fordsmand
Software Mentions: 3
Published: about 3 years ago

10.1186/1471-2148-9-215

The small heat shock protein (sHSP) genes in the silkworm, Bombyx mori, and comparative analysis with other insect sHSP genes
Cited by: 104
Author(s): Zi-Wen Li, Xue-zhi Li, Qiuhan Yu, Xiang Zhang, Hirohisa Kishino, Ze Zhang
Software Mentions: 3
Published: about 15 years ago

10.1111/jam.14751

Emerging salt marshes as a source of <i>Trichoderma arenarium</i> sp. nov. and other fungal <i>bio</i> effectors for <i>bio</i> saline agriculture
Cited by: 6
Author(s): Mingyue Ding, Wei Chen, Xingcong Ma, Bing‐Wei Lv, Siqi Jiang, Ya‐Nan Yu, Mohammad Javad Rahimi, Renwei Gao, Zheng Zhao, Feng Cai, Irina S. Druzhinina
Software Mentions: 3
Published: over 4 years ago

10.1099/jgv.0.000902

Polycipiviridae: a proposed new family of polycistronic picorna-like RNA viruses
Cited by: 33
Author(s): Ingrida Olendraitė, Nina I. Lukhovitskaya, Sanford D. Porter, Steven M. Valles, Andrew E. Firth
Software Mentions: 3
Published: about 7 years ago

10.1099/jgv.0.000873

Proposed revision to the taxonomy of the genus Pestivirus, family Flaviviridae
Cited by: 241
Author(s): Donald B. Smith, Gregor Meyers, Jens Bukh, Ernest A. Gould, Thomas P. Monath, A. Scott Muerhoff, Alexander G. Pletnev, Rebeca Rico-Hesse, Jack T. Stapleton, Peter Simmonds, Paul Becher
Software Mentions: 3
Published: over 7 years ago

10.3389/fvets.2020.605704

New Diagnostic Assays for Differential Diagnosis Between the Two Distinct Lineages of Bovine Influenza D Viruses and Human Influenza C Viruses
Cited by: 1
Author(s): Faten A. Okda, Elizabeth C. Griffith, Ahmed Sakr, Eric Nelson, Richard J. Webby
Software Mentions: 3
Published: almost 4 years ago

10.1111/j.1462-2920.2010.02280.x

Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments
Cited by: 293
Author(s): Matthew B. Sullivan, Katherine Huang, J. Cesar Ignacio‐Espinoza, Aaron M. Berlin, Libusha Kelly, Peter Weigele, Alicia S. DeFrancesco, Suzanne E. Kern, Luke R. Thompson, Sarah Young, Chandri Yandava, Ross Fu, Bryan Krastins, Michael R. Chase, David Sarracino, Marcia S. Osburne, Matthew R. Henn, Sallie W. Chisholm
Software Mentions: 3
Published: about 14 years ago

10.1099/ijs.0.063172-0

Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota
Cited by: 223
Author(s): Michaela Stieglmeier, Andreas Klingl, Ricardo J. Eloy Alves, Simon K.-M. R. Rittmann, Michael Melcher, Nikolaus Leisch, Christa Schleper
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1008179

Suppressor mutations in ribosomal proteins and FliY restore Bacillus subtilis swarming motility in the absence of EF-P
Cited by: 12
Author(s): Katherine R. Hummels, Daniel B. Kearns
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1000732

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome
Cited by: 332
Author(s): Regina S. Baucom, James C. Estill, Cristian Chaparro, Naadira C. Upshaw, Ansuya Jogi, Jean-Marc Deragon, Richard P. Westerman, Phillip SanMiguel, Jeffrey L. Bennetzen
Software Mentions: 3
Published: about 15 years ago

10.1186/s12866-019-1402-1

NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission
Cited by: 66
Author(s): Alexandra Dangel, Anja Berger, Regina Konrad, Andreas Sing
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcimb.2018.00313

Joint Genomic and Proteomic Analysis Identifies Meta-Trait Characteristics of Virulent and Non-virulent Staphylococcus aureus Strains
Cited by: 9
Author(s): Emilia Bonar, Michał Bukowski, Marcin Hydzik, Urszula Jankowska, Sylwia Kędracka‐Krok, Magdalena Groborz, Grzegorz Dubin, Viktoria Akkerboom, Jacek Międzobrodzki, Artur J. Sabat, Alexander Friedrich, Benedykt Władyka
Software Mentions: 3
Published: about 6 years ago

10.1099/ijsem.0.004742

Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia
Cited by: 18
Author(s): Milena Serenato Klepa, Luisa Caroline Ferraz Helene, G.W. O’Hara, Mariángela Hungria
Software Mentions: 3
Published: over 5 years ago

10.1099/ijsem.0.004438

Mycolicibacterium nivoides sp. nov isolated from a peat bog
Cited by: 7
Author(s): John L. Dahl, Wayne Gatlin, Phuong M. Tran, Cody S. Sheik
Software Mentions: 3
Published: over 5 years ago

10.1099/mgen.0.000260

EvoMining reveals the origin and fate of natural product biosynthetic enzymes
Cited by: 35
Author(s): Nelly Sélem-Mójica, César Aguilar, Karina Gutiérrez-García, Christian E. Martínez-Guerrero
Software Mentions: 3
Published: almost 5 years ago

10.1099/mgen.0.000187

Using glycolysis enzyme sequences to inform Lactobacillus phylogeny
Cited by: 8
Author(s): Katelyn Brandt, Rodolphe Barrangou
Software Mentions: 3
Published: over 6 years ago

10.1099/mgen.0.000183

The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut
Cited by: 19
Author(s): Korin Albert, Asha Rani, David A. Sela
Software Mentions: 3
Published: over 6 years ago

10.7554/eLife.42542

Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes
Cited by: 15
Author(s): Nimisha Chaturvedi, Evguenia S. Svarovskaia, Hongmei Mo, Anu Osinusi, Diana M. Brainard, G. Mani Subramanian, John G. McHutchison, Stefan Zeuzem, Jacques Fellay
Software Mentions: 2
Published: about 5 years ago

10.1099/acmi.0.000055

First report of Lasiodiplodia pseudotheobromae keratitis susceptible to voriconazole in an Indian mango grower
Cited by: 3
Author(s): Hari Pankaj Vanam, Mohammed Ather, K S Madhura, Shivaprakash M. Rudramurthy
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2148-8-219

An amphioxus orthologue of the estrogen receptor that does not bind estradiol: Insights into estrogen receptor evolution
Cited by: 72
Author(s): Mathilde Paris, Katarina Pettersson, Michael Schubert, Stéphanie Bertrand, Ingemar Pongratz, Héctor Escrivà, Vincent Laudet
Software Mentions: 2
Published: over 16 years ago