pypi: hmmer | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1008866

Phylogenetic background and habitat drive the genetic diversification of Escherichia coli
Cited by: 119
Author(s): Marie Touchon, Perrin Amandine, Jorge Moura de Sousa, Belinda Vangchhia, Samantha Burn, Claire O’Brien, Erick Denamur, David M. Gordon, Eduardo P. C. Rocha
Software Mentions: 16
Published: over 4 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

10.1128/mSystems.00316-20

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts
Cited by: 8
Author(s): Rhiannon Mondav, Stefan Bertilsson, Moritz Buck, Silke Langenheder, Eva S. Lindström, Sarahi L. Garcia
Software Mentions: 11
Published: about 4 years ago

10.1099/mgen.0.000503

Rapid molecular evolution of Spiroplasma symbionts of Drosophila
Cited by: 13
Author(s): Michael Gerth, Humberto Martínez-Montoya, Paulino Ramirez, Florent Masson, Joanne S. Griffin, Rodolfo Aramayo, Stefanos Siozios, Bruno Lemaître, Mariana Mateos, Gregory D. D. Hurst
Software Mentions: 11
Published: almost 4 years ago

10.3389/fmicb.2017.00682

Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)
Cited by: 314
Author(s): David W. Waite, Inka Vanwonterghem, Christian Rinke, Donovan H. Parks, Ying Zhang, Ken Takai, Stefan M. Sievert, Jörg Simon, Barbara J. Campbell, Thomas E. Hanson, Tanja Woyke, Martin G. Klotz, Philip Hugenholtz
Software Mentions: 11
Published: over 7 years ago

10.1186/s13059-020-02155-4

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Cited by: 51
Author(s): Paul Saary, Alex L. Mitchell, Alex Bateman
Software Mentions: 8
Published: about 4 years ago

10.1186/s12915-017-0379-1

Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors
Cited by: 55
Author(s): Édouard Evangelisti, Anna Gogleva, Thomas Hainaux, Mehdi Doumane, Frej Tulin, Clément Quan, T. S. Yunusov, Kévin Floch, Sebastián Schornack
Software Mentions: 8
Published: over 7 years ago

10.1186/s12864-020-6764-0

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum
Cited by: 15
Author(s): Alice B. Dennis, Gabriel I. Ballesteros, Stéphanie Robin, Lukas Schrader, Jens Bast, Jan Berghöfer, Leo W. Beukeboom, Maya Belghazi, Anthony Bretaudeau, Jan Buellesbach, Elizabeth Cash, Dominique Colinet, Zoé Dumas, Mohammed Errbii, Patrizia Falabella, Jean‐Luc Gatti, Elzemiek Geuverink, Joshua D. Gibson, Corinne Hertaeg, Stefanie Hartmann, Emmanuelle Jacquin‐Joly, Mark Lammers, Blas I. Lavandero, Ina Lindenbaum, Lauriane Massardier-Galatà, Camille Meslin, Nicolas Montagné, Nina Pak, Marylène Poirié, Rosanna Salvia, Chris R. Smith, Denis Tagu, Sophie Tarès, Heiko Vogel, Tanja Schwander, Jean Simon, Christian C. Figueroa, Christoph Vorburger, Fabrice Legeai, Jürgen Gadau
Software Mentions: 8
Published: over 4 years ago

10.1099/mgen.0.000174

The complete replicons of 16 Ensifer meliloti strains offer insights into intra- and inter-replicon gene transfer, transposon-associated loci, and repeat elements
Cited by: 19
Author(s): Matthew S. Nelson, Joseph Guhlin, Brendan Epstein, Peter Tiffin, Michael J. Sadowsky
Software Mentions: 8
Published: over 6 years ago

10.3390/microorganisms9071368

Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)
Cited by: 0
Author(s): Qianqian Li, Rebecca E. Cooper, Carl‐Eric Wegner, Martin Taubert, Nico Jehmlich, Martin von Bergen, Kirsten Küsel
Software Mentions: 7
Published: over 3 years ago

10.1111/tpj.14349

The genome of cowpea (Vigna unguiculata [L.] Walp.)
Cited by: 215
Author(s): Stefano Lonardi, María Muñoz‐Amatriaín, Qihua Liang, Shengqiang Shu, Steve Wanamaker, Sassoum Lo, Jaakko Tanskanen, Alan H. Schulman, Tingting Zhu, Ming‐Cheng Luo, Hind Alhakami, Rachid Ounit, Abid Hasan, Jérôme Verdier, Philip A. Roberts, Jansen Rodrigo Pereira Santos, Arsenio Ndeve, Jaroslav Doležel, Jan Vrána, S. Hokin, Andrew Farmer, Steven B. Cannon, Timothy J. Close
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pcbi.1008645

Ten simple rules for getting started with command-line bioinformatics
Cited by: 7
Author(s): Parice A. Brandies, Carolyn J. Hogg
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.ppat.1009418

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity
Cited by: 10
Author(s): Cédric Lood, Charlotte Peeters, Quentin Lamy-Besnier, Jeroen Wagemans, Daniël De Vos, Marijke Proesmans, Jean‐Paul Pirnay, Fedoua Echahidi, Denis Piérard, M Thimmesch, Anca Boeras, Katrien Lagrou, Evelien De Canck, Elke De Wachter, Vera van Noort, Rob Lavigne, Peter Vandamme
Software Mentions: 7
Published: over 3 years ago

10.7554/eLife.57347

Universal and taxon-specific trends in protein sequences as a function of age
Cited by: 17
Author(s): Jennifer E. James, Sara M. Willis, Paul Nelson, Catherine Weibel, Luke Kosinski, Joanna Masel
Software Mentions: 6
Published: almost 4 years ago

10.3390/ijms21010269

Genome-Wide Identification and Characterization of the Mitochondrial Transcription Termination Factors (mTERFs) in Capsicum annuum L.
Cited by: 20
Author(s): Bi‐Yu Tang, Lingling Xie, Tao Yi, Junheng Lv, Huiping Yang, Xiang Cheng, Feng Liu, Xuexiao Zou
Software Mentions: 6
Published: almost 5 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

10.1371/journal.pbio.3000534

The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response
Cited by: 112
Author(s): Omri M. Finkel, Isai Salas-González, Gabriel Castrillo, Stijn Spaepen, Theresa F. Law, Paulo José Pereira Lima Teixeira, Corbin D. Jones, Jeffery L. Dangl
Software Mentions: 6
Published: about 5 years ago

10.1371/journal.pcbi.1000071

Discovering Sequence Motifs with Arbitrary Insertions and Deletions
Cited by: 296
Author(s): Martin C. Frith, Neil F. W. Saunders, Boštjan Kobe, Timothy L. Bailey
Software Mentions: 6
Published: over 16 years ago

10.1186/s12859-014-0399-6

Integrating protein structural dynamics and evolutionary analysis with Bio3D
Cited by: 279
Author(s): Lars Skjærven, Xin‐Qiu Yao, Guido Scarabelli, Barry J. Grant
Software Mentions: 6
Published: almost 10 years ago

10.3389/fcimb.2020.600325

Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium
Cited by: 12
Author(s): Charlotte Michaux, Elisabeth E Hansen, Laura Jenniches, Milan Gerovac, Lars Barquist, Jörg Vogel
Software Mentions: 5
Published: almost 4 years ago

10.7717/peerj.6559

Estimating probabilistic context-free grammars for proteins using contact map constraints
Cited by: 7
Author(s): Witold Dyrka, Mateusz Pyzik, F Coste, Hugo Talibart
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2016.01221

Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales
Cited by: 23
Author(s): John Bird, Brett J. Baker, Alexander J. Probst, Mircea Podar, Karen G. Lloyd
Software Mentions: 5
Published: over 8 years ago

10.3389/fmicb.2019.01427

Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
Cited by: 11
Author(s): Scott C. Thomas, Kevin O. Tamadonfar, Cale O. Seymour, Dengxun Lai, Jeremy A. Dodsworth, Senthil K. Murugapiran, Emiley A. Eloe‐Fadrosh, Paul Dijkstra, Brian P. Hedlund
Software Mentions: 5
Published: over 5 years ago

10.1186/s40168-017-0322-2

Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments
Cited by: 147
Author(s): Nina Dombrowski, Kiley W. Seitz, Andreas Teske, Brett J. Baker
Software Mentions: 5
Published: about 7 years ago

10.1186/s12870-016-0860-y

CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors
Cited by: 16
Author(s): Saurabh Gayali, Shankar Acharya, Nilesh Vikram Lande, Ashish Pandey, Subhra Chakraborty, Niranjan Chakraborty
Software Mentions: 5
Published: over 8 years ago

10.1002/ps.6061

Toxicological and molecular profiling of insecticide resistance in a Brazilian strain of fall armyworm resistant to Bt Cry1 proteins
Cited by: 24
Author(s): Debora Boaventura, Benjamin Buer, Niklas Hamaekers, Frank Maiwald, Ralf Nauen
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0233077

Comparative transcriptomics of Diuraphis noxia and Schizaphis graminum fed wheat plants containing different aphid-resistance genes
Cited by: 2
Author(s): Lina Aguirre Rojas, Erin D. Scully, Laramy Enders, Alicia E. Timm, Deepak K. Sinha, C. Michael Smith
Software Mentions: 5
Published: over 4 years ago

10.1099/mgen.0.000341

An assessment of genome annotation coverage across the bacterial tree of life
Cited by: 44
Author(s): Briallen Lobb, Benjamin Tremblay, Gabriel Moreno–Hagelsieb, Andrew C. Doxey
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pgen.1007016

Genomics of parallel adaptation at two timescales in Drosophila
Cited by: 20
Author(s): Li Zhao, David J. Begun
Software Mentions: 5
Published: about 7 years ago

10.7554/eLife.02978

The pseudo GTPase CENP-M drives human kinetochore assembly
Cited by: 107
Author(s): Federica Basilico, Stefano Maffini, John R. Weir, Daniel Prumbaum, Ana M. Rojas, Tomasz Zimniak, De Antoni A, Sadasivam Jeganathan, Beate Voss, Suzan van Gerwen, Veronica Krenn, Lucia Massimiliano, Alfonso Valencia, Ingrid R. Vetter, Franz Herzog, Stefan Raunser, Sebastiano Pasqualato, Andrea Musacchio
Software Mentions: 5
Published: over 10 years ago

10.3389/fgene.2021.589160

Gene and Transposable Element Expression Evolution Following Recent and Past Polyploidy Events in Spartina (Poaceae)
Cited by: 9
Author(s): Delphine Giraud, Oscar Lima, Mathieu Rousseau‐Gueutin, Armel Salmon, Malika L. Aïnouche
Software Mentions: 5
Published: over 3 years ago

10.3390/plants9091149

Response of Downy Oak (Quercus pubescens Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics
Cited by: 7
Author(s): Jean-Philippe Mévy, Béatrice Loriod, Xi Liu, Erwan Corre, Magali Torres, Michael Büttner, Anne Haguenauer, Ilja M. Reiter, Catherine Fernandez, Thierry Gauquelin
Software Mentions: 4
Published: about 4 years ago

10.3390/plants9111589

Effects of Exogenous Salicylic Acid on Drought Response and Characterization of Dehydrins in Impatiens walleriana
Cited by: 11
Author(s): Dragana D Antonić, Angelina Subotić, Milan Dragićević, Danijel Pantelić, Snežana Milošević, Ana Simonović, Ivana Momčilović
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pcbi.1008387

RNA structure prediction using positive and negative evolutionary information
Cited by: 39
Author(s): Elena Rivas
Software Mentions: 4
Published: about 4 years ago

10.1371/journal.pgen.1006401

Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes
Cited by: 52
Author(s): H. Charlotte van der Does, Like Fokkens, Ally Yang, Sarah M. Schmidt, Léon Langereis, Joanna Lukasiewicz, Timothy R. Hughes, Martijn Rep
Software Mentions: 4
Published: about 8 years ago

10.1038/sdata.2018.154

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments
Cited by: 73
Author(s): Paul M. Berube, Steven J. Biller, Thomas Hackl, Brandon M. Satinsky, Jamie W. Becker, Rogier Braakman, Sara B. Collins, Libusha Kelly, Jessie W Berta-Thompson, Allison Coe, Kristin Bergauer, Heather A. Bouman, Thomas J. Browning, Daniele De Corte, Christel Hassler, Yotam Hulata, Jeremy E. Jacquot, Elizabeth W. Maas, Thomas Reinthaler, Eva Sintes, Taichi Yokokawa, Debbie Lindell, Ramunas Stepanauskas, Sallie W. Chisholm
Software Mentions: 4
Published: about 6 years ago

10.1186/s13227-019-0135-4

Comparative transcriptomic analysis of a wing-dimorphic stonefly reveals candidate wing loss genes
Cited by: 16
Author(s): Graham A. McCulloch, Andrew Oliphant, Peter K. Dearden, Andrew J. Veale, Charles W. Ellen, Jonathan M. Waters
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0223680

Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools
Cited by: 51
Author(s): Xiaofang Jiang, Andrew Brantley Hall, Ramnik J. Xavier, Eric J. Alm
Software Mentions: 4
Published: almost 5 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

10.1038/s42003-021-02112-2

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
Cited by: 82
Author(s): Silvia G. Acinas, Pablo Sánchez, Guillem Salazar, Francisco M. Cornejo‐Castillo, Marta Sebastián, Ramiro Logares, Marta Royo-Llonch, Lucas Paoli, Shinichi Sunagawa, Pascal Hingamp, Hiroyuki Ogata, Gipsi Lima‐Mendez, Simon Roux, José M. González, Jesús M. Arrieta, Intikhab Álam, Allan Kamau, Chris Bowler, Jeroen Raes, Stéphane Pesant, Peer Bork, Susana Agustı́, Takashi Gojobori, Dolors Vaqué, Matthew B. Sullivan, Carlos Pedrós‐Alió, Ramón Massana, Carlos M. Duarte, Josep M. Gasol
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0028819

Gentle Masking of Low-Complexity Sequences Improves Homology Search
Cited by: 27
Author(s): Martin C. Frith
Software Mentions: 4
Published: almost 13 years ago

10.1371/journal.pone.0067511

Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes
Cited by: 55
Author(s): Henk C. den Bakker, Christopher A. Desjardins, Allison Griggs, Joseph E. Peters, Qiandong Zeng, Sarah Young, Chinnappa D. Kodira, Chandri Yandava, Theresa A. Hepburn, Brian J. Haas, Bruce W. Birren, Martin Wiedmann
Software Mentions: 4
Published: over 11 years ago

10.7554/eLife.24414

Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria
Cited by: 38
Author(s): M. Sabrina Pankey, Randi L Foxall, Ian M Ster, Lauren A Perry, Brian G. Schuster, Rachel A Donner, Matthew Coyle, Vaughn S. Cooper, Cheryl A. Whistler
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0228722

Iron metabolic pathways in the processes of sponge plasticity
Cited by: 8
Author(s): Alexander D. Finoshin, Kim I. Adameyko, Kirill V. Mikhailov, О. И. Кравчук, Anton Georgiev, Н. Г. Горностаев, Igor A. Kosevich, Victor S. Mikhailov, Guzel Gazizova, Elena Shagimardanova, Oleg Gusev, Yu. V. Lyupina
Software Mentions: 4
Published: over 4 years ago

10.1186/s12864-017-3967-0

Regulation of gene expression in roots of the pH-sensitive Vaccinium corymbosum and the pH-tolerant Vaccinium arboreum in response to near neutral pH stress using RNA-Seq
Cited by: 15
Author(s): Miriam Payá‐Milans, Gerardo H. Nunez, James W. Olmstead, Timothy A. Rinehart, Margaret Staton
Software Mentions: 4
Published: over 7 years ago

10.1038/s41396-018-0343-2

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi
Cited by: 74
Author(s): Joel A. Boyd, Sean P. Jungbluth, Andy O. Leu, Paul N. Evans, Ben J. Woodcroft, Grayson L. Chadwick, Victoria J. Orphan, Jan P. Amend, Michael S. Rappé, Gene W. Tyson
Software Mentions: 4
Published: almost 6 years ago

10.1186/gb-2013-14-12-r141

Obligate mutualism within a host drives the extreme specialization of a fig wasp genome
Cited by: 79
Author(s): Jin‐Hua Xiao, Zhen Yue, Ling-Yi Jia, Xinhua Yang, Lihua Niu, Zhuo Wang, Peng Zhang, Bao‐Fa Sun, Shunmin He, Zi Li, Tuanlin Xiong, Xintian Wen, Haifeng Gu, Bo Wang, John H. Werren, Robert W. Murphy, David A. Wheeler, Li‐Ming Niu, Guang-Chang Ma, Ting Tang, Sheng‐Nan Bian, Ningxin Wang, Caiqiong Yang, Nan Wang, Yanlong Fu, Wenzhu Li, Soojin V. Yi, Xingyu Yang, Qing Zhou, Changxin Lu, Chunyan Xu, Li He, Lili Yu, Ming Chen, Yawen Zheng, Shaowei Wang, Shuang Zhao, Yanhong Li, Yangyang Yu, Xiaoju Qian, Yuchen Cai, Lianle Bian, Shu Zhang, Junyi Wang, Ye Yin, Hui Xiao, Guan-Hong Wang, Hui Yu, Wei-Jian Wu, James M. Cook, Jun Wang, Dawei Huang
Software Mentions: 4
Published: almost 12 years ago

10.1099/mgen.0.000426

Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings
Cited by: 4
Author(s): Benjamin J. Perry, John T. Sullivan, Elena Colombi, Riley Murphy, Joshua P. Ramsay, Clive W. Ronson
Software Mentions: 4
Published: about 4 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: about 6 years ago

10.1128/mSystems.00299-20

Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms
Cited by: 44
Author(s): Elizabeth A. McDaniel, Brittany F. Peterson, Sarah Stevens, Patricia Q. Tran, Karthik Anantharaman, Katherine D. McMahon
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2021.668644

Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood
Cited by: 9
Author(s): Vojtěch Tláskal, Victor Satler Pylro, Lucia Žifčáková, Petr Baldrián
Software Mentions: 4
Published: over 3 years ago

10.1128/mBio.00530-17

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea
Cited by: 53
Author(s): Connor T. Skennerton, Karuna Chourey, Ramsunder Iyer, Robert L. Hettich, Gene W. Tyson, Victoria J. Orphan
Software Mentions: 4
Published: about 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

10.1093/bioinformatics/bty545

Kinome-wide identification of phosphorylation networks in eukaryotic proteomes
Cited by: 6
Author(s): Luca Parca, Bruno Ariano, Andrea Cabibbo, Martina Paoletti, Annalaura Tamburrini, Antonio Palmeri, Gabriele Ausiello, Manuela Helmer-Citterich
Software Mentions: 3
Published: over 6 years ago

10.1186/s12862-019-1353-z

Origin and diversification of the plasminogen activation system among chordates
Cited by: 26
Author(s): Andrés Chana-Muñoz, Agnieszka Jendroszek, Malene Sønnichsen, Tobias Wang, Michael Ploug, Jan K. Jensen, Peter A. Andreasen, Christian Berthou, Frank Panitz
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-018-4739-1

Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus
Cited by: 14
Author(s): Xiaozhen Ye, Zhenhui Zhong, Hongyi Liu, Lian‐Yu Lin, Mengmeng Guo, Wenhui Guo, Zonghua Wang, Qinghua Zhang, Li Feng, Guodong Lu, Feiping Zhang, Quanzhu Chen
Software Mentions: 3
Published: over 6 years ago

10.1093/gbe/evab126

The Assembled and Annotated Genome of the Fairy-Ring Fungus Marasmius oreades
Cited by: 9
Author(s): Markus Hiltunen, Sandra Lorena Ament‐Velásquez, Hanna Johannesson
Software Mentions: 3
Published: over 3 years ago

10.1186/s12864-020-06980-6

Comparative genomic analysis of Vibrios yields insights into genes associated with virulence towards C. gigas larvae
Cited by: 8
Author(s): Hanna Kehlet-Delgado, Claudia C. Häse, Robert F. Mueller
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2164-12-534

Comparative Genomics of Helicobacter pylori and the human-derived Helicobacter bizzozeronii CIII-1 strain reveal the molecular basis of the zoonotic nature of non-pylori gastric Helicobacter infections in humans
Cited by: 40
Author(s): Thomas Schott, Pradeep Kumar Kondadi, Marja‐Liisa Hänninen, Mirko Rossi
Software Mentions: 3
Published: about 13 years ago

10.1093/gigascience/giy074

Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub
Cited by: 18
Author(s): Fei Gao, Xue Wang, Xuming Li, Mingyue Xu, Huayun Li, Merhaba Abla, Han Sun, Shanjun Wei, Jinchao Feng, Yijun Zhou
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

10.3390/genes12091374

Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods
Cited by: 5
Author(s): Yibing Liu, Ying Yu, Ai Hong, Fengxia Zhang, Xitong Zhao, Huatao Liu, Yong Shi, Kai Xing, Chuduan Wang
Software Mentions: 3
Published: about 3 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

10.1186/s12864-017-3684-8

Iron-regulated small RNA expression as Neisseria gonorrhoeae FA 1090 transitions into stationary phase growth
Cited by: 8
Author(s): Lydgia A. Jackson, Michael Day, Jennie Allen, Edgar J. Scott, David W. Dyer
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-07149-x

Systemic paralogy and function of retinal determination network homologs in arachnids
Cited by: 16
Author(s): Guilherme Gainett, Jesús A. Ballesteros, Charlotte R. Kanzler, Jakob T. Zehms, John M. Zern, Shlomi Aharon, Efrat Gavish‐Regev, Prashant P. Sharma
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12862-015-0319-z

The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history
Cited by: 28
Author(s): Lidija Berke, Berend Snel
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0181399

The antenna transcriptome changes in mosquito Anopheles sinensis, pre- and post- blood meal
Cited by: 14
Author(s): Qian Chen, Di Pei, Jianyong Li, Chengyu Jing, Wenjian Wu, Yahui Man
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2019.00345

Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family
Cited by: 23
Author(s): Jacob S. Stai, Akhilesh Yadav, Carole Sinou, Anne Bruneau, Jeff J. Doyle, David Fernández-Baca, Steven B. Cannon
Software Mentions: 3
Published: over 5 years ago

10.3389/fphar.2020.01075

A Multiomics Approach Unravels New Toxins With Possible In Silico Antimicrobial, Antiviral, and Antitumoral Activities in the Venom of Acanthoscurria rondoniae
Cited by: 16
Author(s): Guilherme A Câmara, Milton Yutaka Nishiyama-Jr, Eduardo S. Kitano, Úrsula Castro de Oliveira, Pedro I. da Silva, Inácio L.M. Junqueira-de-Azevedo, Alexandre Keiji Tashima
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0215492

Bulked segregant analysis RNA-seq (BSR-Seq) validated a stem resistance locus in Aegilops umbellulata, a wild relative of wheat
Cited by: 19
Author(s): Erena A. Edae, Matthew N. Rouse
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2019.01914

Soil Metatranscriptomes Under Long-Term Experimental Warming and Drying: Fungi Allocate Resources to Cell Metabolic Maintenance Rather Than Decay
Cited by: 28
Author(s): Adriana L. Romero‐Olivares, Germán Meléndrez-Carballo, Asunción Lago‐Lestón, Kathleen K. Treseder
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.01228-21

Alternative Transmission Patterns in Independently Acquired Nutritional Cosymbionts of Dictyopharidae Planthoppers
Cited by: 15
Author(s): Anna Michalik, Diego Castillo Franco, Michał Kobiałka, Teresa Szklarzewicz, Adam Stroiński, Piotr Łukasik
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0078858

Comparative and Phylogenomic Evidence That the Alphaproteobacterium HIMB59 Is Not a Member of the Oceanic SAR11 Clade
Cited by: 33
Author(s): Jenny Viklund, Joran Martijn, Thijs J. G. Ettema, Siv G. E. Andersson
Software Mentions: 3
Published: about 11 years ago

10.1186/s12864-015-1588-z

Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica
Cited by: 87
Author(s): Selene L. Fernández-Valverde, Andrew Calcino, Bernard M. Degnan
Software Mentions: 3
Published: over 9 years ago

10.1038/s42003-018-0141-4

PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation
Cited by: 53
Author(s): Julia Jehn, Daniel Gebert, Frank Pipilescu, Sarah Stern, Julian Simon Thilo Kiefer, Charlotte Hewel, David Rosenkranz
Software Mentions: 3
Published: about 6 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

10.1038/s41597-020-0480-0

An improved high-quality genome assembly and annotation of Tibetan hulless barley
Cited by: 23
Author(s): Xingquan Zeng, Tong Xu, Zhihao Ling, Yulin Wang, Xiangfeng Li, Shuqing Xu, Qijun Xu, Zha Sang, Wangmu Qimei, Yuzhen Basang, Jiabu Dunzhu, Mingzhai Yu, Hongjun Yuan, Nyima Tashi
Software Mentions: 3
Published: over 4 years ago

10.1186/s13059-018-1498-x

Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation
Cited by: 38
Author(s): Lakshmipuram S. Swapna, Alyssa M. Molinaro, Nicole Lindsay-Mosher, Bret J. Pearson, John Parkinson
Software Mentions: 3
Published: about 6 years ago

10.1186/s13059-015-0858-z

KIAA0556 is a novel ciliary basal body component mutated in Joubert syndrome
Cited by: 50
Author(s): Anna A. W. M. Sanders, Erik de Vrieze, Anas M. Alazami, Fatema Alzahrani, Erik B. Malarkey, Nasrin Sorusch, Lars Tebbe, Stefanie Kuhns, Teunis J. P. van Dam, Amal Alhashem, Brahim Tabarki, Qianhao Lu, Nils J. Lambacher, Julie Kennedy, Rachel V. Bowie, Lisette Hetterschijt, Sylvia van Beersum, Jeroen van Reeuwijk, Karsten Boldt, Hannie Kremer, Robert A. Kesterson, Dorota Monies, Mohamed Abouelhoda, Ronald Roepman, Martijn A. Huynen, Marius Ueffing, Rob B. Russell, Uwe Wolfrum, Bradley K. Yoder, Erwin van Wijk, Fowzan S. Alkuraya, Oliver E. Blacque
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-021-07467-8

Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes
Cited by: 22
Author(s): Shoubo Tian, Panling Lu, Zhaohui Zhang, Jian Wu, Hui Zhang, Haibin Shen
Software Mentions: 3
Published: over 3 years ago

10.1186/gb-2006-7-2-r12

Cited by: 382
Author(s): Tobias Sargeant, Matthias Marti, Elisabet Caler, Jane M. Carlton, Ken M. Simpson, Terence P. Speed, Alan F. Cowman
Software Mentions: 3
Published: almost 19 years ago

10.1186/1471-2105-13-42

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community
Cited by: 142
Author(s): Konstantinos Krampis, Tim Booth, Brad Chapman, Brijesh K. Tiwari, Mesude Bicak, Dawn Field, Karen E. Nelson
Software Mentions: 3
Published: over 12 years ago

10.1038/sdata.2018.146

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea
Cited by: 33
Author(s): Johannes Alneberg, John Sundh, Christin M. Bennke, Sara Beier, Daniel Lundin, Luisa W. Hugerth, Jarone Pinhassi, Veljo Kisand, Lasse Riemann, Klaus Jürgens, Matthias Labrenz, Anders F. Andersson
Software Mentions: 3
Published: over 6 years ago

10.1186/s13068-016-0534-x

Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies
Cited by: 107
Author(s): Simon Güllert, Martin Fischer, Dmitrij Turaev, Britta Noebauer, Nele Ilmberger, Bernd Wemheuer, Malik Alawi, Thomas Rattei, Rolf Daniel, Ruth A. Schmitz, Adam Grundhoff, Wolfgang R. Streit
Software Mentions: 3
Published: over 8 years ago

10.1186/1748-7188-8-14

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search
Cited by: 15
Author(s): Sebastian Will, Michael Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, Rolf Backofen
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2105-14-S3-S12

Concomitant prediction of function and fold at the domain level with GO-based profiles
Cited by: 4
Author(s): Daniel López, Florencio Pazos
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12864-014-1205-6

Transcriptomic characterisation and genomic glimps into the toxigenic dinoflagellate Azadinium spinosum, with emphasis on polykeitde synthase genes
Cited by: 39
Author(s): Jan M. Meyer, Christian Rödelsperger, Karsten Eichholz, Urban Tillmann, Allan Cembella, Angela McGaughran, Uwe John
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12864-020-07226-1

Contrasting genetic variation and positive selection followed the divergence of NBS-encoding genes in Asian and European pears
Cited by: 6
Author(s): Manyi Sun, Mingyue Zhang, Jugpreet Singh, Bobo Song, Zikai Tang, Yueyuan Liu, Runze Wang, Mengfan Qin, Jiaming Li, Awais Khan, Wu Jun
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2164-10-641

Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
Cited by: 157
Author(s): Haley F. Oliver, Renato H. Orsi, Lalit Ponnala, Uri Keich, Wei Wang, Qi Sun, Samuel Cartinhour, Melanie J. Filiatrault, Martin Wiedmann, Kathryn J. Boor
Software Mentions: 2
Published: almost 15 years ago

10.1186/1471-2164-13-564

Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group
Cited by: 16
Author(s): Edgar J. Scott, David W. Dyer
Software Mentions: 2
Published: about 12 years ago

10.1186/s12864-019-5757-3

Genome-wide analysis of HSP70 family genes in cabbage (Brassica oleracea var. capitata) reveals their involvement in floral development
Cited by: 15
Author(s): Henan Su, Miaomiao Xing, Xing Liu, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Yong Wang, Honghao Lv
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-020-07317-z

Analysis across diverse fish species highlights no conserved transcriptome signature for proactive behaviour
Cited by: 5
Author(s): Sónia Rey, Xing‐Kun Jin, Børge Damsgård, Marie‐Laure Bégout, Simon Mackenzie
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12864-018-4780-0

Dietary aquaculture by-product hydrolysates: impact on the transcriptomic response of the intestinal mucosa of European seabass (Dicentrarchus labrax) fed low fish meal diets
Cited by: 42
Author(s): Alexandre Leduc, Céline Zatylny-Gaudin, Marie Robert, Erwan Corre, Gildas Le Corguillé, Hélène Castel, Antoine Lefevre-Scelles, Valérie Fournier, Enric Gisbert, Karl B. Andrée, Joël Henry
Software Mentions: 2
Published: over 6 years ago

10.1186/s12870-014-0316-1

Transcriptome analysis of ripe and unripe fruit tissue of banana identifies major metabolic networks involved in fruit ripening process
Cited by: 80
Author(s): Mehar Hasan Asif, Deepika Lakhwani, Sumya Pathak, Parul Gupta, Sumit K. Bag, Paras Nath, Prabodh Kumar Trivedi
Software Mentions: 2
Published: almost 10 years ago

10.1186/1756-0500-7-928

The loose evolutionary relationships between transcription factors and other gene products across prokaryotes
Cited by: 2
Author(s): Marc del Grande, Gabriel Moreno–Hagelsieb
Software Mentions: 2
Published: almost 11 years ago

10.1080/08927014.2016.1233325

Profiling of adhesive-related genes in the freshwater cnidarianHydra magnipapillataby transcriptomics and proteomics
Cited by: 36
Author(s): Marcos Rodrigues, Thomas Ostermann, Leopold Kremeser, Herbert Lindner, Christian Beisel, Eugène Berezikov, Bert Hobmayer, Peter Ladurner
Software Mentions: 2
Published: about 8 years ago

10.3390/md16050140

Genome-Wide Comparison Reveals a Probiotic Strain Lactococcus Lactis WFLU12 Isolated from the Gastrointestinal Tract of Olive Flounder (Paralichthys Olivaceus) Harboring Genes Supporting Probiotic Action
Cited by: 14
Author(s): Thanh Luan Nguyen, Do-Hyung Kim
Software Mentions: 2
Published: over 6 years ago

10.1099/mgen.0.000560

Niche-specific adaptation of Lactobacillus helveticus strains isolated from malt whisky and dairy fermentations
Cited by: 3
Author(s): Yoshihiko Kido, Shintaro Maeno, Hiroki Tanno, Yuko Kichise, Yuh Shiwa, Akihito Endo
Software Mentions: 2
Published: over 3 years ago

10.1099/mgen.0.000043

Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes
Cited by: 139
Author(s): Paul O. Sheridan, Jennifer C. Martin, Trevor D. Lawley, Hilary P. Browne, Hugh M. B. Harris, Annick Bernalier-Donadille, Sylvia H. Duncan, Paul W. O’Toole, Karen P. Scott, Harry J. Flint
Software Mentions: 2
Published: almost 9 years ago

10.1099/mgen.0.000455

Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes
Cited by: 15
Author(s): Fanny Berglund, Maria Elisabeth Böhm, Anton Martinsson, Stefan Ebmeyer, Tobias Österlund, Anna Johnning, D. G. Joakim Larsson, Erik Kristiansson
Software Mentions: 2
Published: about 4 years ago

Projects: pypi: hmmer

Papers Mentioning hmmer 196