Ecosyste.ms: Papers

10.1038/s41598-019-39576-6

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

10.1371/journal.pone.0000671

Analysis of Expressed Sequence Tags of the Cyclically Parthenogenetic Rotifer Brachionus plicatilis
Cited by: 50
Author(s): K. Suga, David B. Mark Welch, Yukari Tanaka, Yoshitaka Sakakura, Atsushi Hagiwara
Software Mentions: 5
Published: over 17 years ago

10.1186/1471-2105-9-420

XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
Cited by: 54
Author(s): Daniel N. Frank
Software Mentions: 5
Published: about 16 years ago

10.1186/1471-2105-10-391

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
Cited by: 6
Author(s): Chunguang Liang, Alexander Schmid, María José López‐Sánchez, Andrés Moya, Roy Gross, Jörg Bernhardt, Thomas Dandekar
Software Mentions: 5
Published: about 15 years ago

10.7717/peerj.2768

Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America
Cited by: 44
Author(s): Jana M. U’Ren, A. Elizabeth Arnold
Software Mentions: 4
Published: about 8 years ago

10.1371/currents.RRN1237

Molecular data and ploidal levels indicate several putative allopolyploidization events in the genus Potentilla (Rosaceae)
Cited by: 26
Author(s): Mats Töpel, Magnus Lundberg, Torsten Eriksson, Bente Eriksen
Software Mentions: 4
Published: over 13 years ago

10.3389/fmicb.2019.00635

Denitrifying Bacteria Active in Woodchip Bioreactors at Low-Temperature Conditions
Cited by: 31
Author(s): Jeonghwan Jang, Emily L. Anderson, Rodney T. Venterea, Michael J. Sadowsky, Carl J. Rosen, Gary W. Feyereisen, Satoshi Ishii
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-14-523

Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains
Cited by: 38
Author(s): Yuanyuan Li, Xiao Chang, Wen-Bang Yu, Hao Li, Zhiqiang Ye, Hui Yu, Baohong Liu, Yan Zhang, Siliang Zhang, Bang‐Ce Ye, Yixue Li
Software Mentions: 4
Published: almost 12 years ago

10.1186/1476-4598-9-213

Loss, mutation and deregulation of L3MBTL4 in breast cancers
Cited by: 46
Author(s): Lynda Addou-Klouche, José Adélaı̈de, Pascal Finetti, Nathalie Cervera, Anthony Ferrari, Ismahane Bekhouche, Fabrice Sircoulomb, Christos Sotiriou, Patrice Viens, Soraya Moulessehoul, François Bertucci, Daniel Birnbaum, Max Chaffanet
Software Mentions: 4
Published: over 14 years ago

10.1186/1471-2164-13-136

A second generation framework for the analysis of microsatellites in expressed sequence tags and the development of EST-SSR markers for a conifer, Cryptomeria japonica
Cited by: 60
Author(s): S. Ueno, Yoshinari Moriguchi, Kentaro Uchiyama, Tokuko Ujino‐Ihara, Norihiro Futamura, Tetsuya Sakurai, Kenji Shinohara, Yoshihiko Tsumura
Software Mentions: 4
Published: almost 13 years ago

10.1186/1752-0509-6-72

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum
Cited by: 12
Author(s): Daniela Beißer, Markus A. Grohme, Joachim Kopka, Marcus Frohme, Ralph O. Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W. Klau, Marcus Dittrich, Tobias Müller
Software Mentions: 4
Published: over 12 years ago

10.1186/s12864-020-6635-8

Tracy: basecalling, alignment, assembly and deconvolution of sanger chromatogram trace files
Cited by: 48
Author(s): Tobias Rausch, Markus Hsi-Yang Fritz, Andreas Untergasser, Vladimı́r Beneš
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-018-19554-0

Human migration and the spread of malaria parasites to the New World
Cited by: 65
Author(s): Priscila T. Rodrigues, Hugo O. Valdivia, Thaís Crippa de Oliveira, João M. P. Alves, Ana Maria Ribeiro de Castro Duarte, Crispim Cerutti-Junior, Julyana Cerqueira Buery, Cristiana Ferreira Alves de Brito, Júlio César de Souza, Zelinda Maria Braga Hirano, Marina Galvão Bueno, José Luiz Catão‐Dias, Rosely S. Malafronte, Simone Ladeia‐Andrade, Toshihiro Mita, Ana María Santamaría, Igor Calzada, Indah Setyawati Tantular, Fumihiko Kawamoto, Leonie R. J. Raijmakers, Ivo Müeller, M. Andreína Pacheco, Ananías A. Escalante, Ingrid Felger, Marcelo U. Ferreira
Software Mentions: 4
Published: almost 7 years ago

10.1186/1743-422X-8-406

Sequencing of bovine herpesvirus 4 v.test strain reveals important genome features
Cited by: 18
Author(s): Léonor Palmeira, Bénédicte Machiels, Céline Lété, Alain Vanderplasschen, Laurent Gillet
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pgen.1000570

Coevolution of Interacting Fertilization Proteins
Cited by: 131
Author(s): Nathan L. Clark, Joe Gasper, Masashi Sekino, Stevan A. Springer, Charles F. Aquadro, Willie J. Swanson
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0236907

Novel candidates of pathogenic variants of the BRCA1 and BRCA2 genes from a dataset of 3,552 Japanese whole genomes (3.5KJPNv2)
Cited by: 7
Author(s): Hideki Tokunaga, Keita Iida, Atsushi Hozawa, Soichi Ogishima, Yoh Watanabe, Shogo Shigeta, Muneaki Shimada, Yumi Yamaguchi-Kabata, Shu Tadaka, Fumiki Katsuoka, Itó S, Kazuki Kumada, Yohei Hamanaka, Nobuo Fuse, Kengo Kinoshita, Masayuki Yamamoto, Nobuo Yaegashi, Jun Yasuda
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-11-38

SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read
Cited by: 159
Author(s): Juan Falgueras, Antonio Jiménez Lara, Noé Fernández-Pozo, Francisco R. Cantón, Guillermo Pérez-Trabado, M. Gonzalo Claros
Software Mentions: 3
Published: almost 15 years ago

10.1186/1471-2105-5-187

Cited by: 120
Author(s): James D. Wasmuth, Mark Blaxter
Software Mentions: 3
Published: almost 21 years ago

10.4056/sigs.4258318

Genome sequence of the Litoreibacter arenae type strain (DSM 19593T), a member of the Roseobacter clade isolated from sea sand
Cited by: 8
Author(s): Thomas Riedel, Anne Fiebig, Jörn Petersen, Sabine Gronow, Nikos C. Kyrpides, Markus Göker, Hans‐Peter Klenk
Software Mentions: 3
Published: about 11 years ago

10.1186/1471-2164-12-73

Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies
Cited by: 33
Author(s): Minxiao Wang, Song Sun, Chaolun Li, Xin Shen
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0010598

The Human Nasal Microbiota and Staphylococcus aureus Carriage
Cited by: 351
Author(s): Daniel N. Frank, Leah M. Feazel, Mary Bessesen, Connie S. Price, Edward N. Janoff, Norman R. Pace
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-11-168

Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer
Cited by: 47
Author(s): Brahim Mali, Markus A. Grohme, Frank Förster, Thomas Dandekar, Martina Schnölzer, Dirk Reuter, Weronika Wełnicz, Ralph O. Schill, Marcus Frohme
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0031886

Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain
Cited by: 29
Author(s): John D. Kriesel, Maurine R. Hobbs, Brandt Jones, Brett Milash, Rashed M. Nagra, Kael F. Fischer
Software Mentions: 2
Published: almost 13 years ago

10.1111/j.1365-2052.2008.01848.x

Monophyletic origin of domestic bactrian camel (<i>Camelus bactrianus</i>) and its evolutionary relationship with the extant wild camel (<i>Camelus bactrianus ferus</i>)
Cited by: 86
Author(s): Rimutu Ji, Pin Cui, Feng Ding, Jian Guo Geng, Hongwei Gao, H. Zhang, Jie-Ying Yu, Shigang Hu, Hongzhe Meng
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0110113

Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)
Cited by: 17
Author(s): Daniela Holtgräwe, Thomas Rosleff Sörensen, Prisca Viehöver, Jessica Schneider, Britta Schulz, Dietrich Borchardt, Thomas Kraft, Heinz Himmelbauer, Bernd Weißhaar
Software Mentions: 2
Published: about 10 years ago

10.1002/mgg3.411

Whole‐exome sequencing for variant discovery in blepharospasm
Cited by: 16
Author(s): Jun Tian, Satya R. Vemula, Jianfeng Xiao, Enza Maria Valente, Giovanni Defazio, Simona Petrucci, Angelo Fabio Gigante, Monika Rudzińska‐Bar, Zbigniew K. Wszołek, Kathleen D. Kennelly, Ryan J. Uitti, Jay A. van Gerpen, Peter Hedera, Elizabeth J. Trimble, Mark S. LeDoux
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0206732

Past vicariance promoting deep genetic divergence in an endemic frog species of the Espinhaço Range in Brazil: The historical biogeography of Bokermannohyla saxicola (Hylidae)
Cited by: 13
Author(s): Augusto César Nascimento, Anderson V. Chaves, Felipe Sá Fortes Leite, Paula Cabral Eterovick, Fabrício R. Santos
Software Mentions: 2
Published: about 6 years ago

10.1186/1471-2105-9-5

EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration
Cited by: 47
Author(s): Javier Forment, Francisco Jurado Gilabert, Antonio Robles, Vicente Conejero, F. Nuez, José Blanca
Software Mentions: 2
Published: almost 17 years ago

10.1186/1471-2164-7-49

Development of a chicken 5 K microarray targeted towards immune function
Cited by: 31
Author(s): Jacqueline Smith, David Speed, Paul Hocking, Richard Talbot, W.G.J. Degen, Virgil E.J.C. Schijns, Elizabeth J. Glass, David W. Burt
Software Mentions: 2
Published: almost 19 years ago

10.1186/1471-2148-11-120

Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes
Cited by: 38
Author(s): Kelly E. O’Quin, Daniel A. Smith, Zan Naseer, Jane E. Schulte, Samuel D Engel, Yong-Hwee Eddie Loh, J. Todd Streelman, Jeffrey L. Boore, Karen L. Carleton
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-9-423

Development of genomic resources for Citrus clementina: Characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences
Cited by: 82
Author(s): Javier Terol, Miguel A. Gutiérrez–Naranjo, Patrick Ollitrault, Manuel Talón
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2164-8-462

Construction and characterization of an expressed sequenced tag library for the mosquito vector Armigeres subalbatus
Cited by: 12
Author(s): George F. Mayhew, Lyric C. Bartholomay, Hang-Yen Kou, Thomas A. Rocheleau, Jeremy F. Fuchs, Matthew T. Aliota, I-Yu Tsao, Chiung-Yen Huang, Tze-Tze Liu, Kwang‐Jen Hsiao, Shih‐Feng Tsai, Ueng Cheng Yang, Nicole T. Perna, Wen-Long Cho, Bruce M. Christensen, Cheng-Chen Chen
Software Mentions: 2
Published: about 17 years ago

10.3389/fpls.2020.00156

A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping
Cited by: 6
Author(s): Daniela Holtgräwe, Thomas Rosleff Soerensen, Ludger Hausmann, Boas Pucker, Prisca Viehöver, Reinhard Töpfer, Bernd Weißhaar
Software Mentions: 2
Published: almost 5 years ago

10.1186/1756-0500-3-257

A direct comparison of the KB™ Basecaller and phred for identifying the bases from DNA sequencing using chain termination chemistry
Cited by: 10
Author(s): Richard W. Hyman, Hui Jiang, Marilyn Fukushima, Ronald W. Davis
Software Mentions: 2
Published: about 14 years ago

10.1186/1756-0500-4-254

The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones
Cited by: 7
Author(s): Paula Moolhuijzen, A.E. Lew-Tabor, Jess A. T. Morgan, M. Rodriguez-Valle, Daniel G. Peterson, Scot E. Dowd, Felix D. Guerrero, M. Bellgard, R. Appels
Software Mentions: 2
Published: over 13 years ago

10.1186/gb-2007-8-1-r9

Cited by: 52
Author(s): John Wang, Stephanie Jemielity, Paolo Uva, Yannick Wurm, Johannes Gräff, Laurent Keller
Software Mentions: 2
Published: almost 18 years ago

10.1186/gb-2007-8-4-r45

Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags
Cited by: 74
Author(s): Jan Gorodkin, Susanna Cirera, Jakob Hedegaard, Michael J. Gilchrist, Frank Panitz, Claus B. Jørgensen, Karsten Scheibye-Knudsen, Troels Arvin, Steen Lumholdt, Milena Sawera, Trine Green, Bente J. Nielsen, Jakob Hull Havgaard, Carina Rosenkilde, Junjun Wang, Heng Li, Ruiqiang Li, Bin Liu, Songnian Hu, Wei Dong, Li Wei, Jun Yu, Jian Wang, Hans‐Henrik Stærfeldt, Rasmus Wernersson, Lone Bruhn Madsen, Bo Thomsen, Henrik Hornshøj, Bin Zhan, Xuegang Wang, Xuefei Wang, Lars Bolund, Søren Brunak, Huanming Yang, Christian Berthou, Merete Fredholm
Software Mentions: 2
Published: almost 18 years ago

10.1371/journal.pgen.1000869

KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading
Cited by: 293
Author(s): Anna C. Groner, Sylvain Meylan, Angela Ciuffi, Nadine Zangger, Giovanna Ambrosini, Nicolas Dénervaud, Philipp Bücher, Didier Trono
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pgen.1000516

Change of Gene Structure and Function by Non-Homologous End-Joining, Homologous Recombination, and Transposition of DNA
Cited by: 27
Author(s): Wolfgang Goettel, Joachim Messing
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pgen.1000471

Widespread Genomic Signatures of Natural Selection in Hominid Evolution
Cited by: 401
Author(s): Graham McVicker, David Gordon, Colleen Davis, Phil Green
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-6-43

Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens
Cited by: 61
Author(s): Stefan A. Rensing, Dana Fritzowsky, Daniel Lang, Ralf Reski
Software Mentions: 2
Published: almost 20 years ago

10.1371/journal.pone.0014234

Evolution of Disease Response Genes in Loblolly Pine: Insights from Candidate Genes
Cited by: 24
Author(s): Elhan S. Ersoz, Mark H. Wright, Santiago C. González‐Martínez, Charles H. Langley, David B. Neale
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-12-530

Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels
Cited by: 26
Author(s): Isabelle Boutet, Raymond Ripp, Odile Lecompte, Carole Dossat, Erwan Corre, Arnaud Tanguy, François H. Lallier
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0064621

Transcriptome and Proteome Data Reveal Candidate Genes for Pollinator Attraction in Sexually Deceptive Orchids
Cited by: 44
Author(s): Khalid E. M. Sedeek, Weihong Qi, Monica A. Schauer, Alok Gupta, Lucy Poveda, Shuqing Xu, Zhong‐Jian Liu, Ueli Grossniklaus, Florian P. Schiestl, Philipp M. Schlüter
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0007811

Culture-Independent Microbiological Analysis of Foley Urinary Catheter Biofilms
Cited by: 78
Author(s): Daniel N. Frank, Shandra Wilson, Allison L. St. Amand, Norman R. Pace
Software Mentions: 2
Published: about 15 years ago

10.1186/1471-2164-15-506

ShrimpGPAT: a gene and protein annotation tool for knowledge sharing and gene discovery in shrimp
Cited by: 7
Author(s): Parpakron Korshkari, Sirintra Vaiwsri, Timothy W. Flegel, Sudsanguan Ngamsuriyaroj, Burachai Sonthayanon, Anuphap Prachumwat
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0035168

The Mitochondrial Genome of the Lycophyte Huperzia squarrosa: The Most Archaic Form in Vascular Plants
Cited by: 37
Author(s): Yang Liu, Binbin Wang, Peng Cui, Libo Li, Jia‐Yu Xue, Jianing Yu, Yin‐Long Qiu
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0184196

Complete chloroplast genome of green tide algae Ulva flexuosa (Ulvophyceae, Chlorophyta) with comparative analysis
Cited by: 26
Author(s): Chuner Cai, Lingke Wang, Liang Zhou, Peimin He, Binghua Jiao
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0250968

Screening and verification of extranuclear genetic markers in green tide algae from the Yellow Sea
Cited by: 11
Author(s): Chuner Cai, Kai Gu, Hui Zhao, Sophie Steinhagen, Peimin He, Thomas Wichard
Software Mentions: 1
Published: over 3 years ago

10.3389/fbioe.2020.553474

A Single Amino Acid Change to Taq DNA Polymerase Enables Faster PCR, Reverse Transcription and Strand-Displacement
Cited by: 6
Author(s): Wayne M. Barnes, Zhian Zhang, Milko B. Kermekchiev
Software Mentions: 1
Published: almost 4 years ago

10.3389/fpls.2015.00979

A Genome-wide Combinatorial Strategy Dissects Complex Genetic Architecture of Seed Coat Color in Chickpea
Cited by: 24
Author(s): Deepak Bajaj, Shouvik Das, Hari D. Upadhyaya, Rajeev Ranjan, Saurabh Badoni, Vinod Kumar, Shailesh Tripathi, C. L. L. Gowda, Shuchi Sharma, Sube Singh, Akhilesh K. Tyagi, Swarup K. Parida
Software Mentions: 1
Published: about 9 years ago

10.1128/genomeA.01060-13

Genome Sequence of the Thermophilic Cyanobacterium <i>Thermosynechococcus</i> sp. Strain NK55a
Cited by: 15
Author(s): Sergey Stolyar, Zhenfeng Liu, Vera Thiel, Lynn P. Tomsho, Nicolás Pinel, Karen E. Nelson, Stephen R. Lindemann, Margaret F. Romine, Shin Haruta, Stephan C. Schuster, Donald A. Bryant, Jim K. Fredrickson
Software Mentions: 1
Published: almost 11 years ago

10.1186/gb-2005-6-7-r60

Cited by: 89
Author(s): Charles L. Magness, P Campion Fellin, Matthew Thomas, Marcus J. Korth, Michael B. Agy, Sean Proll, Matthew Fitzgibbon, Christina Scherer, Douglas G. Miner, Michael G. Katze, Shawn P. Iadonato
Software Mentions: 1
Published: almost 20 years ago

10.1186/gb-2009-10-8-r85

Community-wide analysis of microbial genome sequence signatures
Cited by: 470
Author(s): Gregory J. Dick, Anders F. Andersson, Brett J. Baker, Stephanie Simmons, Brian C. Thomas, Alexis P Yelton, Jillian F. Banfield
Software Mentions: 1
Published: almost 16 years ago

10.1002/jobm.201000117

Novel application of the MSSCP method in biodiversity studies
Cited by: 6
Author(s): Karolina Tomczyk-Żak, Szymon Kaczanowski, Magdalena Górecka, Urszula Zieenkiewicz
Software Mentions: 1
Published: over 13 years ago

10.1038/srep28969

A novel role for pigment genes in the stress response in rainbow trout (Oncorhynchus mykiss)
Cited by: 17
Author(s): Uniza W. Khan, Øyvind Øverli, Patricia M. Hinkle, Farhan Ahmad Pasha, Ida Beitnes Johansen, Ingunn Berget, Patricia I.M. Silva, Silje Kittilsen, Erik Höglund, Stig W. Omholt, Dag Inge Våge
Software Mentions: 1
Published: over 8 years ago

10.1007/s10739-018-9538-7

The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project
Cited by: 37
Author(s): Kathryn Maxson Jones, Rachel A. Ankeny, Robert Cook-Deegan
Software Mentions: 1
Published: about 6 years ago

10.1155/2007/17542

Temporal Gene Expression Profiling of the Wheat Leaf Rust Pathosystem Using cDNA Microarray Reveals Differences in Compatible and Incompatible Defence Pathways
Cited by: 35
Author(s): Bourlaye Fofana, Travis Banks, Brent D. McCallum, Stephen E. Strelkov, Sylvie Cloutier
Software Mentions: 1
Published: about 17 years ago

10.1186/s13028-019-0493-x

Association between single-nucleotide polymorphisms within candidate genes and fertility in Landrace and Duroc pigs
Cited by: 2
Author(s): Nina Hårdnes Tremoen, Maren van Son, Ina Andersen-Ranberg, Eli Grindflek, Frøydis Deinboll Myromslien, Ann Helen Gaustad, Dag Inge Våge
Software Mentions: 1
Published: about 5 years ago

10.1098/rsob.130010

Genomics and genetics of<i>Sulfolobus islandicus</i>LAL14/1, a model hyperthermophilic archaeon
Cited by: 56
Author(s): Carole Jaubert, Chloë Danioux, Jacques Oberto, Diego Cortez, Ariane Bize, Mart Krupovìč, Qunxin She, Patrick Forterre, David Prangishvili, Guennadi Sezonov
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-7-185

Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server
Cited by: 3
Author(s): H. Alexander Ebhardt, Kay C. Wiese, Peter J. Unrau
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2105-7-115

MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools
Cited by: 17
Author(s): Chun Liang, Feng Sun, Haiming Wang, Junfeng Qu, Robert M. Freeman, Lee H. Pratt, Marie‐Michèle Cordonnier‐Pratt
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2407-10-426

Distinguishing between cancer driver and passenger gene alteration candidates via cross-species comparison: a pilot study
Cited by: 18
Author(s): Xinglai Ji, Jie Tang, Richard B. Halberg, Dana Busam, Steve Ferriera, Maria Marjorette O. Peña, Chinnambally Venkataramu, Timothy J. Yeatman, Shaying Zhao
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2148-12-60

The phylogenetics of Anguillicolidae (Nematoda: Anguillicoloidea), swimbladder parasites of eels
Cited by: 58
Author(s): Dominik R. Laetsch, Emanuel Heitlinger, Horst Taraschewski, Steven A. Nadler, Mark Blaxter
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2148-12-229

Analyses of expressed sequence tags in Neurosporareveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi
Cited by: 12
Author(s): Kristiina Nygren, Andreas Wållberg, Nicklas Samils, Jason E. Stajich, Jeffrey P. Townsend, Magnus Karlsson, Hanna Johannesson
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2156-10-66

Automated DNA mutation detection using universal conditions direct sequencing: application to ten muscular dystrophy genes
Cited by: 13
Author(s): Richard Rodney Bennett, Hal E. Schneider, Elicia Estrella, Stephanie L. Burgess, Andrew Cheng, Caitlín E. Barrett, Va Lip, Poh San Lai, Yiping Shen, Bai-Lin Wu, Basil T. Darras, Alan H. Beggs, Louis M. Kunkel
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2156-9-41

Variation at the Calpain 3 gene is associated with meat tenderness in zebu and composite breeds of cattle
Cited by: 64
Author(s): W. Barendse, B. E. Harrison, R. J. Bunch, Morgane Thomas
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2156-8-17

Mutation screen and association studies in the Diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13
Cited by: 30
Author(s): Susann Friedel, Kathrin Reichwald, André Scherag, Harald Brumm, Anne-Kathrin Wermter, Hans-Rudolf Fries, Kerstin Koberwitz, Martin Wabitsch, Thomas Meitinger, Matthias Platzer, Heike Biebermann, Anke Hinney, Johannes Hebebrand
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-6-34

Marine Genomics: A clearing-house for genomic and transcriptomic data of marine organisms
Cited by: 37
Author(s): David J. McKillen, Yian Ann Chen, Chuming Chen, Matthew J. Jenny, Harold F. Trent, Javier Robalino, David C. McLean, Paul S. Gross, R. W. Chapman, Gregory W. Warr, Jonas S. Almeida
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-11-407

Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes
Cited by: 47
Author(s): Eduardo R. Macagno, Terry Gaasterland, Lee Edsall, Vineet Bafna, Marcelo B. Soares, Todd E. Scheetz, Thomas L. Casavant, Corinne Da Silva, Patrick Wincker, Aurélie Tasiemski, Michel Salzet
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-13-112

The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110
Cited by: 69
Author(s): Patrick Schwientek, Rafael Szczepanowski, Christian Rückert, Jörn Kalinowski, Andreas Klein, Klaus Selber, Udo F. Wehmeier, Jens Stoye, Alfred Pühler
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-10-386

Generation, annotation, and analysis of ESTs from midgut tissue of adult female Anopheles stephensi mosquitoes
Cited by: 8
Author(s): Deepak P. Patil, Santosh S. Atanur, Dhiraj Dhotre, D Anantharam, Vineet Mahajan, Sandeep A. Walujkar, Rakesh K Chandode, Girish Kulkarni, Pankaj S. Ghate, Abhishek Srivastav, Kannayakanahalli M. Dayananda, Neha Gupta, Bhakti Bhagwat, Rajendra Joshi, Devendra T. Mourya, Milind S. Patole, Yogesh S. Shouche
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2164-9-318

A genome-wide 20 K citrus microarray for gene expression analysis
Cited by: 49
Author(s): Maria Ángeles Martínez-Godoy, Nuria Mauri, José Juárez, María Carmen Marques, Julia Santiago, Javier Forment, J. Gadea
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-8-416

An optimized procedure greatly improves EST vector contamination removal
Cited by: 75
Author(s): Yi‐An Chen, Chang-Chun Lin, Chin-Di Wang, Huan-Bin Wu, Pei-Ing Hwang
Software Mentions: 1
Published: about 17 years ago

10.1186/1471-2164-12-389

De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity
Cited by: 176
Author(s): Massimo Iorizzo, Douglas Senalik, Dariusz Grzebelus, Megan J. Bowman, Pablo Federico Cavagnaro, Marta Matvienko, Hamid Ashrafi, Allen Van Deynze, Philipp W. Simon
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-9-96

Annotation of expressed sequence tags for the East African cichlid fish Astatotilapia burtoni and evolutionary analyses of cichlid ORFs
Cited by: 49
Author(s): Walter Salzburger, Susan C. P. Renn, Dirk Steinke, Ingo Braasch, Hans A. Hofmann, Axel Meyer
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-8-31

Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance
Cited by: 74
Author(s): Javier Terol, Ana Conesa, Jose M. Colmenero, Manuel Cercós, Francisco R. Tadeo, Javier Agustí, Enriqueta Alós, Fernando Andrés, Guillermo Soler, Javier Brumós, Domingo J. Iglesias, Stefan Götz, Francisco Legaz, Xavier Argout, B. Courtois, Patrick Ollitrault, Carole Dossat, Patrick Wincker, Raphaël Morillón, Manuel Talón
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-9-6

A first glimpse at the transcriptome of Physarum polycephalum
Cited by: 42
Author(s): Gernot Glöckner, Georg Golderer, Gabriele Werner-Felmayer, Sonja Meyer, Wolfgang Marwan
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-8-217

Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes
Cited by: 29
Author(s): John K. Colbourne, Brian D. Eads, Joseph R. Shaw, Elizabeth A. Bohuski, Darren J. Bauer, Justen Andrews
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-8-448

Functional annotation of 19,841 Populus nigra full-length enriched cDNA clones
Cited by: 35
Author(s): Tokihiko Nanjo, Tetsuya Sakurai, Yasushi Totoki, Atsushi Toyoda, Mitsuru Nishiguchi, Tomoyuki Kado, Tomohiro Igasaki, Norihiro Futamura, Motoaki Seki, Yoshiyuki Sakaki, Kazuo Shinozaki, Kenji Shinohara
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-8-75

Expansion of the Bactericidal/Permeability Increasing-like (BPI-like) protein locus in cattle
Cited by: 24
Author(s): Thomas T. Wheeler, Kylie Hood, Nauman J. Maqbool, John C. McEwan, Colin D. Bingle, Shaying Zhao
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-10-258

Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont
Cited by: 146
Author(s): Shinichi Sunagawa, Emily Wilson, Michael Thaler, Marc L. Smith, Carlo Caruso, John R. Pringle, Virginia M. Weis, Mónica Medina, Jodi Schwarz
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-11-210

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics
Cited by: 171
Author(s): Koh Aoki, Kentarô Yano, Ayako Suzuki, Shingo Kawamura, Nozomu Sakurai, Kenichi Suda, Atsushi Kurabayashi, Tatsuya Suzuki, Taneaki Tsugane, Masao Watanabe, Kazuhide Ooga, Maiko Torii, Takanori Narita, Tadasu Shin-I, Yuji Kohara, Nobuto Yamamoto, Hideki Takahashi, Yuichiro Watanabe, Mayumi Egusa, Motoichiro Kodama, Yuki Ichinose, Mari Kikuchi, Sumire Fukushima, Akiko Okabe, Tsutomu Arie, Yuko Sato, Katsumi Yazawa, Shinobu Satoh, Toshikazu Omura, Hiroshi Ezura, Daisuke Shibata
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-14-137

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation
Cited by: 55
Author(s): Glenn T. Howe, Jianbin Yu, Brian J. Knaus, Richard Cronn, Scott E. Kolpak, Peter C. Dolan, W. Walter Lorenz, Jeffrey F. D. Dean
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-12-163

Comparative analysis of mitochondrial genomes between a wheat K-type cytoplasmic male sterility (CMS) line and its maintainer line
Cited by: 75
Author(s): Huitao Liu, Peng Cui, Kai Zhan, Qiang Lin, Guoyin Zhuo, Xiaoli Guo, Feng Ding, Wenlong Yang, Dongcheng Liu, Songnian Hu, Jun Yu, Aimin Zhang
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-8-241

A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus): an evolutionary history of camelidae
Cited by: 70
Author(s): Peng Cui, Rimutu Ji, Feng Ding, Dandan Qi, Hongwei Gao, He Meng, Jun Yu, Songnian Hu, Heping Zhang
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-14-870

Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen
Cited by: 32
Author(s): Sini Junttila, Asta Laiho, Attila Gyenesei, Stephen Rudd
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-10-136

A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta
Cited by: 64
Author(s): Xin Shen, Xiaoyin Ma, Jianfeng Ren, Fangqing Zhao
Software Mentions: 1
Published: almost 16 years ago

10.1186/1471-2180-6-7

Generation, annotation, and analysis of an extensive Aspergillus niger EST collection
Cited by: 38
Author(s): N Semova, Reginald Storms, Tricia John, Pascale Gaudet, Peter Ulycznyj, Xiang Jia Min, Jian Sun, Gregory Butler, Adrian Tsang
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2229-8-69

A blackberry (Rubus L.) expressed sequence tag library for the development of simple sequence repeat markers
Cited by: 35
Author(s): Kim S. Lewers, Chris Saski, Brandon J. Cuthbertson, David C Henry, Meg Staton, Dorrie Main, Anik L. Dhanaraj, Lisa J. Rowland, J. P. Tomkins
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2229-12-133

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles
Cited by: 35
Author(s): Joanne A. Labate, Larry D. Robertson
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2229-11-86

Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis viniferaL.) based on curation and mining of large-scale EST data sets
Cited by: 37
Author(s): Richard L. Tillett, Ali Ergül, Rebecca L. Albion, Karen Schlauch, Grant R. Cramer, John C. Cushman
Software Mentions: 1
Published: over 13 years ago

10.1016/j.mce.2005.11.049

The evolution and genomic landscape of CGB1 and CGB2 genes
Cited by: 37
Author(s): Pille Hallast, Kristiina Rull, Maris Laan
Software Mentions: 1
Published: almost 18 years ago

10.3390/molecules25215058

Teratopyrones A–C, Dimeric Naphtho-γ-Pyrones and Other Metabolites from Teratosphaeria sp. AK1128, a Fungal Endophyte of Equisetum arvense
Cited by: 1
Author(s): Ya Ming Xu, A. Elizabeth Arnold, Jana M. U Ren, Xuan Li, Wen Qiong Wang, A. A. Leslie Gunatilaka
Software Mentions: 1
Published: about 4 years ago

10.1186/1297-9716-44-64

Small ruminant lentivirus genetic subgroups associate with sheep TMEM154 genotypes
Cited by: 19
Author(s): L. H. Sider, Michael P. Heaton, Carol G. Chitko-McKown, Gregory P Harhay, Timothy P. L. Smith, K. A. Leymaster, William W. Laegreid, Marion Clawson
Software Mentions: 1
Published: over 11 years ago

10.1080/21505594.2021.1899616

Reductive evolution of virulence repertoire to drive the divergence between community- and hospital-associated methicillin-resistant <i>Staphylococcus aureus</i> of the ST1 lineage
Cited by: 7
Author(s): Marina Farrel Cortês, Ana Botelho, Paula Terra Bandeira, William Mouton, Cédric Badiou, Michèle Bes, Nicholas Costa Barroso Lima, André Elias Rodrigues Soares, Rangel Celso Souza, Luiz Gonzaga Paula de Almeida, Patrícia Martins-Simões, Ana Tereza Ribeiro de Vasconcelos, Marisa Fabiana Nicolás, Frédéric Laurent, Paul J. Planet, Agnes Marie Sá Figueiredo
Software Mentions: 1
Published: almost 4 years ago

10.1186/s40851-017-0084-5

Paternal phylogeographic structure of the brown bear (Ursus arctos) in northeastern Asia and the effect of male-mediated gene flow to insular populations
Cited by: 41
Author(s): Daisuke Hirata, Tsutomu Mano, Alexei V. Abramov, Gennady Baryshnikov, П. А. Косинцев, Koichi Murata, Ryuichi Masuda
Software Mentions: 1
Published: about 7 years ago

10.1186/s13071-018-2907-4

A new Aura virus isolate in Brazil shows segment duplication in the variable region of the nsP3 gene
Cited by: 3
Author(s): Ana Luiza Pamplona Mosimann, Mirian Krystel de Siqueira, Lígia Fernanda Ceole, Claudia Nunes Duarte dos Santos
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.0010005

Evidence for Domesticated and Wild Populations of Saccharomyces cerevisiae
Cited by: 350
Author(s): Justin C. Fay, Joseph A. Benavides
Software Mentions: 1
Published: over 19 years ago

10.1371/journal.pgen.1001085

Commercially Available Outbred Mice for Genome-Wide Association Studies
Cited by: 124
Author(s): Binnaz Yalcin, Jérôme Nicod, Amarjit Bhomra, Sean Davidson, James Cleak, Laurent Farinelli, Magne Østerås, Adam Whitley, Yuan Wei, Xiangchao Gan, Martin Goodson, Paul Klenerman, Ansuman T. Satpathy, Diane Mathis, Christophe Benoist, David J. Adams, Richard Mott, Jonathan Flint
Software Mentions: 1
Published: over 14 years ago