Ecosyste.ms: Papers

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: almost 4 years ago

10.1242/dev.193060

Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish
Cited by: 4
Author(s): Stefan Redl, António Miguel de Jesus Domingues, Edoardo Caspani, Stefanie Möckel, Willi Salvenmoser, María Méndez-Lago, René F. Ketting
Software Mentions: 10
Published: over 4 years ago

10.7717/peerj.8965

CFSP: a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classification
Cited by: 2
Author(s): Huan Peng
Software Mentions: 9
Published: over 4 years ago

10.1186/s13029-016-0059-5

A bedr way of genomic interval processing
Cited by: 19
Author(s): Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei‐Fei Liu, Paul C. Boutros
Software Mentions: 9
Published: almost 8 years ago

10.1186/1471-2164-13-556

Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry
Cited by: 117
Author(s): Kapila Gunasekera, Daniel Wüthrich, Sophie Braga-Lagache, Manfred Heller, Torsten Ochsenreiter
Software Mentions: 8
Published: almost 12 years ago

10.1186/1471-2105-10-121

SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data
Cited by: 29
Author(s): Yoko Fukuda, Yukiko Nakahara, Hidetoshi Date, Yūji Takahashi, Jun Goto, Akinori Miyashita, Ryozo Kuwano, Hiroki Adachi, Eiji Nakamura, Shoji Tsuji
Software Mentions: 6
Published: over 15 years ago

10.1186/1939-8433-6-15

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress
Cited by: 82
Author(s): Palitha Dharmawardhana, Liya Ren, Vindhya Amarasinghe, Marcela K. Monaco, Jim Thomason, Dean Ravenscroft, Susan R. McCouch, Doreen Ware, Pankaj Jaiswal
Software Mentions: 5
Published: over 11 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: about 17 years ago

10.7717/peerj.3893

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
Cited by: 49
Author(s): Ruth Timme, Hugh Rand, Martin Shumway, Eija Trees, Mustafa Simmons, Richa Agarwala, S. Scott Davis, Glenn E. Tillman, Stephanie Defibaugh-Chávez, Heather Carleton, William Klimke, Lee S. Katz
Software Mentions: 5
Published: almost 7 years ago

10.3390/genes12071058

Exposure to Fine Particulate Matter Air Pollution Alters mRNA and miRNA Expression in Bone Marrow-Derived Endothelial Progenitor Cells from Mice
Cited by: 4
Author(s): Xiaohong Li, Petra Haberzettl, Daniel J. Conklin, Aruni Bhatnagar, Eric C. Rouchka, Mei Zhang, Timothy E. O’Toole
Software Mentions: 5
Published: about 3 years ago

10.3762/bjnano.2.48

Towards a scalable and accurate quantum approach for describing vibrations of molecule–metal interfaces
Cited by: 18
Author(s): David M. Benoit, Bruno Madebène, Inga S. Ulusoy, Luis Mancera, Yohann Scribano, Sergey K. Chulkov
Software Mentions: 4
Published: about 13 years ago

10.1093/gigascience/giy034

Improving the annotation of the Heterorhabditis bacteriophora genome
Cited by: 15
Author(s): Florence McLean, Duncan Berger, Dominik R. Laetsch, Hillel T. Schwartz, Mark Blaxter
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.11020

Differential gene expression in a tripartite interaction:<i>Drosophila</i>,<i>Spiroplasma</i>and parasitic wasps
Cited by: 4
Author(s): Victor Manuel Higareda Alvear, Mariana Mateos, Diego Cortez, Cécilia Tamborindeguy, Esperanza Martínez‐Romero
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0163106

Tanscriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants
Cited by: 21
Author(s): Micheline N. Ngaki, Bing Wang, Binod Bihari Sahu, Subodh Srivastava, Mohammad Samir Farooqi, Kondapalli Venkata Gowri Chandra Sekhar, Sundararaman Swaminathan, Madan K. Bhattacharyya
Software Mentions: 4
Published: almost 8 years ago

10.1007/s13222-020-00362-8

From Blackboard to Green Screen
Cited by: 0
Author(s): Torsten Grust
Software Mentions: 4
Published: over 3 years ago

10.1371/journal.pone.0129059

Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data
Cited by: 33
Author(s): Gordon Daly, Richard M. Leggett, Will Rowe, Sam Stubbs, Maxim Wilkinson, Ricardo H. Ramírez-González, Mario Cáccamo, William Bernal, Jonathan L. Heeney
Software Mentions: 3
Published: about 9 years ago

10.3389/fimmu.2018.02280

A Web Resource for Designing Subunit Vaccine Against Major Pathogenic Species of Bacteria
Cited by: 28
Author(s): Gandharva Nagpal, Salman Sadullah Usmani, Gajendra P. S. Raghava
Software Mentions: 3
Published: almost 6 years ago

10.1093/bioinformatics/btv660

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization
Cited by: 16
Author(s): Göksel Mısırlı, Matteo Cavaliere, William Waites, Matthew Pocock, Curtis Madsen, Owen Gilfellon, Ricardo Honorato-Zimmer, Paolo Zuliani, Vincent Danos, Anil Wipat
Software Mentions: 3
Published: almost 9 years ago

10.1186/1471-2105-15-61

CDSbank: taxonomy-aware extraction, selection, renaming and formatting of protein-coding DNA or amino acid sequences
Cited by: 2
Author(s): Bart Hazes
Software Mentions: 3
Published: over 10 years ago

10.1186/s13059-018-1483-4

Chromatin loop anchors are associated with genome instability in cancer and recombination hotspots in the germline
Cited by: 42
Author(s): Vera B. Kaiser, Colin A. Semple
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms22094936

Identification of SYS1 as a Host Factor Required for Shiga Toxin-Mediated Cytotoxicity in Vero Cells
Cited by: 5
Author(s): Chisato Sakuma, Tsuyoshi Sekizuka, Makoto Kuroda, Kentaro Hanada, Taiki Yamaji
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2105-8-8

Least-squares methods for identifying biochemical regulatory networks from noisy measurements
Cited by: 23
Author(s): Jongrae Kim, Declan G. Bates, Ian Postlethwaite, J. S. Heslop-Harrison, Kwang-Hyun Cho
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0111018

Identification of the PLK2-Dependent Phosphopeptidome by Quantitative Proteomics
Cited by: 8
Author(s): Cinzia Franchin, Luca Cesaro, Lorenzo A. Pinna, Giorgio Arrigoni, Mauro Salvi
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0105062

Genome-Wide Association Studies and Heritability Estimates of Body Mass Index Related Phenotypes in Bangladeshi Adults
Cited by: 20
Author(s): Molly Scannell Bryan, Maria Argos, Brandon L. Pierce, Tong Lin, Muhammad Rakibuz-Zaman, Alauddin Ahmed, Mahfuzar Rahman, Tariqul Islam, Muhammad Yunus, Faruque Parvez, Shantanu Roy, Farzana Jasmine, John A. Baron, Muhammad G. Kibriya, Habibul Ahsan
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0084995

Genomic Analysis of Xanthomonas translucens Pathogenic on Wheat and Barley Reveals Cross-Kingdom Gene Transfer Events and Diverse Protein Delivery Systems
Cited by: 41
Author(s): Donald M. Gardiner, Narayana M. Upadhyaya, Jiri Stiller, Jeff Ellis, Peter N. Dodds, Kemal Kazan, John M. Manners
Software Mentions: 2
Published: over 10 years ago

10.3390/genes11091110

Survey and Diversity of Grapevine Pinot gris virus in Algeria and Comprehensive High-Throughput Small RNA Sequencing Analysis of Two Isolates from Vitis vinifera cv. Sabel Revealing High Viral Diversity
Cited by: 5
Author(s): Aleš Eichmeier, Eliška Peňázová, Jana Čechová, Akila Berraf-Tebbal
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2105-12-S13-S13

Near-membrane ensemble elongation in the proline-rich LRP6 intracellular domain may explain the mysterious initiation of the Wnt signaling pathway
Cited by: 6
Author(s): Chengcheng Liu, Mingxi Yao, Christopher W. V. Hogue
Software Mentions: 2
Published: almost 13 years ago