Ecosyste.ms: Papers

10.1186/1471-2164-13-462

NG6: Integrated next generation sequencing storage and processing environment
Cited by: 54
Author(s): Jérôme Mariette, Frédéric Escudié, Nicolas Allias, Gérald Salin, Céline Noirot, Sylvain Thomas, Christophe Klopp
Software Mentions: 10
Published: almost 13 years ago

10.1186/s12864-015-1303-0

Genome-wide comparison of PU.1 and Spi-B binding sites in a mouse B lymphoma cell line
Cited by: 34
Author(s): Lauren A. Solomon, Stephen K. H. Li, Jan Piskorz, Li Xu, Rodney P. DeKoter
Software Mentions: 6
Published: over 9 years ago

10.1186/1471-2105-13-154

TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data
Cited by: 50
Author(s): Aaron L. Sarver, Jesse Erdman, Timothy K. Starr, David A. Largaespada, Kevin A.T. Silverstein
Software Mentions: 6
Published: over 12 years ago

10.12688/f1000research.6157.2

ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines
Cited by: 21
Author(s): Michael T. Wolfinger, Jörg Fallmann, Florian Eggenhofer, Fabian Amman
Software Mentions: 6
Published: over 9 years ago

10.1111/pbi.12852

The transcriptome, extracellular proteome and active secretome of agroinfiltrated<i>Nicotiana benthamiana</i>uncover a large, diverse protease repertoire
Cited by: 52
Author(s): Friederike Grosse‐Holz, Steven L. Kelly, Svenja Blaskowski, Farnusch Kaschani, Markus Kaiser, Renier A. L. van der Hoorn
Software Mentions: 5
Published: almost 7 years ago

10.1098/rsob.200253

The role of antioxidants in restoring MAPK 14 and a DNA damage marker level following autophagy suppression
Cited by: 3
Author(s): Abdalla Elbialy
Software Mentions: 4
Published: almost 4 years ago

10.1186/1471-2105-15-44

The HTS barcode checkerpipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data
Cited by: 19
Author(s): Youri Lammers, Tamara Peelen, Rutger A. Vos, Barbara Gravendeel
Software Mentions: 4
Published: almost 11 years ago

10.3389/fmicb.2018.02043

Protists Within Corals: The Hidden Diversity
Cited by: 23
Author(s): Camille Clérissi, Sébastien Brunet, Jérémie Vidal-Dupiol, Mehdi Adjeroud, Pierre Lepage, Laure Guillou, Jean-Michel Escoubas, Ève Toulza
Software Mentions: 4
Published: about 6 years ago

10.3389/fmicb.2019.00483

Bacterial Communities Associated With Spherical Nostoc Macrocolonies
Cited by: 8
Author(s): Pablo S. Aguilar, Cristina Dorador, Irma Vila, Rubén Sommaruga
Software Mentions: 3
Published: over 5 years ago

10.1186/s12863-017-0584-5

An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench)
Cited by: 20
Author(s): Adugna Abdi Woldesemayat, Peter van Heusden, Bongani K. Ndimba, Alan Christoffels
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms22126437

BrPP5.2 Overexpression Confers Heat Shock Tolerance in Transgenic Brassica rapa through Inherent Chaperone Activity, Induced Glucosinolate Biosynthesis, and Differential Regulation of Abiotic Stress Response Genes
Cited by: 5
Author(s): Muthusamy Muthusamy, Jong Hee Kim, Suk Hee Kim, So Young Park, Soo In Lee
Software Mentions: 3
Published: over 3 years ago

10.1186/s12014-018-9188-y

Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization
Cited by: 37
Author(s): Melanie Christine Föll, Matthias Fahrner, Victor Oginga Oria, Markus Kühs, Martin L. Biniossek, Martin Werner, Peter Bronsert, Oliver Schilling
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-018-5217-5

Dissecting clinical outcome of porcine circovirus type 2 with in vivo derived transcriptomic signatures of host tissue responses
Cited by: 4
Author(s): Nicolaas Van Renne, Ruifang Wei, Nathalie Pochet, Hans Nauwynck
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-019-2663-2

SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data
Cited by: 45
Author(s): Yoann Dufresne, Franck Lejzerowicz, Laure Apotheloz Perret-Gentil, Jan Pawłowski, Tristan Cordier
Software Mentions: 2
Published: over 5 years ago

10.1155/2021/1596834

Immunoinformatics and Molecular Docking Studies Predicted Potential Multiepitope-Based Peptide Vaccine and Novel Compounds against Novel SARS-CoV-2 through Virtual Screening
Cited by: 21
Author(s): Muhammad Waqas, Haider Ali, Abdur Rehman, Muhammad Qasim, Ahitsham Umar, Muhammad Sufyan, Hafiza Nisha Akram, Asif Mir, Roha Razzaq, Danish Rasool, Rana Adnan Tahir, Sheikh Arslan Sehgal
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms8121898

Shared Extended-Spectrum β-Lactamase-Producing Salmonella Serovars between Agricultural and Aquatic Environments Revealed through invA Amplicon Sequencing
Cited by: 9
Author(s): Cecilia Mahlatse Raseala, Mutshiene Deogratias Ekwanzala, Maggy Ndombo Benteke Momba
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1001134

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome
Cited by: 461
Author(s): Robert S. Illingworth, Ulrike Gruenewald-Schneider, Shaun Webb, Alastair Kerr, Keith James, Daniel J. Turner, Colin Smith, David J. Harrison, Robert Andrews, Adrian Bird
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0191566

Mobile tablet-based therapies following stroke: A systematic scoping review of administrative methods and patient experiences
Cited by: 29
Author(s): Michael Pugliese, Tim Ramsay, Dylan Johnson, Dar Dowlatshahi
Software Mentions: 2
Published: almost 7 years ago

10.3389/fmicb.2020.00311

Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome
Cited by: 42
Author(s): Camille Clérissi, Julien de Lorgeril, Bruno Petton, Aude Lucasson, Jean-Michel Escoubas, Yannick Gueguen, Lionel Dégremont, Guillaume Mitta, Ève Toulza
Software Mentions: 2
Published: over 4 years ago

10.1186/s13742-015-0063-8

BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ
Cited by: 2
Author(s): Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai, Olivier Collin
Software Mentions: 2
Published: over 9 years ago

10.1186/s40249-020-00752-w

Reverse vaccinology assisted designing of multiepitope-based subunit vaccine against SARS-CoV-2
Cited by: 54
Author(s): Muhammad Tahir ul Qamar, Farah Shahid, Sadia Aslam, Usman Ali Ashfaq, Sidra Aslam, Israr Fatima, Muhammad Mazhar Fareed, Ali Zohaib, Ling Ling Chen
Software Mentions: 2
Published: about 4 years ago

10.1002/jbm4.10383

TET1 Directs Chondrogenic Differentiation by Regulating SOX9 Dependent Activation of Col2a1 and Acan In Vitro
Cited by: 8
Author(s): Piera Smeriglio, Fiorella C. Grandi, Sarah Taylor, Antoine Zalc, Nidhi Bhutani
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-019-50454-z

Role of NF-kappaB2-p100 in regulatory T cell homeostasis and activation
Cited by: 11
Author(s): Atika Dhar, M. L. Chawla, Somdeb Chattopadhyay, Neelam Oswal, Danish Umar, Suman Gupta, Vineeta Bal, Satyajit Rath, Anna George, Aneeshkumar G. Arimbasseri, Soumen Basak
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.20640

Modularity and determinants of a (bi-)polarization control system from free-living and obligate intracellular bacteria
Cited by: 26
Author(s): Matthieu Bergé, Sébastien Campagne, Johann Mignolet, Séamus Holden, Laurence Théraulaz, Suliana Manley, Frédéric H.‐T. Allain, Patrick H. Viollier
Software Mentions: 2
Published: almost 8 years ago

10.3390/ijms221910489

Establishment of Bovine-Induced Pluripotent Stem Cells
Cited by: 12
Author(s): Yue Su, Ling Wang, Zhiqiang Fan, Ying Liu, Jiaqi Zhu, Deborah Kaback, Julia Oudiz, Tayler Patrick, Siu Pok Yee, X. Cindy Tian, Irina A. Polejaeva, Yaning Tang
Software Mentions: 2
Published: about 3 years ago

10.1007/s12020-021-02753-7

Screening for extremely rare pathogenic variants of monogenic diabetes using targeted panel sequencing
Cited by: 3
Author(s): Tomasz Płoszaj, Karolina Antosik, Paulina Jakiel, Agnieszka Zmysłowska, Maciej Borowiec
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0094011

MNK1-Induced eIF-4E Phosphorylation in Myeloma Cells: A Pathway Mediating IL-6-Induced Expansion and Expression of Genes Involved in Metabolic and Proteotoxic Responses
Cited by: 12
Author(s): Yijiang Shi, Patrick Frost, Bao Hoang, Yonghui Yang, Carolyne Bardeleben, Joseph Gera, Alan Lichtenstein
Software Mentions: 1
Published: over 10 years ago

10.3389/fcell.2021.647485

MicroRNA-1205 Regulation of FRYL in Prostate Cancer
Cited by: 4
Author(s): Michelle Naidoo, Fayola Levine, Tamara Gillot, Akintunde T. Orunmuyi, E.O. Olapade-Olaopa, Thahmina Ali, Konstantinos Krampis, Chun Hsu Pan, Princesca Dorsaint, Andrea Sboner, Olorunseun O. Ogunwobi
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0007162

Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets
Cited by: 18
Author(s): Peter B. McGarvey, Hongzhan Huang, Raja Mazumder, Jian Zhang, Yongxing Chen, Chengdong Zhang, Stephen Cammer, Rebecca Will, Margie Odle, Bruno W. S. Sobral, M. Moore, Cathy H. Wu
Software Mentions: 1
Published: about 15 years ago

10.15252/msb.202010019

Levels of autonomy in synthetic biology engineering
Cited by: 6
Author(s): Jacob Beal, Miles Rogers
Software Mentions: 1
Published: almost 4 years ago

10.1093/molbev/msu249

Purifying Selection on Splice-Related Motifs, Not Expression Level nor RNA Folding, Explains Nearly All Constraint on Human lincRNAs
Cited by: 50
Author(s): Andreas Schüler, Avazeh T. Ghanbarian, Laurence D. Hurst
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-015-2360-0

Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus
Cited by: 26
Author(s): Robert Reichelt, Antonia Gindner, Michael Thomm, Winfried Hausner
Software Mentions: 1
Published: almost 9 years ago