cran: CAST | Projects | Ecosyste.ms: Papers

10.1186/s13071-021-04851-x

Data-driven and interpretable machine-learning modeling to explore the fine-scale environmental determinants of malaria vectors biting rates in rural Burkina Faso
Cited by: 9
Author(s): Paul Taconet, Angélique Porciani, Dieudonné Diloma Soma, Karine Mouline, Frédéric Simard, Alphonsine A. Koffi, Cédric Pennetier, Roch K. Dabiré, Morgan Mangeas, Nicolas Moiroux
Software Mentions: 21
Published: over 3 years ago

10.1186/1471-2105-16-S11-S2

VisRseq: R-based visual framework for analysis of sequencing data
Cited by: 59
Author(s): Hamid Younesy, Torsten B. Möller, Matthew C. Lorincz, Mehdi Karimi, Steven J.M. Jones
Software Mentions: 15
Published: about 9 years ago

10.1186/s12915-020-00863-8

Functional signatures of evolutionarily young CTCF binding sites
Cited by: 7
Author(s): Dhoyazan Azazi, Jonathan M. Mudge, Duncan T. Odom, Paul Flicek
Software Mentions: 8
Published: about 4 years ago

10.1016/j.celrep.2021.108739

Natural genetic variation determines microglia heterogeneity in wild-derived mouse models of Alzheimer’s disease
Cited by: 40
Author(s): Hongtian Yang, Kristen D. Onos, Kwangbom Choi, Kelly J. Keezer, Daniel A. Skelly, Gregory W. Carter, Gareth R. Howell
Software Mentions: 6
Published: almost 4 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

10.1371/journal.pone.0239154

Assessing the low complexity of protein sequences via the low complexity triangle
Cited by: 4
Author(s): Pablo Mier, Miguel A. Andrade‐Navarro
Software Mentions: 6
Published: almost 4 years ago

10.1186/1471-2105-13-S10-S7

A systematic comparison of genome-scale clustering algorithms
Cited by: 45
Author(s): Jeremy J. Jay, John D. Eblen, Yun Zhang, Mikael Benson, Andy D. Perkins, Arnold M. Saxton, Brynn H. Voy, Elissa J. Chesler, Michael A. Langston
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0179364

DoEstRare: A statistical test to identify local enrichments in rare genomic variants associated with disease
Cited by: 6
Author(s): Elodie Persyn, Matilde Karakachoff, Solena Le Scouarnec, Camille Le Clézio, Dominique Campion, Emmanuelle Génin, Jean‐Jacques Schott, Richard Redon, Lise Bellanger, Christian Dina
Software Mentions: 4
Published: over 7 years ago

10.1186/s12859-017-1906-3

fLPS: Fast discovery of compositional biases for the protein universe
Cited by: 57
Author(s): Paul M. Harrison
Software Mentions: 4
Published: almost 7 years ago

10.15252/msb.20156505

A cell‐based model system links chromothripsis with hyperploidy
Cited by: 113
Author(s): Balca R. Mardin, Alexandros P. Drainas, Sebastian M. Waszak, Joachim Weischenfeldt, Mayumi Isokane, Adrian M. Stütz, Benjamin Raeder, Theocharis Efthymiopoulos, Christopher Buccitelli, Maia Segura-Wang, Paul A. Northcott, Stefan M. Pfister, Peter Lichter, Jan Ellenberg, Jan Korbel
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-018-28999-2

Spiking neurons with short-term synaptic plasticity form superior generative networks
Cited by: 22
Author(s): Luziwei Leng, Roman Martel, Oliver Breitwieser, Ilja Bytschok, Walter Senn, Johannes Schemmel, K. Meier, Mihai A. Petrovici
Software Mentions: 4
Published: over 6 years ago

10.1093/bib/bbw058

Graphics processing units in bioinformatics, computational biology and systems biology
Cited by: 53
Author(s): Marco S. Nobile, Paolo Cazzaniga, Andrea Tangherloni, Daniela Besozzi
Software Mentions: 4
Published: over 8 years ago

10.1186/s12920-020-0684-3

Adaptive Fisher method detects dense and sparse signals in association analysis of SNV sets
Cited by: 2
Author(s): Xiaoyu Cai, Lo‐Bin Chang, Jordan Potter, Chi Song
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-017-00712-9

Longitudinal data analysis for rare variants detection with penalized quadratic inference function
Cited by: 1
Author(s): Hongyan Cao, Li Zhi, Yang Huang, Yuehua Cui, Yanbo Zhang
Software Mentions: 3
Published: over 7 years ago

10.1186/1756-0500-2-142

Network module detection: Affinity search technique with the multi-node topological overlap measure
Cited by: 44
Author(s): Li Ai, Steve Horvath
Software Mentions: 3
Published: almost 16 years ago

10.1038/s41598-020-66194-4

Pseudomonas aeruginosa core metabolism exerts a widespread growth-independent control on virulence
Cited by: 28
Author(s): Stavria Panayidou, Kaliopi Georgiades, Theodoulakis Christofi, Stella Tamana, Vasilis J. Promponas, Yiorgos Apidianakis
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.0030145

Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells
Cited by: 80
Author(s): Marica Grs̆ković, Christina Chaivorapol, Alexandre Gaspar-Maia, Hao Li, Miguel Ramalho-Santos
Software Mentions: 3
Published: about 17 years ago

10.1523/JNEUROSCI.0586-21.2021

RIM-Binding Protein 2 Organizes Ca<sup>2+</sup> Channel Topography and Regulates Release Probability and Vesicle Replenishment at a Fast Central Synapse
Cited by: 12
Author(s): Tanvi Butola, Theocharis Alvanos, Anika Hintze, Peter Koppensteiner, David Kleindienst, Ryuichi Shigemoto, Carolin Wichmann, Tobias Moser
Software Mentions: 3
Published: over 3 years ago

10.18632/oncotarget.8921

c-MYC inhibition impairs hypoxia response in glioblastoma multiforme
Cited by: 20
Author(s): Maria Patrizia Mongiardi, Mauro Savino, Maria Laura Falchetti, Barbara Illi, Francesca Bozzo, Cristiana Valle, Manuela Helmer-Citterich, Fabrizio Ferrè, Sergio Nasi, Andrea Levi
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pgen.1004916

PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination
Cited by: 125
Author(s): Christopher L. Baker, Shimpei Kajita, Michael Walker, Ruth L. Saxl, Narayanan Raghupathy, Kwangbom Choi, Petko M. Petkov, Kenneth Paigen
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep44804

Renal Medulla is More Sensitive to Cisplatin than Cortex Revealed by Untargeted Mass Spectrometry-Based Metabolomics in Rats
Cited by: 29
Author(s): Pei Zhang, Jiaqing Chen, Wanqiu Huang, Wei Li, Yin Huang, Zunjian Zhang, Fengguo Xu
Software Mentions: 3
Published: over 7 years ago

10.1016/j.ajhg.2017.05.015

A Fast Association Test for Identifying Pathogenic Variants Involved in Rare Diseases
Cited by: 33
Author(s): Daniel Greene, Nihr BioResource, Sylvia Richardson, Ernest Turro
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-26453-x

Blood lipid-related low-frequency variants in LDLR and PCSK9 are associated with onset age and risk of myocardial infarction in Japanese
Cited by: 14
Author(s): Tomoyuki Tajima, Hiroyuki Morita, Kei Ito, Tsutomu Yamazaki, Michiaki Kubo, Issei Komuro, Yukihide Momozawa
Software Mentions: 3
Published: over 6 years ago

10.1017/S1041610214000416

Review of brief cognitive tests for patients with suspected dementia
Cited by: 158
Author(s): Latha Velayudhan, Seung‐Ho Ryu, Malgorzata Raczek, Michael Philpot, James Lindesay, Matthew Critchfield, Gill Livingston
Software Mentions: 3
Published: over 10 years ago

10.1186/1752-0509-7-52

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum
Cited by: 21
Author(s): Katherine Lawler, K. E. Hammond‐Kosack, Alvis Brāzma, Richard M. R. Coulson
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pgen.1000274

Mutations in AtPS1 (Arabidopsis thaliana Parallel Spindle 1) Lead to the Production of Diploid Pollen Grains
Cited by: 125
Author(s): Isabelle d’Erfurth, Sylvie Jolivet, Nicole Froger, Olivier Catrice, Maria Novatchkova, Simon Mathieu, Eric Jenczewski, Raphaël Mercier
Software Mentions: 3
Published: almost 16 years ago

10.1038/srep27640

Comprehensive analysis of multi-tissue transcriptome data and the genome-wide investigation of GRAS family in Phyllostachys edulis
Cited by: 11
Author(s): Hansheng Zhao, Lili Dong, Huayu Sun, Lichao Li, Yonggen Lou, Lili Wang, Zuyao Li, Zhimin Gao
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0004001

TranscriptomeBrowser: A Powerful and Flexible Toolbox to Explore Productively the Transcriptional Landscape of the Gene Expression Omnibus Database
Cited by: 29
Author(s): Fabrice Lopez, Julien Textoris, Aurélie Bergon, Gilles Didier, Élisabeth Rémy, Samuel Granjeaud, Jean Imbert, Catherine Nguyen, Denis Puthier
Software Mentions: 3
Published: almost 16 years ago

10.1186/gb-2004-5-11-r94

Cited by: 131
Author(s): Stephen Swift, Allan Tucker, Veronica Vinciotti, Nigel Martin, Christine A. Orengo, Xiaohui Liu, Paul Kellam
Software Mentions: 3
Published: almost 21 years ago

10.1186/1741-7007-8-96

Serious limitations of the QTL/Microarray approach for QTL gene discovery
Cited by: 29
Author(s): Ricardo A. Verdugo, Charles R. Farber, Craig H Warden, Juan F. Medrano
Software Mentions: 3
Published: over 14 years ago

10.1186/s12864-015-1384-9

Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds
Cited by: 108
Author(s): Caihong Wei, Huihua Wang, Gang Liu, Mingming Wu, Jiaxve Cao, Zhen Liu, Ruizao Liu, Fuping Zhao, Li Zhang, Jian Lü, Chousheng Liu, Lixin Du
Software Mentions: 3
Published: over 9 years ago

10.3390/ijerph16183502

Early Autism Screening: A Comprehensive Review
Cited by: 68
Author(s): Fadi Thabtah, David Peebles
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0207677

The impact of a fine-scale population stratification on rare variant association test results
Cited by: 27
Author(s): Elodie Persyn, Richard Redon, Lise Bellanger, Christian Dina
Software Mentions: 3
Published: almost 6 years ago

10.1093/bfgp/elu012

Methodology for the analysis of rare genetic variation in genome-wide association and re-sequencing studies of complex human traits
Cited by: 17
Author(s): Loukas Moutsianas, Andrew P. Morris
Software Mentions: 3
Published: over 10 years ago

10.15252/emmm.201607308

Attenuated <scp>PDGF</scp> signaling drives alveolar and microvascular defects in neonatal chronic lung disease
Cited by: 29
Author(s): Prajakta Oak, Tina Pritzke, Isabella Thiel, Markus Koschlig, Daphne S. Mous, Anita Windhorst, Noopur Jain, Oliver Eickelberg, Kai Foerster, Andreas Schulze, Wolfgang Goepel, Tobias Reicherzer, Harald Ehrhardt, Robbert J. Rottier, Peter Ahnert, Ludwig Gortner, Tushar J. Desai, Anne Hilgendorff
Software Mentions: 3
Published: about 7 years ago

10.1002/gepi.21743

VAAST 2.0: Improved Variant Classification and Disease‐Gene Identification Using a Conservation‐Controlled Amino Acid Substitution Matrix
Cited by: 128
Author(s): Hao Hu, Chad Huff, Barry Moore, Steven Flygare, Martin G. Reese, Mark Yandell
Software Mentions: 3
Published: over 11 years ago

10.1038/s41598-018-35033-y

A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes
Cited by: 85
Author(s): Frédéric Cadet, Nicolas Fontaine, Guangyue Li, Joaquı́n Sanchis, Matthieu Ng Fuk Chong, Rudy Pandjaitan, Iyanar Vetrivel, Bernard Offmann, Manfred T. Reetz
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pcbi.1005293

Normal Modes Expose Active Sites in Enzymes
Cited by: 9
Author(s): Yitav Glantz-Gashai, Tomer Meirson, Abraham O. Samson
Software Mentions: 2
Published: almost 8 years ago

10.1186/1753-6561-8-S1-S43

Analysis of Genetic Analysis Workshop 18 data with gene-based penalized regression
Cited by: 1
Author(s): Kristin L. Ayers, Heather J. Cordell
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2105-8-250

Nearest Neighbor Networks: clustering expression data based on gene neighborhoods
Cited by: 63
Author(s): Curtis Huttenhower, Avi I. Flamholz, Jessica Landis, Sauhard Sahi, Chad L. Myers, Kellen L. Olszewski, Matthew A. Hibbs, Nathan O. Siemers, Olga G. Troyanskaya, Hilary A. Coller
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pcbi.1000188

Cavities and Atomic Packing in Protein Structures and Interfaces
Cited by: 75
Author(s): Shrihari Sonavane, Pinak Chakrabarti
Software Mentions: 2
Published: about 16 years ago

10.1186/s12870-016-0720-9

Transcriptome and comparative gene expression analysis of Phyllostachys edulis in response to high light
Cited by: 29
Author(s): Hansheng Zhao, Yonggen Lou, Huayu Sun, Lichao Li, Lili Wang, Lili Dong, Zhimin Gao
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2105-12-207

HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information
Cited by: 39
Author(s): Rong Liu, Jianjun Hu
Software Mentions: 2
Published: over 13 years ago

10.1186/1472-6831-14-119

Assessing caries status according to the CAST instrument and WHO criterion in epidemiological studies
Cited by: 29
Author(s): Ana Luiza de Figueiredo Souza, Soraya Coelho Leal, Ewald M. Bronkhorst, Jo E. Frencken
Software Mentions: 2
Published: about 10 years ago

10.1186/s12883-021-02348-9

Prognostic analysis of different therapeutic regimens in patients with acute cardiogenic cerebral embolism
Cited by: 2
Author(s): Lan Hu, Duan Guangxin, Yuan Xu, Yongjun Cao
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0053911

The Multifaceted Effects of Agmatine on Functional Recovery after Spinal Cord Injury through Modulations of BMP-2/4/7 Expressions in Neurons and Glial Cells
Cited by: 31
Author(s): Yu Mi Park, Won Taek Lee, Kiran Kumar Bokara, Seunggi Seo, Seung Hwa Park, Jaehwan Kim, Midori A. Yenari, Kyung Ah Park, Jong Eun Lee
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2180-12-249

Evolution and diversity of periplasmic proteins involved in copper homeostasis in gamma proteobacteria
Cited by: 55
Author(s): Georgina Hernández-Montes, José M. Argüello, Brenda Valderrama
Software Mentions: 2
Published: about 12 years ago

10.1186/1742-2094-9-5

NADPH oxidase and reactive oxygen species contribute to alcohol-induced microglial activation and neurodegeneration
Cited by: 211
Author(s): Liya Qin, Fulton T. Crews
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12920-018-0344-z

Exact association test for small size sequencing data
Cited by: 1
Author(s): Joowon Lee, Seungyeoun Lee, Jin‐Young Jang, Taesung Park
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-11-417

FACT: Functional annotation transfer between proteins with similar feature architectures
Cited by: 27
Author(s): Tina Koestler, Arndt von Haeseler, Ingo Ebersberger
Software Mentions: 2
Published: about 14 years ago

10.3390/s17051003

OpenSHS: Open Smart Home Simulator
Cited by: 52
Author(s): Nasser Alshammari, Talal Alshammari, Mohamed Sedky, Justin Champion, Carolin Bauer
Software Mentions: 2
Published: over 7 years ago

10.1186/s12877-019-1337-2

Acceptability of oral liquid pharmaceutical products in older adults: palatability and swallowability issues
Cited by: 15
Author(s): Émilie Belissa, Thibault Vallet, Sandra Laribe-Caget, A. Chevallier, François-Xavier Chedhomme, Fattima Abdallah, Nathalie Bachalat, Sid-Ahmed Belbachir, Imad Boulaich, Vanessa Bloch, Anne Delahaye, Mathieu Depoisson, Amélie Dufaÿ Wojcicki, Stéphane Gibaud, Anne-Sophie Grancher, Caroline Guinot, C. Lachuer, L. Lechowski, Patrick Léglise, Abdel Mahiou, Sylvie Meaume, Corinne Michel, Hugues Michelon, Yann Orven, Ines Perquy, M. Piccoli, Marie-Thérèse Rabus, Annie-Claude Ribemont, Jean-Paul Rwabihama, Jean‐Hugues Trouvin, Fabrice Ruiz, Vincent Boudy
Software Mentions: 2
Published: almost 5 years ago

10.1038/s41598-021-98370-5

Controlling for human population stratification in rare variant association studies
Cited by: 7
Author(s): Matthieu Bouaziz, Jimmy Mullaert, Benedetta Bigio, Yoann Seeleuthner, Jean‐Laurent Casanova, Alexandre Alcaïs, Laurent Abel, Aurélie Cobat
Software Mentions: 2
Published: about 3 years ago

10.3390/s130708612

A Bandwidth-Efficient Service for Local Information Dissemination in Sparse to Dense Roadways
Cited by: 8
Author(s): Estrella M. Garcia-Lozano, Celeste Campo, Carlos García-Rubio, Alberto Cortés-Martín, Alicia Rodríguez-Carrión, Patricia Noriega-Vivas
Software Mentions: 2
Published: over 11 years ago

10.1128/mBio.01516-16

Tuberculosis Susceptibility and Vaccine Protection Are Independently Controlled by Host Genotype
Cited by: 99
Author(s): Clare M. Smith, Megan K. Proulx, Andrew J. Olive, Dominick J. Laddy, Bibhuti B. Mishra, Caitlin E. Moss, Nuria Martinez Gutierrez, Michelle M. Bellerose, Palmira Barreira-Silva, Jia Yao Phuah, Richard E. Baker, Samuel M. Behar, Hardy Kornfeld, Thomas G. Evans, Gillian Beamer, Christopher M. Sassetti
Software Mentions: 2
Published: about 8 years ago

10.3390/pharmaceutics11080368

Sex Differences in Medicine Acceptability: A New Factor to Be Considered in Medicine Formulation
Cited by: 10
Author(s): Fabrice Ruiz, Alexander Keeley, Patrick Léglise, Catherine Tuleu, C. Lachuer, Jean-Paul Rwabihama, Nathalie Bachalat, Imad Boulaich, Fattima Abdallah, Marie-Thérèse Rabus, Annie-Claude Ribemont, Hugues Michelon, Amélie Dufaÿ Wojcicki, Mine Orlu, Thibault Vallet, Vincent Boudy
Software Mentions: 2
Published: over 5 years ago

10.1038/srep38889

High-resolution transcript profiling reveals shoot abscission process of spruce dwarf mistletoe Arceuthobium sichuanense in response to ethephon
Cited by: 2
Author(s): Yonglin Wang, Dan Xiong, Ning Jiang, Xuewu Li, Yang Qiqing, Chengming Tian
Software Mentions: 2
Published: almost 8 years ago

10.1039/d1cb00101a

Targeting protein–protein interactions in the DNA damage response pathways for cancer chemotherapy
Cited by: 7
Author(s): Kerry Silva McPherson, Dmitry M. Korzhnev
Software Mentions: 2
Published: almost 4 years ago

10.1186/gb-2009-10-10-r112

Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels
Cited by: 37
Author(s): Ian Sudbery, Jim Stalker, Jared T. Simpson, Thomas Keane, Alistair G. Rust, Matthew E. Hurles, Klaudia Walter, Dee Lynch, Lydia Teboul, Steve Brown, Heng Li, Zemin Ning, Joseph H. Nadeau, Colleen M. Croniger, Richard Durbin, David J. Adams
Software Mentions: 2
Published: almost 16 years ago

10.1186/1743-422X-10-247

Molecular characterization and phylogenetic study of African swine fever virus isolates from recent outbreaks in Uganda (2010–2013)
Cited by: 35
Author(s): David Kalenzi Atuhaire, Mathias Afayoa, Sylvester Ochwo, Savannah Mwesigwa, Julius Boniface Okuni, W. Olaho-Mukani, Lonzy Ojok
Software Mentions: 2
Published: over 11 years ago

10.1126/sciadv.abc9863

Robust inference of positive selection on regulatory sequences in the human brain
Cited by: 19
Author(s): Jialin Liu, Marc Robinson‐Rechavi
Software Mentions: 2
Published: almost 4 years ago

10.1007/s12035-020-01907-4

Human Pluripotent Stem Cell-Derived Neurons Are Functionally Mature In Vitro and Integrate into the Mouse Striatum Following Transplantation
Cited by: 17
Author(s): Andrea Comella-Bolla, Javier G. Orlandi, Andrés Miguez, Marco Straccia, María García‐Bravo, Georgina Bombau, Mireia Galofré, Phil Sanders, Jordi Carrère, José C. Segovia, Joan Blasi, Nicholas Denby Allen, Jordi Alberch, Jordi Soriano, Josep M. Canals
Software Mentions: 2
Published: over 4 years ago

10.3389/fgene.2015.00149

A review of study designs and statistical methods for genomic epidemiology studies using next generation sequencing
Cited by: 41
Author(s): Qian Wang, Qiongshi Lu, Hongyu Zhao
Software Mentions: 2
Published: over 9 years ago

10.3390/genes3020291

The Chlamydiales Pangenome Revisited: Structural Stability and Functional Coherence
Cited by: 10
Author(s): Fotis Psomopoulos, Victoria I. Siarkou, Nikolas Papanikolaou, Ioannis Iliopoulos, Athanasios Tsaftaris, Vasilis J. Promponas, Christos A. Ouzounis
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-15-324

Deep mRNA sequencing reveals stage-specific transcriptome alterations during microsclerotia development in the smoke tree vascular wilt pathogen, Verticillium dahliae
Cited by: 56
Author(s): Dan Xiong, Yonglin Wang, Jie Ma, Steven J. Klosterman, Shuxiao Xiao, Chengming Tian
Software Mentions: 2
Published: over 10 years ago

10.3390/e20030159

IBVis: Interactive Visual Analytics for Information Bottleneck Based Trajectory Clustering
Cited by: 1
Author(s): Yuejun Guo, Qing Xu, Mateu Sbert
Software Mentions: 2
Published: over 6 years ago

10.1140/epjc/s10052-016-4372-6

TREX-DM: a low-background Micromegas-based TPC for low-mass WIMP detection
Cited by: 32
Author(s): F.J. Iguaz, J.G. Garza, Francisco Aznar, J. Castel, S. Cebrián, T. Dafní, Juan Antonio Garcı́a, I. G. Irastorza, A. Lagraba, G. Luzón, A. Peiró
Software Mentions: 2
Published: about 8 years ago

10.3389/fgene.2014.00323

A comprehensive evaluation of collapsing methods using simulated and real data: excellent annotation of functionality and large sample sizes required
Cited by: 13
Author(s): Carmen Dering, Inke R. König, Laura B. Ramsey, Mary V. Relling, Wenjian Yang, Andreas Ziegler
Software Mentions: 2
Published: about 10 years ago

10.1002/brb3.1195

Electroconvulsive treatment prevents chronic restraint stress-induced atrophy of the hippocampal formation-A stereological study
Cited by: 12
Author(s): Johanne L. Alemu, Frederik Elberling, Bushra Azam, Bente Pakkenberg, Mikkel V. Olesen
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0189984

The effect of subject measurement error on joint kinematics in the conventional gait model: Insights from the open-source pyCGM tool using high performance computing methods
Cited by: 11
Author(s): Mathew Schwartz, Philippe C. Dixon
Software Mentions: 2
Published: almost 7 years ago

10.1186/1752-153X-1-7

PocketPicker: analysis of ligand binding-sites with shape descriptors
Cited by: 279
Author(s): Martin Weisel, Ewgenij Proschak, Gisbert Schneider
Software Mentions: 2
Published: over 17 years ago

10.1186/s12544-021-00495-1

Identifying port maritime communities: application to the Spanish case
Cited by: 1
Author(s): Nicanor García, Belarmino Adenso‐Díaz, Laura Calzada-Infante
Software Mentions: 2
Published: over 3 years ago

10.3390/metabo6040046

Current and Future Perspectives on the Structural Identification of Small Molecules in Biological Systems
Cited by: 101
Author(s): Daniel A. Dias, Oliver A.H. Jones, David J. Beale, Berin A. Boughton, Devin Benheim, Konstantinos A. Kouremenos, Jean‐Luc Wolfender, David S. Wishart
Software Mentions: 2
Published: almost 8 years ago

10.1099/mgen.0.000429

Ancestral state reconstruction of metabolic pathways across pangenome ensembles
Cited by: 3
Author(s): Fotis Psomopoulos, Jacques van Helden, Claudine Médigue, Anastasia Chasapi, Christos A. Ouzounis
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2164-9-183

Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants
Cited by: 20
Author(s): Matthieu Conte, Sylvain Gaillard, Gaëtan Droc, Christophe Périn
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2105-15-197

KVFinder: steered identification of protein cavities as a PyMOL plugin
Cited by: 93
Author(s): Saulo H. P. de Oliveira, Felipe A. N. Ferraz, Rodrigo Vargas Honorato, José Xavier‐Neto, Tiago J. P. Sobreira, Paulo Sérgio Lopes de Oliveira
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0079450

Measuring the Reliability of Picture Story Exercises like the TAT
Cited by: 14
Author(s): Nicole Gruber, Ludwig Kreuzpointner
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0221261

Dosage form suitability in vulnerable populations: A focus on paracetamol acceptability from infants to centenarians
Cited by: 13
Author(s): Fabrice Ruiz, Thibault Vallet, Amélie Dufaÿ Wojcicki, Émilie Belissa, Jean-Eudes Fontan, Loïc de Pontual, Sylvie Nathanson, A. Chevallier, Sandra Laribe-Caget, Vincent Boudy
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0069226

A Linkage Disequilibrium–Based Approach to Selecting Disease-Associated Rare Variants
Cited by: 10
Author(s): Rajesh Talluri, Sanjay Shete
Software Mentions: 2
Published: over 11 years ago

10.1111/acel.13112

Age‐related changes to macrophages are detrimental to fracture healing in mice
Cited by: 58
Author(s): Daniel Clark, Sloane Brazina, Frank Yang, Diane Hu, Christine L. Hsieh, Eréne C. Niemi, Theodore Miclau, Mary C. Nakamura, Ralph Marcucio
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2164-15-703

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations
Cited by: 74
Author(s): Gloria Sheynkman, James E. Johnson, Pratik Jagtap, Michael R. Shortreed, Getiria Onsongo, Brian L. Frey, Timothy J. Griffin, Lloyd M. Smith
Software Mentions: 2
Published: about 10 years ago

10.1186/s13073-015-0138-2

Rare variant association studies: considerations, challenges and opportunities
Cited by: 172
Author(s): Paul L. Auer, Guillaume Lettre
Software Mentions: 2
Published: almost 10 years ago

10.1186/gb-2008-9-7-r120

Whole proteome identification of plant candidate G-protein coupled receptors in Arabidopsis, rice, and poplar: computational prediction and in-vivo protein coupling
Cited by: 79
Author(s): Timothy E. Gookin, Junhyong Kim, Sarah M. Assmann
Software Mentions: 2
Published: almost 17 years ago

10.1136/bmjopen-2018-022802

Development and prospective external validation of a tool to predict poor recovery at 9 months after acute ankle sprain in UK emergency departments: the SPRAINED prognostic model
Cited by: 4
Author(s): Michael Maia Schlüssel, David Keene, Gary S. Collins, Jennifer Bostock, Chris Byrne, Steve Goodacre, Stephen Gwilym, Daryl Hagan, Kirstie L. Haywood, Jacqueline Thompson, Mark A. Williams, Sarah E Lamb
Software Mentions: 1
Published: about 6 years ago

10.1186/1472-6807-6-19

Cited by: 410
Author(s): Bingding Huang, Michael Schroeder
Software Mentions: 1
Published: almost 19 years ago

10.1186/1472-6807-14-18

A simple method for finding a protein’s ligand-binding pockets
Cited by: 13
Author(s): Seyed Majid Saberi Fathi, Jack A. Tuszyński
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2105-13-39

Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets
Cited by: 13
Author(s): Paul Ashford, David S. Moss, Alexander Alex, Siew Kuen Yeap, Alice Povia, Irene Nobeli, Mark A. Williams
Software Mentions: 1
Published: over 12 years ago

10.1186/1753-6561-5-S9-S115

Comparison of collapsing methods for the statistical analysis of rare variants
Cited by: 5
Author(s): Carmen Dering, Andreas Ziegler, Inke R. König, Claudia Hemmelmann
Software Mentions: 1
Published: almost 13 years ago

10.1186/1753-6561-5-S9-S114

Improved power by collapsing rare and common variants based on a data-adaptive forward selection strategy
Cited by: 2
Author(s): Yilin Dai, Ling Guo, Jing Dong, Rong Jiang
Software Mentions: 1
Published: almost 13 years ago

10.3390/ani11061791

Unmitigated Surgical Castration in Calves of Different Ages: Electroencephalographic and Neurohormonal Findings
Cited by: 4
Author(s): L. Bergamasco, Lily N. Edwards‐Callaway, Nora M. Bello, Sage Mijares, Charley A. Cull, Ruby A. Mosher, Johann F. Coetzee
Software Mentions: 1
Published: over 3 years ago

10.1186/1472-6831-14-74

Dental caries in primary and permanent molars in 7-8-year-old schoolchildren evaluated with Caries Assessment Spectrum and Treatment (CAST) index
Cited by: 44
Author(s): Joanna Bagińska, Ewa Rodakowska, Robert Milewski, Anna Kierklo
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-8-S4-S3

CORRIE: enzyme sequence annotation with confidence estimates
Cited by: 16
Author(s): Benjamin Audit, Emmanuel D. Levy, Walter R. Gilks, Leon Goldovsky, Christos A. Ouzounis
Software Mentions: 1
Published: over 17 years ago

10.1186/s12903-018-0583-6

Comparison of caries lesion detection methods in epidemiological surveys: CAST, ICDAS and DMF
Cited by: 38
Author(s): Ana Luiza Sarno Castro, Maria Isabel Pereira Vianna, Carlos Maurício Cardeal Mendes
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-10-239

Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis
Cited by: 85
Author(s): Roberto Ternes Arrial, Roberto Coiti Togawa, Marcelo M. Brigido
Software Mentions: 1
Published: over 15 years ago

10.1371/journal.pone.0004473

Investigation of Atomic Level Patterns in Protein—Small Ligand Interactions
Cited by: 55
Author(s): Ke Chen, Lukasz Kurgan
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2369-9-18

The association between renal function and structural parameters: a pig study
Cited by: 15
Author(s): Anders Bergh Lødrup, Kristian Karstoft, Thomas H. Dissing, Jens Randel Nyengaard, Michael Pedersen
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pgen.0030094

Determinants of Cell- and Gene-Specific Transcriptional Regulation by the Glucocorticoid Receptor
Cited by: 276
Author(s): Alex Yick-Lun So, Christina Chaivorapol, Eric Bolton, Hao Li, Keith R. Yamamoto
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pgen.1002393

Mining the LIPG Allelic Spectrum Reveals the Contribution of Rare and Common Regulatory Variants to HDL Cholesterol
Cited by: 31
Author(s): Sumeet A. Khetarpal, Andrew C. Edmondson, Avanthi Raghavan, Hemanth Neeli, Weijun Jin, Karen O. Badellino, Serkalem Demissie, Alisa K. Manning, Stephanie DerOhannessian, Megan L. Wolfe, L. Adrienne Cupples, Mingyao Li, Sekar Kathiresan, Daniel J. Rader
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12891-017-1879-4

The effect of low intensity shockwave treatment (Li-SWT) on human myoblasts and mouse skeletal muscle
Cited by: 5
Author(s): Lise Hansen, Henrik Daa Schrøder, Lars Lund, Karthikeyan Rajagopal, Vrisha Maduri, Jeeva Sellathurai
Software Mentions: 1
Published: almost 7 years ago

10.1186/1471-2105-11-365

Knowledge-based annotation of small molecule binding sites in proteins
Cited by: 15
Author(s): Ratna R. Thangudu, Manoj Tyagi, Benjamin A. Shoemaker, Stephen H. Bryant, Anna R. Panchenko, Thomas Madej
Software Mentions: 1
Published: over 14 years ago

Projects: cran: CAST

Papers Mentioning CAST 219