Ecosyste.ms: Papers

10.1093/bioinformatics/bty1063

Simulation of heterogeneous tumour genomes with HeteroGenesis and <i>in silico</i> whole exome sequencing
Cited by: 3
Author(s): Georgette Tanner, David R. Westhead, Alastair P. Droop, Lucy F. Stead
Software Mentions: 2
Published: almost 6 years ago

10.1093/bioinformatics/btt330

Automated design of paralogue ratio test assays for the accurate and rapid typing of copy number variation
Cited by: 9
Author(s): Colin Veal, Hang Xu, Katherine Reekie, Robert C. Free, Robert J. Hardwick, David G. McVey, Anthony J. Brookes, Edward J. Hollox, Chris J. Talbot
Software Mentions: 2
Published: over 11 years ago

10.1155/2015/238139

Constructing a Genome-Wide LD Map of Wild<i>A. gambiae</i>Using Next-Generation Sequencing
Cited by: 2
Author(s): Xiaohong Wang, Yaw A. Afrane, Guiyun Yan, Jun Li
Software Mentions: 2
Published: almost 10 years ago

10.1093/bib/bbt081

A bioinformatician's guide to the forefront of suffix array construction algorithms
Cited by: 30
Author(s): Anish Man Singh Shrestha, Martin C. Frith, Paul Horton
Software Mentions: 2
Published: almost 11 years ago

10.26508/lsa.201900564

Meiotic sex chromosome cohesion and autosomal synapsis are supported by<i>Esco2</i>
Cited by: 7
Author(s): François McNicoll, Anne Kühnel, Uddipta Biswas, Kai Hempel, Gabriela Whelan, Gregor Eichele, Rolf Jessberger
Software Mentions: 2
Published: almost 5 years ago

10.1128/MRA.01444-18

Draft Genome Sequence of Azole-Resistant Aspergillus thermomutatus (Neosartorya pseudofischeri) Strain HMR-AF-39, Isolated from a Human Nasal Septum Abscess Aspirate
Cited by: 4
Author(s): Maxime Parent-Michaud, Philippe J. Dufresne, Éric Fournier, Christine Martineau, Sandrine Moreira, Vincent Perkins, Louis de Repentigny, Simon F. Dufresne
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.2339

CardioTF, a database of deconstructing transcriptional circuits in the heart system
Cited by: 1
Author(s): Yang Zhen
Software Mentions: 2
Published: about 8 years ago

10.7717/peerj-cs.516

VisTAS: blockchain-based visible and trusted remote authentication system
Cited by: 2
Author(s): Ahmad Ali, Mansoor Ahmed, Abid Khan, Adeel Anjum, Muhammad Ilyas, Markus Helfert
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pcbi.1005897

Fluctuating Finite Element Analysis (FFEA): A continuum mechanics software tool for mesoscale simulation of biomolecules
Cited by: 24
Author(s): Albert Solernou, Benjamin S. Hanson, Robin A. Richardson, Robert C. Welch, Daniel J. Read, Oliver G. Harlen, Sarah A. Harris
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pcbi.1003792

VASP-E: Specificity Annotation with a Volumetric Analysis of Electrostatic Isopotentials
Cited by: 19
Author(s): Brian Y. Chen
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pcbi.1005494

Erroneous energy-generating cycles in published genome scale metabolic networks: Identification and removal
Cited by: 79
Author(s): Claus Jonathan Fritzemeier, Daniel Hartleb, Balázs Szappanos, Balázs Papp, Martin J. Lercher
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1008565

Online analysis of microendoscopic 1-photon calcium imaging data streams
Cited by: 22
Author(s): Johannes Friedrich, Andrea Giovannucci, Eftychios A. Pnevmatikakis
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pgen.1005496

Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data
Cited by: 23
Author(s): Frederick E. Dewey, Megan E. Grove, James R. Priest, Daryl Waggott, Puneet Batra, Clint L. Miller, Matthew T. Wheeler, Amin Zia, Cuiping Pan, Konrad J. Karzcewski, Christina Y. Miyake, Michelle Whirl‐Carrillo, Teri E. Klein, Somalee Datta, Russ B. Altman, M Snyder, Thomas Quertermous, Euan A. Ashley
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0003820

NMRDyn: A Program for NMR Relaxation Studies of Protein Association
Cited by: 1
Author(s): Conan K. Wang, Horst Joachim Schirra, David J. Craik
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0127659

QuantiFly: Robust Trainable Software for Automated Drosophila Egg Counting
Cited by: 27
Author(s): Dominic Waithe, Peter Rennert, Gabriel J. Brostow, Matthew D. W. Piper
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0001751

Automatic Physiological Waveform Processing for fMRI Noise Correction and Analysis
Cited by: 14
Author(s): Daniel J. Kelley, Terrence R. Oakes, Lawrence L. Greischar, Moo K. Chung, John M. Ollinger, Andrew L. Alexander, Steven E. Shelton, Ned H. Kalin, Richard J. Davidson
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0004421

Cepred: Predicting the Co-Expression Patterns of the Human Intronic microRNAs with Their Host Genes
Cited by: 47
Author(s): Dong Wang, Ming Lu, Jing Miao, Tingting Li, Edwin Wang, Qinghua Cui
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0075433

Simulating Society Transitions: Standstill, Collapse and Growth in an Evolving Network Model
Cited by: 2
Author(s): Guanghua Xu, Junjie Yang, Guoqing Li
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0119306

Prediction of Protein Structural Features from Sequence Data Based on Shannon Entropy and Kolmogorov Complexity
Cited by: 16
Author(s): Robert P. Bywater
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0116570

UFSRAT: Ultra-Fast Shape Recognition with Atom Types –The Discovery of Novel Bioactive Small Molecular Scaffolds for FKBP12 and 11βHSD1
Cited by: 12
Author(s): Steven Shave, Elizabeth A. Blackburn, Jillian Adie, Douglas R. Houston, Manfred Auer, Scott P. Webster, Paul Taylor, Malcolm D. Walkinshaw
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0039987

FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data
Cited by: 52
Author(s): Richard W. Francis, Katherine Thompson-Wicking, Kim W. Carter, Denise Anderson, Ursula R. Kees, Alex H. Beesley
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0208138

On the use of local weather types classification to improve climate understanding: An application on the urban climate of Toulouse
Cited by: 26
Author(s): Julia Hidalgo, Renaud Jougla
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0036740

The Metagenome of an Anaerobic Microbial Community Decomposing Poplar Wood Chips
Cited by: 85
Author(s): Daniël van der Lelie, Safiyh Taghavi, Sean McCorkle, Luen Luen Li, Stephanie Malfatti, Denise C. Monteleone, Bryon S. Donohoe, Shi You Ding, William S. Adney, Michael E. Himmel, Susannah G. Tringe
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0039158

An Ultra-Fast Metabolite Prediction Algorithm
Cited by: 1
Author(s): Zheng Yang, Murray Grant
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0112168

Understanding the Relationship between Cotton Fiber Properties and Non-Cellulosic Cell Wall Polysaccharides
Cited by: 15
Author(s): Dhivyaa Rajasundaram, Jean-Luc Runavot, Xiaoyuan Guo, William G. T. Willats, Frank Meulewaeter, Joachim Selbig
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0144937

From Insect to Man: Photorhabdus Sheds Light on the Emergence of Human Pathogenicity
Cited by: 28
Author(s): Geraldine Mulley, Michael L. Beeton, Paul Wilkinson, Isabella Vlisidou, Nina Ockendon-Powell, Alexia Hapeshi, Nicholas J. Tobias, Friederike I. Nollmann, Helge B. Bode, Jean M. H. van den Elsen, Richard H. ffrench-Constant, Nicholas R. Waterfield
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0024162

Large-Scale Bi-Level Strain Design Approaches and Mixed-Integer Programming Solution Techniques
Cited by: 78
Author(s): Joonhoon Kim, Jennifer L. Reed, Christos T. Maravelias
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0107497

visPIG - A Web Tool for Producing Multi-Region, Multi-Track, Multi-Scale Plots of Genetic Data
Cited by: 38
Author(s): Matthew Scales, Roland Jäger, G Migliorini, Richard S. Houlston, Marc Henrion
Software Mentions: 2
Published: about 10 years ago

10.1007/978-3-030-53288-8_26

SAW: A Tool for Safety Analysis of Weakly-Hard Systems
Cited by: 8
Author(s): Chao Huang, Kai‐Fu Chang, Chung Wei Lin, Qi Zhu
Software Mentions: 2
Published: almost 5 years ago

10.1186/1742-7622-9-9

A tutorial in estimating the prevalence of disease in humans and animals in the absence of a gold standard diagnostic
Cited by: 66
Author(s): Fraser Lewis, Paul R. Torgerson
Software Mentions: 2
Published: almost 12 years ago

10.12688/f1000research.2-217.v2

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data
Cited by: 16
Author(s): Guillermo Barturen, Antonio Rueda, José Luis Tejera Oliver, Michael Hackenberg
Software Mentions: 2
Published: over 10 years ago

10.3389/fcell.2014.00070

Integrative workflows for metagenomic analysis
Cited by: 31
Author(s): Efthymios Ladoukakis, Fragiskos N. Kolisis, Aristotelis Chatziioannou
Software Mentions: 2
Published: about 10 years ago

10.3389/fchem.2017.00100

Discovering Novel Alternaria solani Succinate Dehydrogenase Inhibitors by in Silico Modeling and Virtual Screening Strategies to Combat Early Blight
Cited by: 13
Author(s): Sehrish Iftikhar, Ahmad Ali Shahid, Sobia Ahsan Halim, Pieter J. Wolters, Vivianne G. A. A. Vleeshouwers, Ajmal Khan, Ahmed Al‐Harrasi, Shahbaz Ahmad
Software Mentions: 2
Published: about 7 years ago

10.3389/fchem.2018.00189

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein
Cited by: 5
Author(s): Mingyuan Xu, Tong Zhu, John Z. H. Zhang
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2019.02367

Minimizing Batch Effects in Mass Cytometry Data
Cited by: 73
Author(s): Ronald P. Schuyler, Conner Jackson, Josselyn E. Garcia-Perez, Ryan M. Baxter, Sidney Ogolla, Rosemary Rochford, Debashis Ghosh, Pratyaydipta Rudra, Elena W.Y. Hsieh
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2021.631603

IL-33 Gene Polymorphisms as Potential Biomarkers of Disease Susceptibility and Response to TNF Inhibitors in Rheumatoid Arthritis, Ankylosing Spondylitis, and Psoriatic Arthritis Patients
Cited by: 17
Author(s): Milena Iwaszko, Joanna Wielińska, Jerzy Świerkot, Katarzyna Kolossa, Renata Sokolik, Bartosz Bugaj, Monika Chaszczewska-Markowska, Sławomir Jeka, Katarzyna Bogunia‐Kubik
Software Mentions: 2
Published: over 3 years ago

10.3389/fninf.2013.00032

Brain extraction using the watershed transform from markers
Cited by: 33
Author(s): Richard Beare, Jian Chen, Christopher Adamson, Tim Silk, Deanne K. Thompson, Joseph Yuan-Mou Yang, Vladyslav Anderson, Marc L. Seal, Amanda G. Wood
Software Mentions: 2
Published: almost 12 years ago

10.3389/fninf.2013.00050

Fast parallel image registration on CPU and GPU for diagnostic classification of Alzheimer's disease
Cited by: 330
Author(s): Denis P. Shamonin, Esther E. Bron, Boudewijn P. F. Lelieveldt, Marion Smits, Stefan Klein, Marius Staring
Software Mentions: 2
Published: almost 12 years ago

10.3389/fnins.2020.590029

Changes in Day/Night Activity in the 6-OHDA-Induced Experimental Model of Parkinson’s Disease: Exploring Prodromal Biomarkers
Cited by: 7
Author(s): Catalina Requejo, Karmele López de Ipiña, José Ángel Ruiz-Ortega, Elsa Fernández, Pilar M. Calvo, Teresa Morera-Herreras, Cristina Miguélez, Laura Cardona-Grifoll, Hodei Cepeda, Luisa Ugedo, José Vicente Lafuente
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2020.00688

Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae)
Cited by: 14
Author(s): Do Yoon Hyun, Sebastin Raveendar, Kyung Jun Lee, Gi-An Lee, Myoung-Jae Shin, Seong Hoon Kim, Jung-Ro Lee, Gyu‐Taek Cho
Software Mentions: 2
Published: over 4 years ago

10.3389/frobt.2020.00098

Efficacy of Modern Neuro-Evolutionary Strategies for Continuous Control Optimization
Cited by: 19
Author(s): Paolo Pagliuca, Nicola Milano, Stefano Nolfi
Software Mentions: 2
Published: over 4 years ago

10.3389/frobt.2019.00022

Model-Based Control of Soft Actuators Using Learned Non-linear Discrete-Time Models
Cited by: 40
Author(s): Phillip Hyatt, David Wingate, Marc D. Killpack
Software Mentions: 2
Published: over 5 years ago

10.1186/gb-2011-12-10-r104

High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing
Cited by: 106
Author(s): David Sims, Ana M. Mendes-Pereira, Jessica Frankum, Darren J. Burgess, Maria-Antonietta Cerone, C. Lombardelli, Costas Mitsopoulos, Jarle Hakas, Nirupa Murugaesu, Clare M. Isacke, Kerry Fenwick, Ioannis Assiotis, Iwanka Kozarewa, Marketa Zvelebil, Alan Ashworth, Christopher J. Lord
Software Mentions: 2
Published: almost 14 years ago

10.1093/gigascience/giy157

LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly
Cited by: 116
Author(s): Gui-Cai Xu, Tianjun Xu, Rui Zhu, Yan Zhang, Shang-Qi Li, Hongwei Wang, Jiong-Tang Li
Software Mentions: 2
Published: almost 6 years ago

10.1093/gigascience/giy148

Prot-SpaM: fast alignment-free phylogeny reconstruction based on whole-proteome sequences
Cited by: 17
Author(s): Chris-André Leimeister, Jendrik Schellhorn, Svenja Dörrer, Michael Gerth, Christoph Bleidorn, Burkhard Morgenstern
Software Mentions: 2
Published: almost 6 years ago

10.1186/1758-2946-4-1

Making SharePoint® Chemically Aware™
Cited by: 43
Author(s): Kartik Tallapragada, Joseph H. Chewning, David C. Kombo, Beverly Ludwick
Software Mentions: 2
Published: almost 13 years ago

10.1038/sdata.2014.50

Multi-modal ultra-high resolution structural 7-Tesla MRI data repository
Cited by: 50
Author(s): Birte U. Forstmann, Max C. Keuken, Andreas Schäfer, Pierre‐Louis Bazin, Anneke Alkemade, Robert Turner
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep26536

QwikMD — Integrative Molecular Dynamics Toolkit for Novices and Experts
Cited by: 141
Author(s): João V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, J. C. Phillips, Peter L. Freddolino, Klaus Schulten
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-017-14885-w

Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids
Cited by: 23
Author(s): Christopher Saski, Brian E. Scheffler, Amanda M. Hulse‐Kemp, Bo Liu, Qingxin Song, Atsumi Ando, David M. Stelly, Jodi A. Scheffler, Jane Grimwood, Don C. Jones, Daniel G. Peterson, Jeremy Schmutz, Z Jeffrey Chen
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-018-36318-y

Gut microbiota community characteristics and disease-related microorganism pattern in a population of healthy Chinese people
Cited by: 29
Author(s): Wen Zhang, Juan Li, Shan Lu, Ning Han, Jiaojiao Miao, Tingting Zhang, Yujun Qiang, Yanhua Kong, Hong Wang, Tongxin Gao, Yuqing Liu, Xiuwen Li, Peng Xu, Xia Chen, Xiaofei Zhao, Jie Che, Ling Zhang, Xi Chen, Zhang Qing, Ming Hu, Qun Li, Biao Kan
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-019-47505-w

Genetic Risk for Rheumatoid Arthritis is Associated with Increased Striatal Volume in Healthy Young Adults
Cited by: 1
Author(s): Reut Avinun, Adam Nevo, Ahmad R. Hariri
Software Mentions: 2
Published: over 5 years ago

10.3390/s16101769

Underwater Communications for Video Surveillance Systems at 2.4 GHz
Cited by: 11
Author(s): Sandra Sendra, Jaime Lloret, Jose M. Jiménez, Joel J. P. C. Rodrigues
Software Mentions: 2
Published: about 8 years ago

10.3390/s19061469

An IoT Surveillance System Based on a Decentralised Architecture
Cited by: 37
Author(s): Amilcare Francesco Santamaria, Pierfrancesco Raimondo, Mauro Tropea, Floriano De Rango, Carmine Aiello
Software Mentions: 2
Published: over 5 years ago

10.3390/s19235332

Detection of Performance of Hybrid Rice Pot-Tray Sowing Utilizing Machine Vision and Machine Learning Approach
Cited by: 8
Author(s): Wenhao Dong, Ma Xu, Hongwei Li, Suiyan Tan, Linjie Guo
Software Mentions: 2
Published: almost 5 years ago

10.1093/ije/dyy012

Longitudinal analysis strategies for modelling epigenetic trajectories
Cited by: 10
Author(s): James R Staley, Matthew Suderman, Andrew Simpkin, Tom R. Gaunt, Jon Heron, Caroline L Relton, Kate Tilling
Software Mentions: 2
Published: almost 7 years ago

10.1186/s43141-020-00095-x

Molecular docking and simulation investigation: effect of beta-sesquiphellandrene with ionic integration on SARS-CoV2 and SFTS viruses
Cited by: 21
Author(s): Amit Joshi, Sunil Krishnan G, Vikas Kaushik
Software Mentions: 2
Published: almost 4 years ago

10.1007/s00239-018-9828-x

Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics
Cited by: 8
Author(s): Gregory A. Babbitt, Erin E. Coppola, Jamie S. Mortensen, Patrick X. Ekeren, Cosmo Viola, Dallan Goldblatt, André O. Hudson
Software Mentions: 2
Published: almost 7 years ago

10.7554/eLife.02866

Characterization of TSET, an ancient and widespread membrane trafficking complex
Cited by: 110
Author(s): Jennifer Hirst, Alexander Schlacht, J. P. Norcott, David Traynor, Gareth Bloomfield, Robin Antrobus, Robert R. Kay, Joel B. Dacks, Margaret S. Robinson
Software Mentions: 2
Published: over 10 years ago

10.1002/jrs.5808

Infrared and Raman spectra of lignin substructures: Dibenzodioxocin
Cited by: 26
Author(s): P. Bock, Paula Nousiainen, Thomas Elder, Markus Blaukopf, Hassan Amer, Ronald Zirbs, Antje Potthast, Notburga Gierlinger
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.jsb.2009.08.002

Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging
Cited by: 77
Author(s): Giulia Zanetti, James D. Riches, Stephen D. Fuller, John Briggs
Software Mentions: 2
Published: about 15 years ago

10.3791/53450

A Pipeline for 3D Multimodality Image Integration and Computer-assisted Planning in Epilepsy Surgery
Cited by: 9
Author(s): Mark Nowell, Roman Rodionov, Gergely Zombori, Rachel Sparks, Michele Rizzi, Sébastien Ourselin, Anna Miserocchi, Andrew W. McEvoy, John S. Duncan
Software Mentions: 2
Published: over 8 years ago

10.1523/ENEURO.0039-18.2018

Motivation Modulates Brain Networks in Response to Faces Varying in Race and Status: A Multivariate Approach
Cited by: 6
Author(s): Bradley D. Mattan, Jennifer T. Kubota, Tianyi Li, Tzipporah Dang, Jasmin Cloutier
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0013739

Analysis of Thyroid Response Element Activity during Retinal Development
Cited by: 33
Author(s): Nathan Billings, Mark M. Emerson, Constance L. Cepko
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0187771

Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation
Cited by: 19
Author(s): Vishal N. Kopardé, Badar Abdul Razzaq, Tara Suntum, Roy Sabo, Allison F. Scalora, Myrna G. Serrano, Max Jameson-Lee, Charles A. Hall, David J. Kobulnicky, Nihar U. Sheth, Juliana Feltz, Daniel Contaifer, Dayanjan S. Wijesinghe, Jason Reed, Catherine Roberts, Rehan Qayyum, Gregory A. Buck, Michael C. Neale, Amir A. Toor
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0093958

Implicit and Explicit Timing in Oculomotor Control
Cited by: 22
Author(s): Ilhame Ameqrane, Pierre Pouget, Nicolas Wattiez, R. H. S. Carpenter, Marcus Missal
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2105-7-408

Scanning sequences after Gibbs sampling to find multiple occurrences of functional elements
Cited by: 2
Author(s): Kannan Tharakaraman, Leonardo Mariño-Ramírez, Sergey L. Sheetlin, David Landsman, John L. Spouge
Software Mentions: 1
Published: about 18 years ago

10.1371/journal.pcbi.1006712

A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell
Cited by: 8
Author(s): R. John Holash, Brian R. MacIntosh
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0002566

An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)
Cited by: 50
Author(s): Dongying Wu, Amber Hartman, Naomi Ward, Jonathan A. Eisen
Software Mentions: 1
Published: over 16 years ago

10.1186/1746-4811-9-30

Diel leaf growth of soybean: a novel method to analyze two-dimensional leaf expansion in high temporal resolution based on a marker tracking approach (Martrack Leaf)
Cited by: 30
Author(s): Michael Mielewczik, Michael Friedli, Norbert Kirchgeßner, Achim Walter
Software Mentions: 1
Published: over 11 years ago

10.1002/pld3.25

A <scp>GDSL</scp>‐motif esterase/acyltransferase/lipase is responsible for leaf water retention in barley
Cited by: 24
Author(s): Chao Li, Guoxiong Chen, Kohei Mishina, Naoki Yamaji, Jian Feng, Fumiko Yukuhiro, Akemi Tagiri, Cheng Liu, Mohammad Pourkheirandish, Nadia Anwar, Masaru Ohta, Pengshan Zhao, Udda Lundqvist, Xinrong Li, Takao Komatsuda
Software Mentions: 1
Published: about 7 years ago

10.1093/texcom/tgaa044

Abnormal Brain Development in Huntington’ Disease Is Recapitulated in the zQ175 Knock-In Mouse Model
Cited by: 10
Author(s): Chuangchuang Zhang, Qian Wu, Hongshuai Liu, Ling Cheng, Zhipeng Hou, Susumu Mori, Jun Hua, Christopher A. Ross, Jiangyang Zhang, Peggy Nopoulos, Wenzhen Duan
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj-cs.361

On the classification of Microsoft-Windows ransomware using hardware profile
Cited by: 10
Author(s): Sana Aurangzeb, Rao Naveed Bin Rais, Muhammad Aleem, Muhammad Arshad Islam, Muhammad Azhar Iqbal
Software Mentions: 1
Published: almost 4 years ago

10.1038/s42003-021-01881-0

A single donor is sufficient to produce a highly functional in vitro antibody library
Cited by: 11
Author(s): M. Frank Erasmus, Sara D’Angelo, L. Naranjo, Antônio Roberto Franchi Teixeira, Rebecca A. Buonpane, Shaun Stewart, Horacio Nastri, Andrew Bradbury
Software Mentions: 1
Published: over 3 years ago

10.1155/2007/35604

An Integrated Pipeline of Open Source Software Adapted for Multi-CPU Architectures: Use in the Large-Scale Identification of Single Nucleotide Polymorphisms
Cited by: 2
Author(s): B. S. Jayashree, Manindra S. Hanspal, R. Srinivasan, R. Vigneshwaran, Rajeev K. Varshney, N. Spurthi, KE Eshwar, Naveen Ramesh, Subhash Chandra, David Hoisington
Software Mentions: 1
Published: almost 18 years ago

10.7717/peerj.6757

Predicting gene expression using DNA methylation in three human populations
Cited by: 29
Author(s): Huan Zhong, Soyeon Kim, Degui Zhi, Xiangqin Cui
Software Mentions: 1
Published: over 5 years ago

10.3390/s21113910

Power Quality Disturbance Tracking Based on a Proprietary FPGA Sensor with GPS Synchronization
Cited by: 2
Author(s): Oscar N. Pardo-Zamora, René de Jesús Romero-Troncoso, Jesús Roberto Millán-Almaraz, Daniel Moriñigo-Sotelo, Roque Alfredo Osornio-Ríos, José A. Antonino-Daviu
Software Mentions: 1
Published: over 3 years ago

10.1016/j.dib.2020.105924

Dataset of short-term prediction of CO2 concentration based on a wireless sensor network
Cited by: 3
Author(s): Ari Wibisono, Hanif Arief Wisesa, Novian Habibie, Aulia Arshad, Aditya Murdha, Wisnu Jatmiko, Ahmad Gamal, Indra Hermawan, Siti Aminah
Software Mentions: 1
Published: over 4 years ago

10.12688/wellcomeopenres.15518.2

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes
Cited by: 30
Author(s): Kirstyn Brunker, Gurdeep Jaswant, Samuel M. Thumbi, Kennedy Lushasi, Ahmed Lugelo, Anna Czupryna, Fred Ade, Gati Wambura, Veronicah Chuchu, Rachel Steenson, Chanasa Ngeleja, Criselda Bautista, Daria L. Manalo, Ma Ricci R Gomez, Maria Yna Joyce Chu, Mary Elizabeth Miranda, Maya Kamat, Kristyna Rysava, Jason Espineda, Eva Angelica V Silo, Ariane Mae Aringo, Rona P. Bernales, Florencio F Adonay, Michael J. Tildesley, Denise A. Marston, Daisy Jennings, Anthony R. Fooks, Wenlong Zhu, Luke W. Meredith, Sarah C. Hill, Radoslaw Poplawski, Robert J. Gifford, Joshua B. Singer, Mathew Maturi, Athman Mwatondo, Roman Biek, Katie Hampson
Software Mentions: 1
Published: over 4 years ago

10.3390/diagnostics10110901

CoSinGAN: Learning COVID-19 Infection Segmentation from a Single Radiological Image
Cited by: 24
Author(s): Pengyi Zhang, Yunxin Zhong, Yulin Deng, Xiaoying Tang, Xin Li
Software Mentions: 1
Published: about 4 years ago

10.1007/s13346-021-01054-w

Engineering of 2D nanomaterials to trap and kill SARS-CoV-2: a new insight from multi-microsecond atomistic simulations
Cited by: 17
Author(s): Mohammad Khedri, Reza Maleki, Mohammad Dahri, Mohammad Moein Sadeghi, Sima Rezvantalab, Hélder A. Santos, Mohammad‐Ali Shahbazi
Software Mentions: 1
Published: about 3 years ago

10.1002/ece3.6942

Evaluating wildlife translocations using genomics: A bighorn sheep case study
Cited by: 15
Author(s): Elizabeth P. Flesch, Tabitha A. Graves, Jennifer M. Thomson, Kelly M. Proffitt, P. J. White, Thomas R. Stephenson, Robert A. Garrott
Software Mentions: 1
Published: about 4 years ago

10.1186/1471-2105-15-18

ISAAC - InterSpecies Analysing Application using Containers
Cited by: 4
Author(s): Herbert Baier, Jörg Schultz
Software Mentions: 1
Published: almost 11 years ago

10.3390/e20100797

Some Consequences of the Thermodynamic Cost of System Identification
Cited by: 15
Author(s): Chris Fields
Software Mentions: 1
Published: about 6 years ago

10.3390/e20120911

Brute Force Composition Scanning with a CALPHAD Database to Find Low Temperature Body Centered Cubic High Entropy Alloys
Cited by: 14
Author(s): T.P.C. Klaver, Darko Simonovic, Marcel H. F. Sluiter
Software Mentions: 1
Published: almost 6 years ago

10.3390/e22040472

Residue Cluster Classes: A Unified Protein Representation for Efficient Structural and Functional Classification
Cited by: 6
Author(s): Fernando Fontove, Gabriel del Río
Software Mentions: 1
Published: over 4 years ago

10.3390/v13040612

Survival Strategies of Streptococcus pyogenes in Response to Phage Infection
Cited by: 6
Author(s): Dior Beerens, Sandra Franch-Arroyo, Timothy J. Sullivan, Christian Goosmann, Volker Brinkmann, Emmanuelle Charpentier
Software Mentions: 1
Published: over 3 years ago

10.1016/j.ymeth.2016.02.017

An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology
Cited by: 177
Author(s): Rebecca Thompson, Matthew Walker, C. Alistair Siebert, Stephen P. Muench, Neil A. Ranson
Software Mentions: 1
Published: over 8 years ago

10.3390/biom10050712

EffHunter: A Tool for Prediction of Effector Protein Candidates in Fungal Proteomic Databases
Cited by: 19
Author(s): Karla Gisel Carreón-Anguiano, Ignacio Islas‐Flores, Julio Vega-Arreguín, Luis Sáenz, Blondy Canto-Canché
Software Mentions: 1
Published: over 4 years ago

10.12688/f1000research.1-19.v2

A domain sequence approach to pangenomics: applications to Escherichia coli
Cited by: 14
Author(s): Lars-Gustav Snipen, David W. Ussery
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2105-12-S4-S2

Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites
Cited by: 28
Author(s): Kirsten Faber, Karl-Heinz Glatting, Phillip J Mueller, Angela Risch, Agnes Hotz‐Wagenblatt
Software Mentions: 1
Published: over 13 years ago

10.1155/2017/4658584

Expression, Docking, and Molecular Dynamics of Endo-<i>β</i>-1,4-xylanase I Gene of<i>Trichoderma virens</i>in<i>Pichia stipitis</i>
Cited by: 3
Author(s): Gammadde Hewa Ishan Maduka Wickramasinghe, Samith Rathnayake, N.V. Chandrasekharan, Mahindagoda Siril Samantha Weerasinghe, Ravindra Lakshman Chundananda Wijesundera, W.S.S. Wijesundera
Software Mentions: 1
Published: almost 8 years ago

10.12688/f1000research.25484.2

PUblications Metadata Augmentation (PUMA) pipeline
Cited by: 1
Author(s): O. W. Butters, Rebecca Wilson, Hugh Garner, Thomas Burton
Software Mentions: 1
Published: over 3 years ago

10.1186/s12938-016-0225-7

Fully automated, level set-based segmentation for knee MRIs using an adaptive force function and template: data from the osteoarthritis initiative
Cited by: 18
Author(s): Chunsoo Ahn, Toan Duc Bui, Yong-woo Lee, Jitae Shin, Hyunjin Park
Software Mentions: 1
Published: about 8 years ago

10.6026/97320630015295

PocketPipe: A computational pipeline for integrated Pocketome prediction and comparison
Cited by: 3
Author(s): Samdani Ansar, Anupriya Sadhasivam, Umashankar Vetrivel
Software Mentions: 1
Published: over 5 years ago

10.1186/1752-0509-8-66

STI-GMaS: an open-source environment for simulation of sexually-transmitted infections
Cited by: 6
Author(s): M. R. Nelson, Kenneth Sutton, Bindi S. Brook, Daniel G. Mallet, Daniel Simpson, Roger G. Rank
Software Mentions: 1
Published: almost 11 years ago

10.1007/s10703-016-0264-5

Empirical software metrics for benchmarking of verification tools
Cited by: 19
Author(s): Yulia Demyanova, Thomas Pani, Helmut Veith, Florian Zuleger
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-017-1616-x

Multi-scale structural community organisation of the human genome
Cited by: 11
Author(s): Rasha E. Boulos, Nicolas Tremblay, A. Arnéodo, Pierre Borgnat, Benjamin Audit
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-021-04089-5

BugSeq: a highly accurate cloud platform for long-read metagenomic analyses
Cited by: 26
Author(s): Jeremy Fan, Steven K. Huang, Samuel D Chorlton
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-13-122

Web tools for large-scale 3D biological images and atlases
Cited by: 25
Author(s): Zsolt L. Husz, Nick Burton, Bill Hill, Nestor Milyaev, Richard Baldock
Software Mentions: 1
Published: over 12 years ago

10.3389/fgene.2020.00386

De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita
Cited by: 17
Author(s): Paramananda Das, Lakshman Sahoo, Satyajit Das, Amrita Bit, Chaitanya Joshi, Basdeo Kushwaha, Dinesh Kumar, Tejas Shah, Ankit T. Hinsu, Namrata Patel, Siddhi Patnaik, Suyash Agarwal, Manmohan Pandey, Shreya Srivastava, Prem Kumar Meher, P. Jayasankar, Prakash G. Koringa, N. S. Nagpure, Ravindra Kumar, Mahender Singh, Mir Asif Iquebal, Sarika Jaiswal, Neeraj Kumar, Mustafa Raza, Kanta Das Mahapatra, J. K. Jena
Software Mentions: 1
Published: over 4 years ago