Ecosyste.ms: Papers

10.7717/peerj.453

scikit-image: image processing in Python
Cited by: 3,381
Author(s): Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu
Software Mentions: 10
Published: over 10 years ago

10.1186/s12859-016-1003-z

Implementation of a methodology for determining elastic properties of lipid assemblies from molecular dynamics simulations
Cited by: 26
Author(s): Niklaus Johner, Daniel Harries, George Khelashvili
Software Mentions: 8
Published: over 8 years ago

10.1186/s12859-019-2796-3

rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics
Cited by: 15
Author(s): Jaume Bonet, Zander Harteveld, Fabian Sesterhenn, Andreas Scheck, Bruno E. Correia
Software Mentions: 7
Published: over 5 years ago

10.12688/f1000research.9618.2

biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format
Cited by: 2
Author(s): Markus J. Ankenbrand, Niklas Terhoeven, Sonja Hohlfeld, Frank Förster, Alexander Keller
Software Mentions: 7
Published: almost 8 years ago

10.1186/1756-0500-4-331

Agile parallel bioinformatics workflow management using Pwrake
Cited by: 20
Author(s): Hiroyuki Mishima, Kensaku Sasaki, M. Tanaka, Osamu Tatebe, Koh-ichiro Yoshiura
Software Mentions: 7
Published: over 13 years ago

10.1186/1471-2342-8-10

Internet Image Viewer (iiV)
Cited by: 9
Author(s): Joel T. Lee, Kristin Munch, John V. Carlis, José V. Pardo
Software Mentions: 6
Published: over 16 years ago

10.1007/s10237-021-01520-x

Spatiotemporal modeling of first and second wave outbreak dynamics of COVID-19 in Germany
Cited by: 10
Author(s): Dorothee Lippold, Andreas Kergaßner, Christian Burkhardt, Matthias Kergaßner, Jonas Loos, Sarah Nistler, Paul Steinmann, Dominik Budday, Silvia Budday
Software Mentions: 6
Published: about 3 years ago

10.1371/journal.pone.0244616

Integrating morphology and metagenomics to understand taxonomic variability of Amphisorus (Foraminifera, Miliolida) from Western Australia and Indonesia
Cited by: 11
Author(s): Jan Niklas Macher, Martina Prazeres, Sarah Taudien, Jamaluddin Jompa, Aleksey Sadekov, Willem Renema
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pcbi.1002970

Chaste: An Open Source C++ Library for Computational Physiology and Biology
Cited by: 366
Author(s): Gary R. Mirams, Christopher J. Arthurs, Miguel O. Bernabéu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G. Fletcher, Daniel G. Harvey, Megan E. Marsh, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Néjib Zemzemi, David Gavaghan
Software Mentions: 6
Published: almost 12 years ago

10.3390/cells8121510

A New Sensitive Method for the Detection of Mycoplasmas Using Fluorescence Microscopy
Cited by: 10
Author(s): Anna Ligasová, Markéta Vydržalová, Renata Buriánová, Lenka Brůčková, Renata Večeřová, Anna Janošťáková, Karel Koberna
Software Mentions: 5
Published: about 5 years ago

10.7717/peerj-cs.232

On-demand virtual research environments using microservices
Cited by: 10
Author(s): Marco Capuccini, Anders Larsson, Matteo Carone, Jon Ander Novella, Noureddin Sadawi, Jianliang Gao, Salman Toor, Ola Spjuth
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pone.0245710

Isolation of the Buchnera aphidicola flagellum basal body complexes from the Buchnera membrane
Cited by: 1
Author(s): Matthew J. Schepers, James N. Yelland, Nancy A. Moran, David W. Taylor
Software Mentions: 5
Published: over 3 years ago

10.1093/gigascience/giz067

Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C
Cited by: 52
Author(s): Changming Bai, Lusheng Xin, Umberto Rosani, Biao Wu, Qingchen Wang, Xiaoke Duan, Zhihong Liu, Wang Chongming
Software Mentions: 4
Published: over 5 years ago

10.7150/jca.56506

Identification of Hub Genes and Small Molecule Drugs Associated with Acquired Resistance to Gefitinib in Non-Small Cell Lung Cancer
Cited by: 8
Author(s): Guangda Li, You-Zhi Ma, Mingwei Yu, Xiaoxiao Li, Xinjie Chen, Yu Tang Gao, Pei-Yu Cheng, Gan‐Lin Zhang, Xiaomin Wang
Software Mentions: 4
Published: almost 4 years ago

10.1038/s41597-020-0415-9

A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task
Cited by: 8
Author(s): Nand Chandravadia, Daan Liang, Andrea Gómez Palacio Schjetnan, April A Carlson, Maïlys C. M. Faraut, Jeffrey M. Chung, Chrystal M. Reed, Benjamin Dichter, Uri Maoz, Suneil K. Kalia, Taufik A. Valiante, Adam N. Mamelak, Ueli Rutishauser
Software Mentions: 4
Published: almost 5 years ago

10.7717/peerj-cs.156

Comparison and benchmark of name-to-gender inference services
Cited by: 197
Author(s): L. Santamaría, Helena Mihaljević
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1009227

Relating simulation studies by provenance—Developing a family of Wnt signaling models
Cited by: 5
Author(s): Kai Budde, Jacob Smith, Pia Wilsdorf, Fiete Haack, Adelinde M. Uhrmacher
Software Mentions: 4
Published: over 3 years ago

10.12688/f1000research.9453.2

Method-centered digital communities on protocols.io for fast-paced scientific innovation
Cited by: 0
Author(s): Lori Kindler, Alexei Stoliartchouk, Leonid Teytelman, Bonnie Hurwitz
Software Mentions: 4
Published: over 7 years ago

10.3389/fnhum.2021.713114

Visual Field Reconstruction in Hemianopia Using fMRI Based Mapping Techniques
Cited by: 1
Author(s): Hinke N. Halbertsma, Holly Bridge, Joana Carvalho, Frans W. Cornelissen, Sara Ajina
Software Mentions: 4
Published: over 3 years ago

10.3389/fnins.2018.00006

Group Analysis in MNE-Python of Evoked Responses from a Tactile Stimulation Paradigm: A Pipeline for Reproducibility at Every Step of Processing, Going from Individual Sensor Space Representations to an across-Group Source Space Representation
Cited by: 17
Author(s): Lau M. Andersen
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12879-021-06586-7

Antibody seroprevalence and rate of asymptomatic infections with SARS-CoV-2 in Austrian hospital personnel
Cited by: 3
Author(s): Iris Leister, Elisabeth Ponocny‐Seliger, Herwig Kollaritsch, Peter Dungel, Barbara Holzer, Johannes Grillari, Heinz Redl, Ivo Ponocny, Claudia Wilfing, Ludwig Aigner, Markus Exner, Michaela Stainer, Matthias Hackl, T. Hausner, Rainer Mittermayr, Wolfgang Schaden
Software Mentions: 4
Published: over 3 years ago

10.2196/resprot.8397

Influence of Information and Communication Technologies on the Resilience and Coping of Sexual and Gender Minority Youth in the United States and Canada (Project #Queery): Mixed Methods Survey
Cited by: 30
Author(s): Shelley L. Craig, Lauren B. McInroy, Sandra D'Souza, Ashley Austin, Lance T. McCready, Andrew Eaton, Leslie Regan Shade, M. Alex Wagaman
Software Mentions: 3
Published: about 7 years ago

10.12688/f1000research.10137.1

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows
Cited by: 83
Author(s): Brian D. O’Connor, Denis Yuen, Vincent Chung, A. Duncan, Xiang Kun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti
Software Mentions: 3
Published: almost 8 years ago

10.1093/gigascience/gix066

Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection
Cited by: 9
Author(s): Qichao Yu, Wei Zhang, Xiaolong Zhang, Yongli Zeng, Yeming Wang, Yanhui Wang, Liqin Xu, Xiaoyun Huang, Nannan Li, Xinlan Zhou, Jie Lü, Xiaosen Guo, Guibo Li, Yong Hou, Shi Ping Liu, Bo Li
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pbio.2004956

The gender gap in science: How long until women are equally represented?
Cited by: 423
Author(s): Luke Holman, Devi Stuart‐Fox, Cindy E. Hauser
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giaa070

Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat
Cited by: 19
Author(s): Fu-Hao Lu, Neil McKenzie, Laura‐Jayne Gardiner, Ming Luo, Anthony Hall, Michael W. Bevan
Software Mentions: 3
Published: over 4 years ago

10.3389/fneur.2018.00684

Thigh-Derived Inertial Sensor Metrics to Assess the Sit-to-Stand and Stand-to-Sit Transitions in the Timed Up and Go (TUG) Task for Quantifying Mobility Impairment in Multiple Sclerosis
Cited by: 27
Author(s): Harry J. Witchel, Cäcilia Oberndorfer, Robert Needham, Aoife Healy, Carina E. I. Westling, Joseph H. Guppy, Jake Bush, Jens Barth, Chantal Herberz, Daniel Roggen, Bjoern M. Eskofier, Waqar Rashid, Nachiappan Chockalingam, Jochen Klucken
Software Mentions: 3
Published: over 6 years ago

10.1093/gigascience/giz007

Molecular digitization of a botanical garden: high-depth whole-genome sequencing of 689 vascular plant species from the Ruili Botanical Garden
Cited by: 36
Author(s): Huan Liu, Jinpu Wei, Ting Yang, Weixue Mu, Bo Song, Tuo Yang, Yuan Fang, Xuebing Wang, Guohai Hu, Wangsheng Li, Hong Zhou, Xiaoli Chen, Hongyun Chen, Lei Cheng, Xiao Shun He, Hechen Cai, Xianchu Cai, Mei Wang, Yang Li, Sunil Kumar Sahu, Jing Yang, Yu Wang, Ranchang Mu, Jie Liu, Jianming Zhao, Ziheng Huang, Xun Xu, Xin Liu
Software Mentions: 3
Published: almost 6 years ago

10.3389/fphys.2021.627088

Poincaré Plot Area of Gamma-Band EEG as a Measure of Emergence From Inhalational General Anesthesia
Cited by: 5
Author(s): Kazuma Hayase, Atsushi Kainuma, Koichi Akiyama, Mao Kinoshita, Masayuki Shibasaki, Teiji Sawa
Software Mentions: 3
Published: almost 4 years ago

10.1186/s13326-016-0111-z

Consolidating drug data on a global scale using Linked Data
Cited by: 20
Author(s): Milos Jovanovik, Dimitar Trajanov
Software Mentions: 3
Published: almost 8 years ago

10.1200/CCI.19.00110

Exploring Integrative Analysis Using the BioMedical Evidence Graph
Cited by: 4
Author(s): Adam J. Struck, Brian Walsh, Alexander Buchanan, Jordan A. Lee, Ryan Spangler, Joshua M. Stuart, Kyle Ellrott
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0246167

Evidence and magnitude of the effects of meteorological changes on SARS-CoV-2 transmission
Cited by: 12
Author(s): Adam I. Kaplin, Caesar Junker, Anupama Kumar, Mary Anne Ribeiro, Eileen Yu, Michael Wang, Ted Smith, N. Shesh, Aruni Bhatnagar
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0257643

Geographical variation in demand, utilization, and outcomes of hospital services for COVID-19 in Brazil: A descriptive serial cross-sectional study
Cited by: 7
Author(s): Claudia Cristina de Aguiar Pereira, Mônica Martins, Sheyla Maria Lemos Lima, Carla Lourenço Tavares de Andrade, Fernando Ramalho Gameleira Soares, Margareth Crisóstomo Portela
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0234354

Negshell casting: 3D-printed structured and sacrificial cores for soft robot fabrication
Cited by: 5
Author(s): Pornthep Preechayasomboon, Eric Rombokas
Software Mentions: 3
Published: over 4 years ago

10.5195/jmla.2021.1185

Performance of gender detection tools: a comparative study of name-to-gender inference services
Cited by: 47
Author(s): Paul Sebo
Software Mentions: 3
Published: about 3 years ago

10.2196/17496

A Social Media Study on the Associations of Flavored Electronic Cigarettes With Health Symptoms: Observational Study
Cited by: 30
Author(s): Long Chen, Xinyi Lu, Jianbo Yuan, Joyce Luo, Jiebo Luo, Zidian Xie, Dongmei Li
Software Mentions: 2
Published: over 4 years ago

10.15252/msb.20188556

Structured Methods for reproducible science
Cited by: 1
Author(s): Maria Polychronidou
Software Mentions: 2
Published: over 6 years ago

10.1007/s10055-021-00585-4

Harmonize: a shared environment for extended immersive entertainment
Cited by: 6
Author(s): Damiano Oriti, Federico Manuri, Francesco De Pace, Andrea Sanna
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pbio.1002538

Protocols.io: Virtual Communities for Protocol Development and Discussion
Cited by: 42
Author(s): Lenny Teytelman, Alexei Stoliartchouk, Lori Kindler, Bonnie Hurwitz
Software Mentions: 2
Published: over 8 years ago

10.3389/fendo.2021.662769

Brain-Body Control of Glucose Homeostasis—Insights From Model Organisms
Cited by: 4
Author(s): Alastair Macdonald, Yu Hsuan Carol Yang, Cruz Am, Craig Beall, Kate L. J. Ellacott
Software Mentions: 2
Published: over 3 years ago

10.1093/gigascience/gix064

Looking back: forward looking
Cited by: 2
Author(s): Scott Edmunds, Nicole Nogoy, Hans Zauner, Peter Li, Chris Hunter, Sizhe Xiao, Laurie Goodman
Software Mentions: 2
Published: over 7 years ago

10.1093/gigascience/gix067

Deep whole-genome sequencing of 90 Han Chinese genomes
Cited by: 35
Author(s): Tianming Lan, Haoxiang Lin, Wenjuan Zhu, Tellier Christian Asker Melchior Laurent, Mofeng Yang, Xin Liu, Jun Wang, Jian Wang, Huanming Yang, Xun Xu, Xiaosen Guo
Software Mentions: 2
Published: over 7 years ago

10.1093/gigascience/gix047

The metagenomic data life-cycle: standards and best practices
Cited by: 36
Author(s): Petra ten Hoopen, Alex Bateman, Lars Ailo Bongo, Matthieu Le Corre, Bruno Fosso, Folker Meyer, Alex L. Mitchell, Éric Pelletier, Graziano Pesole, Mónica Santamaría, Nils Peder Willassen, Guy Cochrane
Software Mentions: 2
Published: over 7 years ago

10.1093/gigascience/giz127

Key challenges facing data-driven multicellular systems biology
Cited by: 31
Author(s): Paul Macklin
Software Mentions: 2
Published: about 5 years ago

10.1128/JCM.00876-20

Open Development and Clinical Validation of Multiple 3D-Printed Nasopharyngeal Collection Swabs: Rapid Resolution of a Critical COVID-19 Testing Bottleneck
Cited by: 93
Author(s): Cody Callahan, Rose Lee, Katelyn E. Zulauf, Lauren Tamburello, Kenneth P. Smith, Joe Previtera, Annie Cheng, Alexander L. Green, Ahmed Abdul Azim, Amanda Yano, Nancy Doraiswami, James E. Kirby, Ramy Arnaout
Software Mentions: 2
Published: over 4 years ago

10.1038/s41598-021-81767-7

Topological impact of negative links on the stability of resting-state brain network
Cited by: 24
Author(s): Majid Saberi, Reza Khosrowabadi, Ali Khatibi, Bratislav Mišić, G. R. Jafari
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-85602-x

White matter alterations in glaucoma and monocular blindness differ outside the visual system
Cited by: 12
Author(s): Sandra Hanekamp, Branislava Ćurčić‐Blake, Bradley Caron, Brent McPherson, Anneleen Timmer, Doety Prins, Christine C. Boucard, Masaki Yoshida, Masahiro Ida, David Hunt, Nomdo M. Jansonius, Franco Pestilli, Frans W. Cornelissen
Software Mentions: 2
Published: almost 4 years ago

10.1038/s41598-021-96707-8

AI outperformed every dermatologist in dermoscopic melanoma diagnosis, using an optimized deep-CNN architecture with custom mini-batch logic and loss function
Cited by: 27
Author(s): Tri-Cong Pham, Chi-Mai Luong, Vu Hoang, Antoine Doucet
Software Mentions: 2
Published: over 3 years ago

10.3390/s17071513

Analysis of Public Datasets for Wearable Fall Detection Systems
Cited by: 96
Author(s): E. Casilari, José Antonio Santoyo-Ramón, José Manuel Cano-García
Software Mentions: 2
Published: over 7 years ago

10.3390/s20215969

Towards a Safer Internet of Things—A Survey of IoT Vulnerability Data Sources
Cited by: 13
Author(s): Marcin Rytel, Anna Felkner, Marek Janiszewski
Software Mentions: 2
Published: about 4 years ago