10.3389/fmolb.2021.715972

Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks
Cited by: 5
Author(s): Noelia Ferruz, Florian Michel, Francisco Lobos, Steffen Schmidt, Birte Höcker
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pcbi.1009078

lra: A long read aligner for sequences and contigs
Cited by: 50
Author(s): Jimin Ren, Mark Chaisson
Software Mentions: 4
Published: about 5 years ago

10.7717/peerj-cs.144

The Modern Research Data Portal: a design pattern for networked, data-intensive science
Cited by: 24
Author(s): Kyle Chard, Eli Dart, Ian Foster, David J. Shifflett, Steven Tuecke, Jason Williams
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-015-0544-x

Pydna: a simulation and documentation tool for DNA assembly strategies using python
Cited by: 16
Author(s): Filipa Pereira, Flávio Azevedo, Ângela Carvalho, Gabriela Ribeiro, Mark W. Budde, Börje Johansson
Software Mentions: 4
Published: about 11 years ago

10.3389/fneur.2019.00512

Serial S100B Sampling Detects Intracranial Lesion Development in Patients on Extracorporeal Membrane Oxygenation
Cited by: 7
Author(s): Alexander Fletcher‐Sandersjöö, Caroline Lindblad, Eric Peter Thelin, Jiri Bartek, Marko Sallisalmi, Adrian Elmi-Terander, Mikael Svensson, Bo‐Michael Bellander, Lars Broman
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pgen.1000419

Recombinational Landscape and Population Genomics of Caenorhabditis elegans
Cited by: 380
Author(s): Matthew V. Rockman, Leonid Kruglyak
Software Mentions: 4
Published: over 17 years ago

10.3390/bioengineering8020026

An Open-Source COVID-19 CT Dataset with Automatic Lung Tissue Classification for Radiomics
Cited by: 19
Author(s): Paolo Zaffino, Aldo Marzullo, Sara Moccia, Francesco Calimeri, Elena De Momi, Bernardo Bertucci, Pier Paolo Arcuri, Maria Francesca Spadea
Software Mentions: 4
Published: over 5 years ago

10.1083/jcb.201804042

Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities
Cited by: 33
Author(s): Alison E. Casey, Ankit Sinha, Rajat Singhania, Julie Livingstone, Paul Waterhouse, Pirashaanthy Tharmapalan, Jennifer Cruickshank, Mona Shehata, Erik Drysdale, Hui Fang, Hye-Yeon Kim, Ruth Isserlin, Swneke D. Bailey, Tiago da Silva Medina, Geneviève Deblois, Yu-Jia Shiah, Dalia Baršytė-Lovejoy, Stefan Höfer, Gary D. Bader, Mathieu Lupien, C.H. Arrowsmith, S. Knapp, Daniel D De Carvalho, Hal K. Berman, Paul C. Boutros, Thomas Kislinger, Rama Khokha
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-018-20200-y

Cultural effects on computational metrics of spatial and temporal context
Cited by: 3
Author(s): Nicholas D. Wright, Jan Grohn, Chen Song, Geraint Rees, Rebecca Lawson
Software Mentions: 4
Published: over 8 years ago

10.1534/genetics.120.303253

Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes
Cited by: 38
Author(s): Peter L. Ralph, Kevin R. Thornton, Jerome Kelleher
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-019-50885-8

Improved gene co-expression network quality through expression dataset down-sampling and network aggregation
Cited by: 25
Author(s): Franziska Liesecke, Johan-Owen De Craene, Sébastien Besseau, Vincent Courdavault, Marc Clastre, Valentin Vergès, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-021-93528-7

Preoperative nomogram for microvascular invasion prediction based on clinical database in hepatocellular carcinoma
Cited by: 6
Author(s): Shuqi Mao, Xi Yu, Yong Yang, Yuying Shan, Joseph Mugaanyi, Shengping Wu, Caide Lu
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-021-84091-2

A predictive internet-based model for COVID-19 hospitalization census
Cited by: 11
Author(s): Philip Turk, Thao Phuong Tran, Geoffrey Rose, Andrew McWilliams
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-019-42632-w

Combining hippocampal volume metrics to better understand Alzheimer’s disease progression in at-risk individuals
Cited by: 15
Author(s): Kevin McRae-McKee, Stephanie Evans, Christoforos Hadjichrysanthou, Man Sau Wong, Frank de Wolf, Roy M. Anderson
Software Mentions: 4
Published: about 7 years ago

10.1186/1471-2105-8-462

Dynamic simulation of regulatory networks using SQUAD
Cited by: 137
Author(s): Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios, Luis Mendoza
Software Mentions: 4
Published: over 18 years ago

10.1186/s12859-021-04329-8

DI2: prior-free and multi-item discretization of biological data and its applications
Cited by: 2
Author(s): Leonardo Alexandre, Rafael S. Costa, Rui Henriques
Software Mentions: 4
Published: almost 5 years ago

10.18632/aging.202365

Transcriptomic characterization reveals prognostic molecular signatures of sorafenib resistance in hepatocellular carcinoma
Cited by: 7
Author(s): Wei Yuan, Ran Tao, Da Huang, Weiming Yan, Shen Gao, Qin Ning
Software Mentions: 4
Published: over 5 years ago

10.3389/fimmu.2021.693608

Single-Cell RNA Sequencing Reveals the Immunological Profiles of Renal Allograft Rejection in Mice
Cited by: 11
Author(s): Qixia Shen, Yucheng Wang, Jiaoyi Chen, Lifeng Ma, Xiao‐Ru Huang, Sydney C. W. Tang, Hui‐Yao Lan, Hong Jiang, Jianghua Chen
Software Mentions: 4
Published: about 5 years ago

10.1186/s12967-020-02319-7

A LASSO-derived risk model for long-term mortality in Chinese patients with acute coronary syndrome
Cited by: 18
Author(s): Yiming Li, Zhuo-lun Li, Fei Chen, Qi Liu, Yong Peng, Mao Chen
Software Mentions: 4
Published: over 6 years ago

10.1186/1751-0473-8-15

Implementing a new EPR lineshape parameter for organic radicals in carbonaceous matter
Cited by: 1
Author(s): Mathilde Bourbin, Y. Le Du, Laurent Binet, Didier Gourier
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0206531

The music that helps people sleep and the reasons they believe it works: A mixed methods analysis of online survey reports
Cited by: 42
Author(s): Tabitha Trahan, Simon J. Durrant, Daniel Müllensiefen, Victoria J. Williamson
Software Mentions: 4
Published: over 7 years ago

10.3390/s130202220

Architecture for Multi-Technology Real-Time Location Systems
Cited by: 9
Author(s): Javier Rodas, Valentín Barral, Carlos J. Escudero
Software Mentions: 4
Published: over 13 years ago

10.1186/s13059-020-02021-3

Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations
Cited by: 40
Author(s): Gregory P. Way, Michael Zietz, Vincent Rubinetti, Daniel S. Himmelstein, Casey S. Greene
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0242520

On the agreement between bibliometrics and peer review: Evidence from the Italian research assessment exercises
Cited by: 5
Author(s): Alberto Baccini, Lucio Barabesi, Giuseppe De Nicolao
Software Mentions: 4
Published: over 5 years ago

10.1186/2041-1480-5-41

Structuring research methods and data with the research object model: genomics workflows as a case study
Cited by: 26
Author(s): Kristina Hettne, Harish Dharuri, Jun Zhao, Katy Wolstencroft, Khalid Belhajjame, Stian Soiland‐Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, L. Verdes–Montenegro, Julián Garrido, David De Roure, Óscar Corcho, Graham Klyne, Reinout van Schouwen, Peter A C ‘t Hoen, Sean Bechhofer, Carole Goble, Marco Roos
Software Mentions: 4
Published: almost 12 years ago

10.3389/fmolb.2021.617176

BIO-GATS: A Tool for Automated GPCR Template Selection Through a Biophysical Approach for Homology Modeling
Cited by: 3
Author(s): Amara Jabeen, Ramya Vijayram, Shoba Ranganathan
Software Mentions: 4
Published: over 5 years ago

10.1186/s12859-021-04147-y

Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes
Cited by: 1
Author(s): Michal R. Grzadkowski, Hannah D. Holly, Julia Somers, Emek Demir
Software Mentions: 4
Published: about 5 years ago

10.1186/s13029-017-0065-2

LitDB - Keeping Track of Research Papers From Your Institute Made Simple
Cited by: 0
Author(s): Jörn Bethune, Lars Kraemer, Ingo Thomsen, Andreas Keller, David Ellinghaus, André Franke
Software Mentions: 4
Published: over 9 years ago

10.1186/s12916-019-1292-y

Repeated clinical malaria episodes are associated with modification of the immune system in children
Cited by: 33
Author(s): Yaw Bediako, Rebecca N. Adams, Adam J. Reid, John Joseph Valletta, Francis M. Ndungu, Jan Sodenkamp, Jedidah Mwacharo, Joyce M. Ngoi, Domtila Kimani, Oscar Kai, Juliana Wambua, George Nyangweso, Etienne P. de Villiers, Mandy Sanders, Magda E. Lotkowska, Jing-wen Lin, Sabrina Manni, John W.G. Addy, Mario Recker, Chris Newbold, Matthew Berriman, Philip Bejon, Kevin Marsh, Jean Langhorne
Software Mentions: 4
Published: over 7 years ago

10.3390/v13030433

Non-Metabolic Functions of PKM2 Contribute to Cervical Cancer Cell Proliferation Induced by the HPV16 E7 Oncoprotein
Cited by: 7
Author(s): Seoung-Ae Lee, Charles Ho, Madison Troxler, Chin-Yo Lin, Sang-Hyuk Chung
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2105-15-180

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping
Cited by: 135
Author(s): Adam C. English, William Salerno, Jeffrey G. Reid
Software Mentions: 4
Published: about 12 years ago

10.1038/s41598-019-44266-4

Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage Polarization
Cited by: 21
Author(s): Chetan P. Hans, Neekun Sharma, Sidharth Sen, Shuai Zeng, Rishabh Dev, Yuyong Jiang, Advitiya Mahajan, Trupti Joshi
Software Mentions: 4
Published: about 7 years ago

10.1093/gigascience/giz076

Open Humans: A platform for participant-centered research and personal data exploration
Cited by: 39
Author(s): Bastian Greshake Tzovaras, Misha Angrist, Kevin J. Arvai, Mairi Dulaney, Vero Estrada-Galiñanes, Beau Gunderson, T. Head, Dana Lewis, Oded Nov, Orit Shaer, Athina Tzovara, Jason Bobe, Mad Price Ball
Software Mentions: 4
Published: about 7 years ago

10.21105/joss.01294

PyBIDS: Python tools for BIDS datasets
Cited by: 32
Author(s): Tal Yarkoni, Chris Markiewicz, Alejandro de la Vega, Krzysztof J. Gorgolewski, Taylor Salo, Yaroslav O. Halchenko, Quinten McNamara, Krista DeStasio, Jean‐Baptiste Poline, Dmitry Petrov, Valérie Hayot‐Sasson, Dylan M. Nielson, Johan D. Carlin, Gregory Kiar, Kirstie Whitaker, Elizabeth DuPré, Adina Wagner, Lee S. Tirrell, Mainak Jas, Michael Hanke, Russell A. Poldrack, Oscar Estéban, Stefan Appelhoff, Chris Holdgraf, Isla Staden, Bertrand Thirion, Dave F. Kleinschmidt, John A. Lee, Matteo Visconti di Oleggio Castello, Michael Notter, Ross Blair
Software Mentions: 4
Published: almost 7 years ago

10.15252/msb.20167456

A photoconversion model for full spectral programming and multiplexing of optogenetic systems
Cited by: 29
Author(s): Evan J. Olson, Constantine N. Tzouanas, Jeffrey J. Tabor
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2164-12-192

FungalRV: adhesin prediction and immunoinformatics portal for human fungal pathogens
Cited by: 64
Author(s): Rupanjali Chaudhuri, Faraz Alam Ansari, Muthukurussi Varieth Raghunandanan, Srinivasan Ramachandran
Software Mentions: 4
Published: over 15 years ago

10.15252/embj.2019104185

Timeless couples G‐quadruplex detection with processing by <scp>DDX</scp> 11 helicase during <scp>DNA</scp> replication
Cited by: 42
Author(s): Letícia Koch Lerner, Sandro Holzer, M.L. Kilkenny, Saša Šviković, Pierre Murat, Davide Schiavone, Cara Bernadette Eldridge, Alice Bittleston, Joseph D. Maman, Dana Branzei, Katherine Stott, Luca Pellegrini, Julian E. Sale
Software Mentions: 4
Published: about 6 years ago

10.1186/s13007-021-00718-5

Reference-based QUantification Of gene Dispensability (QUOD)
Cited by: 2
Author(s): Katharina Sielemann, Bernd Weißhaar, Boas Pucker
Software Mentions: 4
Published: over 5 years ago

10.1186/s12917-018-1505-1

The value of necropsy reports for animal health surveillance
Cited by: 18
Author(s): Susanne Küker, Céline Faverjon, Lenz Furrer, John Berezowski, Horst Posthaus, Fabio Rinaldi, Flavie Vial
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0242334

Predicting time to graduation at a large enrollment American university
Cited by: 6
Author(s): John M. Aiken, Riccardo De Bin, M. Hjorth‐Jensen, Marcos D. Caballero
Software Mentions: 4
Published: over 5 years ago

10.3233/JAD-200445

Cognitive, Genetic, Brain Volume, and Diffusion Tensor Imaging Markers as Early Indicators of Dementia
Cited by: 4
Author(s): Theresa Müller, Nicola Maria Payton, Grégoria Kalpouzos, Frank Jessen, Giulia Grande, Lars Bäckman, Erika J. Laukka
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0215531

ETDB-Caltech: A blockchain-based distributed public database for electron tomography
Cited by: 36
Author(s): Davi R. Ortega, Catherine M. Oikonomou, H. Ding, Prudence Rees-Lee, Alexandria, Grant J. Jensen
Software Mentions: 4
Published: over 7 years ago

10.1186/s13326-017-0118-0

BioFed: federated query processing over life sciences linked open data
Cited by: 43
Author(s): Ali Hasnain, Qaiser Mehmood, Syeda Sana e Zainab, Muhammad Saleem, Claude N. Warren, Durre Zehra, Stefan Decker, Dietrich Rebholz‐Schuhmann
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pgen.1009164

The PAX-FOXO1s trigger fast trans-differentiation of chick embryonic neural cells into alveolar rhabdomyosarcoma with tissue invasive properties limited by S phase entry inhibition
Cited by: 7
Author(s): Gloria González Curto, Audrey Der Vartanian, Youcef El-Mokhtar Frarma, Line Manceau, Lorenzo Baldi, Selene Prisco, Nabila Elarouci, Frédéric Causeret, Daniil Korenkov, Muriel Rigolet, Frédéric Auradé, Aurélien de Reyniès, Vincent Contremoulins, Frédéric Relaix, Orestis Faklaris, James Briscoe, Pascale Gilardi-Hebenstreit, Vanessa Ribes
Software Mentions: 4
Published: over 5 years ago

10.3389/frai.2020.00023

PECLIDES Neuro: A Personalisable Clinical Decision Support System for Neurological Diseases
Cited by: 12
Author(s): Tamara Müller, Píetro Lió
Software Mentions: 4
Published: over 6 years ago

10.1186/s13049-021-00930-1

Primary versus early secondary referral to a specialized neurotrauma center in patients with moderate/severe traumatic brain injury: a CENTER TBI study
Cited by: 7
Author(s): Charlie Sewalt, Benjamin Gravesteijn, David Menon, Hester F. Lingsma, Andrew I.R. Maas, Nino Stocchetti, Esmée Venema, Fiona Lecky, Cecilia Åkerlund, Krisztina Amrein, Nada Anđelić, Lasse Andreassen, Audny Anke, Anna Antoni, Gérard Audibert, Philippe Azouvi, Maria Luisa Azzolini, Ronald Bartels, Pál Barzó, Romuald Beauvais, Ronny Beer, Bo‐Michael Bellander, Antonio Belli, Habib Benali, Maurizio Berardino, Luigi Beretta, Morten Blaabjerg, Peter Bragge, Alexandra Bražinová, Vibeke Brinck, Joanne Brooker, Camilla Brorsson, András Büki, Monika Bullinger, Manuel Cabeleira, Alessio Caccioppola, Emiliana Calappi, Maria Rosa Calvi, Peter Cameron, Guillermo Carbayo Lozano, Marco Carbonara, Giorgio Chevallard, Arturo Chieregato, Giuseppe Citerio, Maryse C. Cnossen, Mark Coburn, Jonathan P. Coles, David Cooper, Marta Correia, Amra Čović, Nicola Curry, Endre Czeiter, Marek Czosnyka, Claire Dahyot‐Fizelier, Helen Dawes, Véronique De Keyser, Vincent Degos, Francesco Della Corte, Hugo den Boogert, Bart Depreitere, Đula Đilvesi, Abhishek Dixit, Emma Donoghue, Jens P. Dreier, Guy‐Loup Dulière, Ari Ercole, Patrick Esser, Erzsébet Ezer, Martin Fabricius, Valery Feigin, Kelly Foks, Shirin Frisvold, Alex Furmanov, Pablo Gagliardo, Damien Galanaud, Dashiell Gantner, Guoyi Gao, Pradeep George, Alexandre Ghuysen, Lelde Giga, Ben Glocker, Jagoš Golubović, Pedro A. Gómez, Johannes Gratz, Benjamin Gravesteijn, Francesca Grossi, Russell L. Gruen, Deepak Gupta, Juanita A. Haagsma, Iain Haitsma, Raimund Helbok, Eirik Helseth, Lindsay Horton, Jilske Huijben, Peter J. Hutchinson, Bram Jacobs, Stefan Jankowski, Mike Jarrett, Jiyao Jiang, Kelly Jones, Mladen Karan, Angelos Kolias, Erwin J. O. Kompanje, Daniel Kondziella, Evgenios Koraropoulos, Lars‐Owe D. Koskinen, Noémi Kovács, Alfonso Lagares, Linda Lanyon, Steven Laureys, Fiona Lecky, Rolf Lefering, Valérie Legrand, Aurélie Lejeune, Leon Levi, Roger Lightfoot, Hester F. Lingsma, Andrew I.R. Maas, Ana M. Castaño‐León, Marc Maegele, Marek Majdán, Alex Manara, Geoffrey T. Manley, Costanza Martino, Hugues Maréchal, Julia Mattern, Catherine McMahon, Béla Melegh, David Menon, Tomas Menovsky, D Mulazzi, Visakh Muraleedharan, Lynnette Murray, Nandesh Nair, Ancuța Negru, David W. Nelson, Virginia Newcombe, Daan Nieboer, Quentin Noirhomme, József Nyirádi, Otesile Olubukola, Matej Orešič, Fabrizio Ortolano, Aarno Palotie, Paul M. Parizel, Jean‐François Payen, Natascha Perera, Vincent Perlbarg, Paolo Persona, Wilco C. Peul, Anna Piippo-Karjalainen, Matti Pirinen, Horia Pleş, Suzanne Polinder, Iñigo Pomposo, Jussi P. Posti, Louis Puybasset, Andreea Rădoi, Arminas Ragauskas, Rahul Raj, Malinka Rambadagalla, Ruben Real, Jonathan R. Rhodes, Sylvia Richardson, Sophie Richter, Samuli Ripatti, Saulius Ročka, Cecilie Røe, Olav Røise, Jonathan Rosand, Jeffrey V. Rosenfeld, Christina Rosenlund, Guy Rosenthal, Rolf Rossaint, Sandra Rossi, Daniel Rueckert, Martin Rusňák, Juan Sahuquillo, Oliver Sakowitz, Renán Sánchez-Porras, János Sándor, Nadine Schäfer, Silke Schmidt, Herbert Schöechl, Guus Schoonman, Rico Frederik Schou, Elisabeth Schwendenwein, Charlie Sewalt, Toril Skandsen, Peter Smielewski, Abayomi Sorinola, Emmanuel Stamatakis, Simon Stanworth, Ana Kowark, Robert Stevens, William Α. Stewart, Ewout W. Steyerberg, Nino Stocchetti, Nina Sundström, Anneliese Synnot, Riikka Takala, Viktória Tamás, Tomas Tamošuitis, Mark Taylor, Braden Te Ao, Olli Tenovuo, Alice Theadom, Matt Thomas, Dick Tibboel, Marjolein Timmers, Christos M. Tolias, Tony Trapani, Cristina Maria Tudora, Peter Vajkoczy, Shirley Vallance, Egils Valeinis, Zoltán Vámos, Gregory Van der Steen, Joukje van der Naalt, Jeroen T.J.M. van Dijck, Thomas A. van Essen, Wim Van Hecke, Caroline van Heugten, Dominique Van Praag, Thijs Vande Vyvere, Audrey Vanhaudenhuyse, Roel P. J. van Wijk, Alessia Vargiolu, Emmanuel Vega, Kimberley Velt, Jan Verheyden, Paul Vespa, Anne Vik, Rimantas Vilcinis, Victor Volovici, Nicole von Steinbüchel, Daphne Voormolen, Petar Vuleković, Kevin Wang, Eveline Wiegers, Guy Williams, Lindsay Wilson, Stefan Winzeck, Stefan Wolf, Zhihui Yang, Peter Ylén, Alexander Younsi, Frederick A. Zeiler, Veronika Zelinkova, Agate Ziverte, Tommaso Zoerle
Software Mentions: 4
Published: almost 5 years ago

10.3390/s20133645

OpCode-Level Function Call Graph Based Android Malware Classification Using Deep Learning
Cited by: 24
Author(s): Weina Niu, Rong Cao, Xiaosong Zhang, Kangyi Ding, Kaimeng Zhang, Ting Li
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-021-99329-2

Replicated, urban-driven exposure to metallic trace elements in two passerines
Cited by: 5
Author(s): Marion Chatelain, Arnaud Da Silva, Marta Celej, Eliza Kurek, Ewa Bulska, Michela Corsini, Marta Szulkin
Software Mentions: 4
Published: almost 5 years ago

10.1186/1758-5996-5-33

Development and validation of a predictive model of acute glucose response to exercise in individuals with type 2 diabetes
Cited by: 7
Author(s): Bryan Gibson, Sheri R. Colberg, Paul Poirier, Denise Maria Martins Vancea, Jason Jones, Robin L. Marcus
Software Mentions: 4
Published: about 13 years ago

10.3390/antiox10020323

Antioxidant Effect of a Probiotic Product on a Model of Oxidative Stress Induced by High-Intensity and Duration Physical Exercise
Cited by: 17
Author(s): Maravillas Sánchez-Macarro, Vicente Ávila-Gandía, Silvia Pérez-Piñero, Fernando Cánovas, Ana María García-Muñoz, María Salud Abellán-Ruiz, Desirée Victoria-Montesinos, Antonio J. Luque-Rubia, Eric Climent, Salvador Genovés, Daniel Ramón, Empar Chenoll, Francisco Javier López-Román
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/5589829

Pharmacovigilance with Transformers: A Framework to Detect Adverse Drug Reactions Using BERT Fine-Tuned with FARM
Cited by: 4
Author(s): Sajid Hussain, Hammad Afzal, Ramsha Saeed, Naima Iltaf, Mir Yasir Umair
Software Mentions: 4
Published: almost 5 years ago

10.3389/fninf.2018.00041

Using NEURON for Reaction-Diffusion Modeling of Extracellular Dynamics
Cited by: 30
Author(s): Adam J. H. Newton, Robert A. McDougal, Michael L. Hines, William W. Lytton
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0124671

From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
Cited by: 158
Author(s): Dáithí C. Murray, Megan L. Coghlan, Michael Bunce
Software Mentions: 4
Published: over 11 years ago

10.3390/s17061452

MinT: Middleware for Cooperative Interaction of Things
Cited by: 12
Author(s): Seongmin Jeon, Inhwa Jung
Software Mentions: 4
Published: about 9 years ago

10.1186/s13002-020-0360-x

Berries, greens, and medicinal herbs—mapping and assessing wild plants as an ecosystem service in Transylvania (Romania)
Cited by: 5
Author(s): Ágnes Vári, Ildikó Arany, Ágnes Kalóczkai, Katalin Kelemen, Judith Papp, Bálint Czúcz
Software Mentions: 4
Published: over 6 years ago

10.3390/rs12050754

Land-Cover Changes to Surface-Water Buffers in the Midwestern USA: 25 Years of Landsat Data Analyses (1993–2017)
Cited by: 13
Author(s): Tedros M. Berhane, Charles R. Lane, S. G. Mengistu, Jay R. Christensen, Heather E. Golden, Shi Qiu, Zhe Zhu, Qiusheng Wu
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-018-31850-3

Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA
Cited by: 31
Author(s): Satabdi Mishra, Tofayel Ahmed, Anu Tyagi, Jing Shi, Shashi Bhushan
Software Mentions: 4
Published: almost 8 years ago

10.7554/eLife.32481

Molecular structure of human KATP in complex with ATP and ADP
Cited by: 127
Author(s): Kenneth Pak Kin Lee, Jue Chen, Roderick MacKinnon
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0047722

Beyond Streptococcus mutans: Dental Caries Onset Linked to Multiple Species by 16S rRNA Community Analysis
Cited by: 378
Author(s): Erin L. Gross, Clifford J. Beall, Stacey R. Kutsch, Noah D. Firestone, Eugene J. Leys, Ann L. Griffen
Software Mentions: 4
Published: almost 14 years ago

10.1111/ejn.14292

Task‐dependent responses to muscle vibration during reaching
Cited by: 7
Author(s): Johannes Keyser, Rob Ramakers, W. Pieter Medendorp, Luc P. J. Selen
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.9161

Personalized analysis of breast cancer using sample-specific networks
Cited by: 3
Author(s): Ke Zhu, Cong Pian, Qiong Xiang, Xin Liu, Yuanyuan Chen
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pone.0246877

Obesity and mortality after the first ischemic stroke: Is obesity paradox real?
Cited by: 21
Author(s): Durgesh Chaudhary, Ayesha Khan, Mudit Gupta, Yirui Hu, Jiang Li, Vida Abedi, Ramin Zand
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.36629

Structure of the CLC-1 chloride channel from Homo sapiens
Cited by: 80
Author(s): Eunyong Park, Roderick MacKinnon
Software Mentions: 4
Published: about 8 years ago

10.3758/s13428-017-0910-x

How well do network models predict observations? On the importance of predictability in network models
Cited by: 213
Author(s): Jonas M B Haslbeck, Lourens J. Waldorp
Software Mentions: 4
Published: about 9 years ago

10.1038/s41597-020-0542-3

A rasterized building footprint dataset for the United States
Cited by: 28
Author(s): Mehdi P. Heris, Leon Foks, Kenneth J. Bagstad, Austin Troy, Zachary H. Ancona
Software Mentions: 4
Published: about 6 years ago

10.1186/s12859-020-3495-9

YSMR: a video tracking and analysis program for bacterial motility
Cited by: 3
Author(s): Julian Schwanbeck, Ines Oehmig, Jerôme Dretzke, Andreas E. Zautner, Uwe Groß, Wolfgang Bohne
Software Mentions: 4
Published: over 6 years ago

10.7554/eLife.54462

The evolutionary history and genomics of European blackcap migration
Cited by: 39
Author(s): Kira E. Delmore, Juan Carlos Illera, Javier Pérez‐Tris, Gernot Segelbacher, Juan Sebastian Lugo Ramos, Gillian Durieux, Jun Ishigohoka, Miriam Liedvogel
Software Mentions: 4
Published: over 6 years ago

10.3390/diagnostics10121113

Deep Learning Assisted Localization of Polycystic Kidney on Contrast-Enhanced CT Images
Cited by: 15
Author(s): Djeane Debora Onthoni, Ting-Wen Sheng, Prasan Kumar Sahoo, Li-Jen Wang, Pushpanjali Gupta
Software Mentions: 4
Published: over 5 years ago

10.1099/mgen.0.000541

Identification and phylogenetic analysis of RNA binding domain abundant in apicomplexans or RAP proteins
Cited by: 5
Author(s): Thomas Hollin, Lukasz Jaroszewski, Jason E. Stajich, Adam Godzik, Karine G. Le Roch
Software Mentions: 4
Published: over 5 years ago

10.1016/j.cub.2020.06.042

Complete Connectomic Reconstruction of Olfactory Projection Neurons in the Fly Brain
Cited by: 102
Author(s): Alexander Shakeel Bates, Philipp Schlegel, Ruairí J.V. Roberts, Nikolas Drummond, Imaan F M Tamimi, Robert Turnbull, Xincheng Zhao, Elizabeth C. Marin, Patricia Demetria Popovici, Serene Dhawan, Arian R. Jamasb, Alexandre Javier, Laia Serratosa Capdevila, Feng Li, Gerald M. Rubin, Scott Waddell, Davi D. Bock, Marta Costa, Gregory S.X.E. Jefferis
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41396-018-0343-2

Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi
Cited by: 74
Author(s): Joel A. Boyd, Sean P. Jungbluth, Andy O. Leu, Paul N. Evans, Ben J. Woodcroft, Grayson L. Chadwick, Victoria J. Orphan, Jan P. Amend, Michael S. Rappé, Gene W. Tyson
Software Mentions: 4
Published: over 7 years ago

10.1038/sdata.2018.151

High-throughput computational X-ray absorption spectroscopy
Cited by: 86
Author(s): Kiran Mathew, Zheng Chen, Donald Winston, Chi Chen, Alan Dozier, J. J. Rehr, Shyue Ping Ong, Kristin A. Persson
Software Mentions: 4
Published: about 8 years ago

10.3390/e22080849

Application of Imbalanced Data Classification Quality Metrics as Weighting Methods of the Ensemble Data Stream Classification Algorithms
Cited by: 10
Author(s): Weronika Węgier, Paweł Ksieniewicz
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2105-5-195

Cited by: 20
Author(s): Joachim Theilhaber, Anatoly Ulyanov, Anish Malanthara, Jack Cole, Dapeng Xu, Robert Nahf, Michael Heuer, Christoph Brockel, Steven Bushnell
Software Mentions: 4
Published: over 22 years ago

10.1002/ece3.7788

Method for quick DNA barcode reference library construction
Cited by: 11
Author(s): Yanlei Liu, Chao Xu, Yuzhe Sun, Xun Chen, Wenpan Dong, Xiaopan Yang, Shi–Liang Zhou
Software Mentions: 4
Published: almost 5 years ago

10.3389/fgene.2020.00158

TADCompare: An R Package for Differential and Temporal Analysis of Topologically Associated Domains
Cited by: 32
Author(s): Kellen Garrison Cresswell, Mikhail G. Dozmorov
Software Mentions: 4
Published: over 6 years ago

10.4049/jimmunol.1602033

Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells
Cited by: 45
Author(s): Ruth Brignall, Pierre Cauchy, Sarah L Bevington, Bethany Gorman, Angela Oliveira Pisco, James Bagnall, Christopher Boddington, William Rowe, Hazel England, Kevin Rich, Lorraine Schmidt, Nigel P. Dyer, Mark A. Travis, Sascha Ott, Dean A. Jackson, Peter N. Cockerill, Pawel Paszek
Software Mentions: 4
Published: almost 9 years ago

10.1093/gigascience/giaa041

Community standards for open cell migration data
Cited by: 11
Author(s): Alejandra González-Beltrán, Paola Masuzzo, Christophe Ampè, Gert-Jan Bakker, Sébastien Besson, Robert H. Eibl, Peter Friedl, Matthias Gunzer, Mark Kittisopikul, Sylvia E. Le Dévédec, Simone Leo, Josh Moore, Yael Paran, Jaime Prilusky, Philippe Rocca-Serra, Philippe Roudot, Marc Schuster, Gwendolien Sergeant, Staffan Strömblad, Jason R. Swedlow, Merijn van Erp, Marleen Van Troys, Assaf Zaritsky, Susanna Assunta Sansone, Lennart Martens
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.7372

Integrating high‐speed videos in capture‐mark‐recapture studies of insects
Cited by: 0
Author(s): Rassim Khelifa, Hayat Mahdjoub, Leithen K. M’Gonigle, Claire Kremen
Software Mentions: 4
Published: about 5 years ago

10.2196/16117

Predicting Adverse Outcomes for Febrile Patients in the Emergency Department Using Sparse Laboratory Data: Development of a Time Adaptive Model
Cited by: 3
Author(s): Sungjoo Lee, Sungchul Hong, Won Chul, Kyunga Kim
Software Mentions: 4
Published: over 6 years ago

10.3390/ijerph17186853

Infectious or Recovered? Optimizing the Infectious Disease Detection Process for Epidemic Control and Prevention Based on Social Media
Cited by: 6
Author(s): Shiguang Shan, Qi Yan, Yigang Wei
Software Mentions: 4
Published: almost 6 years ago

10.1093/bioinformatics/btw570

Precrec: fast and accurate precision–recall and ROC curve calculations in R
Cited by: 145
Author(s): Takaya Saito, Marc Rehmsmeier
Software Mentions: 4
Published: almost 10 years ago

10.3390/s17010066

A Comparison Study of Classifier Algorithms for Cross-Person Physical Activity Recognition
Cited by: 29
Author(s): Yago Sáez, Alejandro Baldominos, Pedro Isasi
Software Mentions: 4
Published: over 9 years ago

10.3390/insects12010011

Olfactory Choice for Decomposition Stage in the Burying Beetle Nicrophorus vespilloides: Preference or Aversion?
Cited by: 4
Author(s): Pablo J. Delclós, Tammy L. Bouldin, Jeffery K. Tomberlin
Software Mentions: 4
Published: over 5 years ago

10.1186/2041-1480-4-9

Semantic querying of relational data for clinical intelligence: a semantic web services-based approach
Cited by: 21
Author(s): Alexandre Riazanov, Artjom Klein, Arash Shaban-Nejad, Greg Rose, Alan J. Forster, David L. Buckeridge, Christopher J. O. Baker
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0232378

Hydroxyapatite-coated implants provide better fixation in total knee arthroplasty. A meta-analysis of randomized controlled trials
Cited by: 9
Author(s): Tamara Horváth, Lilla Hanák, Péter Hegyi, E.P. Butt, Margit Solymár, Ákos Szücs, Orsolya Varga, Bùi Quốc Thiện, Endre Csonka, Petra Hartmann
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pbio.3001306

Dynamic landscape of protein occupancy across the Escherichia coli chromosome
Cited by: 18
Author(s): Peter L. Freddolino, Haley M. Amemiya, Thomas J. Goss, Saeed Tavazoie
Software Mentions: 4
Published: about 5 years ago

10.3389/fmicb.2020.01012

The Gene Catalog and Comparative Analysis of Gut Microbiome of Big Cats Provide New Insights on Panthera Species
Cited by: 7
Author(s): Parul Mittal, Rituja Saxena, Atul Gupta, Shruti Mahajan, Vineet K. Sharma
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.5261

<i>Staphylococcus aureus</i> viewed from the perspective of 40,000+ genomes
Cited by: 57
Author(s): Robert A. Petit, Timothy D. Read
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0085777

powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions
Cited by: 663
Author(s): Jeff Alstott, Edward T. Bullmore, Dietmar Plenz
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pntd.0008056

Machine learning and dengue forecasting: Comparing random forests and artificial neural networks for predicting dengue burden at national and sub-national scales in Colombia
Cited by: 33
Author(s): Naizhuo Zhao, Katia Charland, Mabel Carabalí, Elaine O. Nsoesie, Mathieu Maheu‐Giroux, Erin E. Rees, Mengru Yuan, César García Balaguera, Gloria Jaramillo Ramirez, Kate Zinszer
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0181463

DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing
Cited by: 49
Author(s): Byunghan Lee, Taesup Moon, Sungroh Yoon, Tsachy Weissman
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-019-39773-3

Environmental structure drives resistance to phages and antibiotics during phage therapy and to invading lysogens during colonisation
Cited by: 34
Author(s): Jorge Moura de Sousa, Eduardo P. C. Rocha
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.24836

Minimal-assumption inference from population-genomic data
Cited by: 21
Author(s): Daniel B. Weissman, Oskar Hallatschek
Software Mentions: 4
Published: about 9 years ago

10.3390/s21010010

MUP: Simplifying Secure Over-The-Air Update with MQTT for Constrained IoT Devices
Cited by: 4
Author(s): Kristina Sahlmann, Vera Clemens, Michael A. Nowak, Bettina Schnor
Software Mentions: 4
Published: over 5 years ago

10.1038/sdata.2018.55

Massively parallel recordings in macaque motor cortex during an instructed delayed reach-to-grasp task
Cited by: 41
Author(s): Thomas Brochier, Lyuba Zehl, Yaoyao Hao, Margaux Duret, Julia Sprenger, Michael Denker, Sonja Grün, Alexa Riehle
Software Mentions: 4
Published: over 8 years ago

10.3389/fpls.2019.01188

Elucidation of Hosts, Native Distribution, and Habitat of the Coffee Berry Borer (Hypothenemus hampei) Using Herbaria and Other Museum Collections
Cited by: 5
Author(s): Fernando E. Vega, Lucy Toulmin Smith, Nina M. Davies, Justin Moat, Tomasz Góral, Robert O’Sullivan, Aaron P. Davis
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pone.0141225

A catalogue of novel bovine long noncoding RNA across 18 tissues
Cited by: 76
Author(s): Lambros T. Koufariotis, Yi‐Ping Phoebe Chen, Amanda J. Chamberlain, Christy Vander Jagt, Ben J. Hayes
Software Mentions: 4
Published: almost 11 years ago

10.1128/mSystems.00299-20

Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms
Cited by: 44
Author(s): Elizabeth A. McDaniel, Brittany F. Peterson, Sarah Stevens, Patricia Q. Tran, Karthik Anantharaman, Katherine D. McMahon
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12893-020-00969-4

A novel nomogram for predicting liver metastasis in patients with gastrointestinal stromal tumor: a SEER-based study
Cited by: 8
Author(s): Guowei Zhou, Keshuai Xiao, Guanwen Gong, Jiabao Wu, Ya Zhang, Xinxin Liu, Zhiwei Jiang, Chaoqun Ma
Software Mentions: 4
Published: over 5 years ago