Ecosyste.ms: Papers

10.12688/f1000research.17548.2

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
Cited by: 8
Author(s): Klara Kaleb, Alex Warwick Vesztrocy, Adrian M. Altenhoff, Christophe Dessimoz
Software Mentions: 13
Published: about 5 years ago

10.12688/f1000research.6767.1

CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API
Cited by: 77
Author(s): Keiichiro Ono, Tanja Muetze, Georgi Kolishovski, Paul Shannon, Barry Demchak
Software Mentions: 8
Published: almost 9 years ago

10.1002/elsc.202000053

Implementing a digital infrastructure for the lab using a central laboratory server and the SiLA2 communication standard
Cited by: 3
Author(s): Marc Porr, F. Lange, Daniel Marquard, Laura Niemeyer, Patrick Lindner, Thomas Scheper, Sascha Beutel
Software Mentions: 8
Published: over 3 years ago

10.34133/2020/3074916

RhizoVision Crown: An Integrated Hardware and Software Platform for Root Crown Phenotyping
Cited by: 65
Author(s): Anand Seethepalli, Haichao Guo, Xiuwei Liu, Marcus Griffiths, Hussien Almtarfi, Zenglu Li, Shuyu Liu, Alina Zare, Felix B. Fritschi, Elison B. Blancaflor, Xuefeng Ma, Larry M. York
Software Mentions: 8
Published: over 4 years ago

10.1016/j.molcel.2019.01.017

System-wide Profiling of RNA-Binding Proteins Uncovers Key Regulators of Virus Infection
Cited by: 122
Author(s): Manuel García-Moreno, Marko Noerenberg, Shuai Ni, Aino I Järvelin, Esther González-Almela, Caroline E. Lenz, Marcel Bach-Pagés, Victoria Cox, Rosario Avolio, Thomas W. Davis, Svenja Hester, Thibault J.M. Sohier, Bingnan Li, Gregory Heikel, Gracjan Michlewski, Miguel Á. Sanz, Luís Carrasco, Emiliano P. Ricci, Vicent Pelechano, Ilan Davis, Bernd Fischer, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 7
Published: about 5 years ago

10.3762/bjnano.6.165

The eNanoMapper database for nanomaterial safety information
Cited by: 82
Author(s): Nina Jeliazkova, Charalampos Chomenidis, Philip Doganis, Bengt Fadeel, Roland C. Grafström, Barry Hardy, Janna Hastings, Markus Hegi, Vedrin Jeliazkov, Nikolay Kochev, Pekka Kohonen, Cristian R. Munteanu, Haralambos Sarimveis, Bart Smeets, Pantelis Sopasakis, Georgia Tsiliki, David Vorgrimmler, Egon Willighagen
Software Mentions: 7
Published: almost 9 years ago

10.1186/s12864-021-07735-7

Non-coding RNAs in the interaction between rice and Meloidogyne graminicola
Cited by: 11
Author(s): Bruno Verstraeten, Mohammad Reza Atighi, Virginia Ruiz‐Ferrer, Carolina Escobar, Tim De Meyer, Tina Kyndt
Software Mentions: 7
Published: almost 3 years ago

10.7717/peerj.2574

<i>YUCCA</i>auxin biosynthetic genes are required for Arabidopsis shade avoidance
Cited by: 60
Author(s): Patricia Müller-Moulé, Kazunari Nozue, Melissa L Pytlak, Christine M. Palmer, Michael F. Covington, Andreah D. Wallace, Stacey L. Harmer, Julin Maloof
Software Mentions: 7
Published: over 7 years ago

10.1093/database/baw160

FirebrowseR: an R client to the Broad Institute’s Firehose Pipeline
Cited by: 123
Author(s): Mario C. Deng, Johannes Brägelmann, Ivan Kryukov, Nuno Saraiva-Agostinho, Sven Perner
Software Mentions: 7
Published: over 7 years ago

10.3390/s150716314

A Smart City Lighting Case Study on an OpenStack-Powered Infrastructure
Cited by: 23
Author(s): Giovanni Merlino, Dario Bruneo, Salvatore Distefano, Francesco Longo, Antonio Puliafito, Adnan Al-Anbuky
Software Mentions: 6
Published: almost 9 years ago

10.3389/frai.2021.644554

Using Twitter Data for the Study of Language Change in Low-Resource Languages. A Panel Study of Relative Pronouns in Frisian
Cited by: 0
Author(s): Jelske Dijkstra, Wilbert Heeringa, Lysbeth Jongbloed-Faber, H. Van de Velde
Software Mentions: 6
Published: about 3 years ago

10.1186/s40168-017-0325-z

Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome
Cited by: 71
Author(s): David Casero, Kirandeep Gill, Vijayalakshmi Sridharan, Igor Koturbash, Gregory A. Nelson, Martin Hauer‐Jensen, Marjan Boerma, Jonathan Braun, Amrita K. Cheema
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pcbi.1003671

Comparison of REST Cistromes across Human Cell Types Reveals Common and Context-Specific Functions
Cited by: 41
Author(s): Shira Rockowitz, Wen-Hui Lien, Erika Pedrosa, Gang Wei, Mingyan Lin, Keji Zhao, Herbert M. Lachman, Elaine Fuchs, Deyou Zheng
Software Mentions: 6
Published: almost 10 years ago

10.1371/journal.pone.0186324

Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant
Cited by: 12
Author(s): Tobias Ahsendorf, Franz‐Josef Müller, V.V. Topkar, Jeremy Gunawardena, Roland Eils
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0134011

A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis.
Cited by: 7
Author(s): Gabriela D. A. Guardia, Luís Ferreira Pires, Ricardo Zorzetto Nicoliello Vêncio, Kelen Cristina Ribeiro Malmegrim, Cléver Ricardo Guareis de Farias
Software Mentions: 6
Published: over 9 years ago

10.7717/peerj.1078

Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox
Cited by: 13
Author(s): A. M. R. Ribeiro, Luís Lacerda, Hugo Alexandre Ferreira
Software Mentions: 6
Published: almost 9 years ago

10.7554/eLife.39209

Reconstructing the functions of endosymbiotic Mollicutes in fungus-growing ants
Cited by: 34
Author(s): Panagiotis Sapountzis, Mariya Zhukova, Jonathan Z. Shik, Morten Schiøtt, Jacobus J. Boomsma
Software Mentions: 6
Published: over 5 years ago

10.3389/fnins.2020.00751

A Radiomics Approach to Predicting Parkinson’s Disease by Incorporating Whole-Brain Functional Activity and Gray Matter Structure
Cited by: 32
Author(s): Xuan Cao, Xiao Wang, Chen Xue, Shaojun Zhang, Qingling Huang, Weiguo Liu
Software Mentions: 5
Published: almost 4 years ago

10.3389/fmicb.2015.01383

Microbiota Plays a Role in Oral Immune Priming in Tribolium castaneum
Cited by: 45
Author(s): Momir Futo, Sophie A. O. Armitage, Joachim Kurtz
Software Mentions: 5
Published: over 8 years ago

10.1186/s12934-015-0226-4

An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture
Cited by: 17
Author(s): Bat-Erdene Jugder, Zhiliang Chen, Darren Tan Tek Ping, Hélène Lebhar, Jeffrey Welch, Christopher P. Marquis
Software Mentions: 5
Published: about 9 years ago

10.1186/s12864-019-6240-x

Didelphis albiventris: an overview of unprecedented transcriptome sequencing of the white-eared opossum
Cited by: 0
Author(s): Íria Gabriela Dias dos Santos, Tiago Antônio de Oliveira Mendes, Gerluza Aparecida Borges Silva, Amanda Maria Sena Reis, Cláudia Barros Monteiro-Vitorello, Patrícia Dayane Carvalho Schaker, Roberto Hirochi Herai, André Brait Carneiro Fabotti, Luiz Lehmann Coutinho, Érika Cristina Jorge
Software Mentions: 5
Published: over 4 years ago

10.1038/srep39002

Phenotypic plasticity in sex pheromone production in Bicyclus anynana butterflies
Cited by: 28
Author(s): Emilie Dion, Antónia Monteiro, Joanne Y. Yew
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pone.0154531

Conserved Senescence Associated Genes and Pathways in Primary Human Fibroblasts Detected by RNA-Seq
Cited by: 63
Author(s): Shiva Marthandan, Mario Baumgart, Stefan Priebe, Marco Groth, Jonas Schaer, Christoph Kaether, Reinhard Guthke, Alessandro Cellerino, Matthias Platzer, Stephan Diekmann, Peter Hemmerich
Software Mentions: 5
Published: about 8 years ago

10.3390/cells8040343

The Petunia CHANEL Gene is a ZEITLUPE Ortholog Coordinating Growth and Scent Profiles
Cited by: 18
Author(s): Marta I. Terry, Fernando Pérez-Sánz, María Victoria Díaz-Galián, Felipe Pérez de los Cobos, Pedro J. Navarro, Marcos Egea‐Cortines, Julia Weiß
Software Mentions: 5
Published: about 5 years ago

10.3390/s20113328

Creating the Internet of Augmented Things: An Open-Source Framework to Make IoT Devices and Augmented and Mixed Reality Systems Talk to Each Other
Cited by: 31
Author(s): Óscar Blanco-Novoa, Paula Fraga‐Lamas, Miguel Vilar-Montesinos, Tiago M. Fernández‐Caramés
Software Mentions: 5
Published: almost 4 years ago

10.1038/s41420-019-0184-4

A six-inhibitor culture medium for improving naïve-type pluripotency of porcine pluripotent stem cells
Cited by: 15
Author(s): Ye Yuan, Jin‐Kyu Park, Yuchen Tian, Jungmin Choi, Rolando Pasquariello, Andrei P. Alexenko, Aihua Dai, Susanta K. Behura, R. Michael Roberts, Toshihiko Ezashi
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-020-07300-8

Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™
Cited by: 2
Author(s): Namit Kumar, Ryan Golhar, Kriti Sen Sharma, James L. Holloway, Srikant Sarangi, Isaac M. Neuhaus, Alice M. Walsh, Zachary W. Pitluk
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0041066

Transcriptional Response of Peripheral Blood Mononuclear Cells from Cattle Infected with Mycobacterium bovis
Cited by: 25
Author(s): Federico Carlos Blanco, Marcelo Soria, María Verónica Bianco, Fabiana Bigi
Software Mentions: 5
Published: almost 12 years ago

10.3390/s19102228

Design and Implementation of an Integrated IoT Blockchain Platform for Sensing Data Integrity
Cited by: 154
Author(s): Hang Lei, Do‐Hyeun Kim
Software Mentions: 5
Published: almost 5 years ago

10.1186/1471-2229-10-150

Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms
Cited by: 129
Author(s): Dennis Janz, Katja Behnke, Jörg‐Peter Schnitzler, Basem Kanawati, Philippe Schmitt‐Kopplin, Andrea Polle
Software Mentions: 5
Published: almost 14 years ago

10.3390/metabo8010016

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites
Cited by: 27
Author(s): Bofei Zhang, Senyang Hu, Elizabeth Baskin, Andrew Patt, Jalal K. Siddiqui, Ewy A. Mathé
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0124564

Differential Gene Expression Reveals Candidate Genes for Drought Stress Response in Abies alba (Pinaceae)
Cited by: 45
Author(s): David Behringer, Heike Zimmermann, Birgit Ziegenhagen, Sascha Liepelt
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pone.0081167

Cytokeratin 15 Marks Basal Epithelia in Developing Ureters and Is Upregulated in a Subset of Urothelial Cell Carcinomas
Cited by: 21
Author(s): Guihua Tai, Parisa Ranjzad, Fiona Marriage, Samrina Rehman, Helen Denley, Jill Dixon, Karen S. Mitchell, Philip J. Day, Adrian S. Woolf
Software Mentions: 5
Published: over 10 years ago

10.1186/s12859-017-1934-z

ImageJ2: ImageJ for the next generation of scientific image data
Cited by: 4,051
Author(s): Curtis Rueden, Johannes Schindelin, Mark Hiner, Barry E. DeZonia, Alison E. Walter, Ellen T. Arena, Kevin W. Eliceiri
Software Mentions: 5
Published: over 6 years ago

10.3389/fpsyg.2020.567499

Reduced Environmental Stimulation in Anorexia Nervosa: An Early-Phase Clinical Trial
Cited by: 8
Author(s): Sahib S. Khalsa, Scott E. Moseman, Hung‐Wen Yeh, Valerie Upshaw, Beth Persac, Eric Breese, Rachel C. Lapidus, Sheridan Chappelle, Martin P. Paulus, Justin S. Feinstein
Software Mentions: 5
Published: over 3 years ago

10.1111/mpp.13003

Chorismate mutase and isochorismatase, two potential effectors of the migratory nematode <i>Hirschmanniella oryzae</i> , increase host susceptibility by manipulating secondary metabolite content of rice
Cited by: 8
Author(s): Lander Bauters, Tina Kyndt, Tim De Meyer, Kris Morreel, Wout Boerjan, Hannes Lefevere, Godelieve Gheysen
Software Mentions: 5
Published: over 3 years ago

10.1107/S1600577517014503

<i>DA+</i> data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines
Cited by: 54
Author(s): Justyna Aleksandra Wojdyla, Jakub Wojciech Kaminski, Ezequiel Panepucci, Simon Ebner, Xiaoqiang Wang, José Gabadinho, Meitian Wang
Software Mentions: 5
Published: over 6 years ago

10.3390/brainsci11060809

A CNN-Based Autoencoder and Machine Learning Model for Identifying Betel-Quid Chewers Using Functional MRI Features
Cited by: 3
Author(s): Ming-Chou Ho, Hsin-An Shen, Yi-Peng Eve Chang, Jun‐Cheng Weng
Software Mentions: 5
Published: almost 3 years ago

10.1186/s13072-021-00395-7

Loss of EZH2-like or SU(VAR)3–9-like proteins causes simultaneous perturbations in H3K27 and H3K9 tri-methylation and associated developmental defects in the fungus Podospora anserina
Cited by: 13
Author(s): Florian Carlier, M. Li, Laetitia Maroc, Robert Debuchy, Charbel Souaid, Daan Noordermeer, Pierre Grognet, Fabienne Malagnac
Software Mentions: 4
Published: about 3 years ago

10.3390/plants10071466

Isolation and Characterization of Pseudomonas chlororaphis Strain ST9; Rhizomicrobiota and in Planta Studies
Cited by: 4
Author(s): Iris Bertani, Elisa Zampieri, Cristina Bez, Andrea Volante, Vittorio Venturi, Stefano Monaco
Software Mentions: 4
Published: almost 3 years ago

10.1186/1471-2105-9-295

Systems biology driven software design for the research enterprise
Cited by: 18
Author(s): John P. Boyle, Christopher C. Cavnor, Sarah Killcoyne, Ilya Shmulevich
Software Mentions: 4
Published: almost 16 years ago

10.1016/j.comtox.2021.100175

COSMOS next generation – A public knowledge base leveraging chemical and biological data to support the regulatory assessment of chemicals
Cited by: 13
Author(s): Chihae Yang, Mark T.D. Cronin, Kirk Arvidson, Bruno Bienfait, Steven J. Enoch, Bart Heldreth, Bryan Hobocienski, Kristi Muldoon-Jacobs, Y. Lan, Judith C. Madden, Tomasz Magdziarz, J. Marusczyk, Aleksandra Mostrąg, Mark Nelms, Daniel Neagu, Katarzyna R. Przybylak, James F. Rathman, J. Park, A.N. Richarz, Ann M. Richard, J.V. Ribeiro, Oliver Sacher, Christof H. Schwab, Vessela Vitcheva, Patra Volarath, Andrew Worth
Software Mentions: 4
Published: almost 3 years ago

10.1371/journal.pone.0019350

Deep Sequencing of Organ- and Stage-Specific microRNAs in the Evolutionarily Basal Insect Blattella germanica (L.) (Dictyoptera, Blattellidae)
Cited by: 82
Author(s): Alexandre S. Cristino, Erica D. Tanaka, Mercedes Rubio, María‐Dolors Piulachs, Xavier Bellés
Software Mentions: 4
Published: about 13 years ago

10.1371/journal.pone.0187150

RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma
Cited by: 13
Author(s): Jennifer K. Grenier, Polly Foureman, Erica A. Sloma, Andrew D. Miller
Software Mentions: 4
Published: over 6 years ago

10.1186/1471-2164-15-884

A comparison of gene transcription profiles of domesticated and wild Atlantic salmon (Salmo salar L.) at early life stages, reared under controlled conditions
Cited by: 46
Author(s): Beatrix Bicskei, James E. Bron, Kevin A. Glover, John B. Taggart
Software Mentions: 4
Published: over 10 years ago

10.3389/fpls.2019.00119

Screening for Sugarcane Root Phenes Reveals That Reducing Tillering Does Not Lead to an Increased Root Mass Fraction
Cited by: 7
Author(s): J. Pierre, Jai M. Perroux, Andrew Rae
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0132450

Construction, De-Novo Assembly and Analysis of Transcriptome for Identification of Reproduction-Related Genes and Pathways from Rohu, Labeo rohita (Hamilton)
Cited by: 11
Author(s): Dinesh Kumar Sahu, Soumya Prasad Panda, Prem Kumar Meher, Paramananda Das, P. Routray, Jitendra Kumar Sundaray, P. Jayasankar, Samiran Nandi
Software Mentions: 4
Published: almost 9 years ago

10.1093/bioinformatics/btw417

SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena
Cited by: 35
Author(s): Yukako Tohsato, Kenneth H. L. Ho, Koji Kyoda, Shuichi Onami
Software Mentions: 4
Published: almost 8 years ago

10.1155/2013/192548

Expression of Bmi-1 in Pediatric Brain Tumors as a New Independent Prognostic Marker of Patient Survival
Cited by: 10
Author(s): Shirin Farivar, Reza Keikha, Reza Shiari, Farzaneh Jadali
Software Mentions: 4
Published: over 11 years ago

10.1186/s12859-015-0846-z

Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features
Cited by: 28
Author(s): Sunil Kumar, Philipp Bücher
Software Mentions: 4
Published: over 8 years ago

10.1186/1471-2164-14-283

Unscrambling butterfly oogenesis
Cited by: 38
Author(s): Jean-Michel Carter, Susan C. Baker, Ryan C. Pink, David R. F. Carter, Aiden Collins, Jeremie Tomlin, Melanie Gibbs, Casper J. Breuker
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0205668

Comprehensive evaluation of candidate reference genes for real-time quantitative PCR (RT-qPCR) data normalization in nutri-cereal finger millet [Eleusine Coracana (L.)]
Cited by: 10
Author(s): Palakolanu Sudhakar Reddy, Mahamaya G. Dhaware, D. Srinivas Reddy, Bommineni Pradeep Reddy, Kummari Divya, Kiran K. Sharma, Pooja Bhatnagar‐Mathur
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pgen.1005457

Runx1 Transcription Factor Is Required for Myoblasts Proliferation during Muscle Regeneration
Cited by: 65
Author(s): Kfir Baruch Umansky, Yael Gruenbaum-Cohen, Michael Tsoory, Ester Feldmesser, Dalia Goldenberg, Ori Brenner, Yoram Groner
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pcbi.1009105

Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis
Cited by: 40
Author(s): Cecilia Wieder, Clément Frainay, Nathalie Poupin, Pablo Rodríguez-Mier, Florence Vinson, Juliette Cooke, Rachel Lai, Jacob G. Bundy, Fabien Jourdan, Timothy M. D. Ebbels
Software Mentions: 4
Published: over 2 years ago

10.3390/s17071691

A Context-Driven Model for the Flat Roofs Construction Process through Sensing Systems, Internet-of-Things and Last Planner System
Cited by: 6
Author(s): María Dolores Andújar-Montoya, Diego Marcos-Jorquera, Francisco Manuel García-Botella, Virgilio Gilart-Iglesias
Software Mentions: 4
Published: almost 7 years ago

10.3390/s18124125

Model Driven Development Applied to Complex Event Processing for Near Real-Time Open Data
Cited by: 6
Author(s): Pedro J. Clemente, Adolfo Lozano-Tello
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-31618-9

Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi L.
Cited by: 21
Author(s): Mehdi Soltani Howyzeh, Seyed Ahmad Sadat Noori, Vahid Shariati J, Mahboubeh Amiripour
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-016-2950-5

The influence of trematode parasite burden on gene expression in a mammalian host
Cited by: 9
Author(s): Bhagya K. Wijayawardena, Dennis J. Minchella, J. Andrew DeWoody
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-020-78997-6

Genes associated with cognitive performance in the Morris water maze: an RNA-seq study
Cited by: 18
Author(s): Vasiliy V. Reshetnikov, Polina E. Kisaretova, Nikita I. Ershov, Anastasia S. Shulyupova, Dmitry Oshchepkov, Н. В. Климова, Anna V. Ivanchihina, T. I. Merkulova, Natalia P. Bondar
Software Mentions: 4
Published: over 3 years ago

10.3390/s21030772

Multi-Layer Blockchain-Based Security Architecture for Internet of Things
Cited by: 58
Author(s): Houshyar Honar Pajooh, M. A. Rashid, Fakhrul Alam, Serge Demidenko
Software Mentions: 4
Published: over 3 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: about 7 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: almost 6 years ago

10.1186/2041-1480-1-8

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows
Cited by: 33
Author(s): Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F. Aoki‐Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Seiichiro Kawashima, Hong‐Woo Chun, Jan Aerts, Bruno Aranda, Lord Hendrix Barboza, Raoul Jean Pierre Bonnal, Richard Bruskiewich, Jan Christian Bryne, José Marı́a Fernández, Akira Funahashi, Paul M. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Tom Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Łukasz Salwiński, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M. Standley, Hideaki Sugawara, Tazuko Tashiro, Oswaldo Trelles, Rutger A. Vos, Mark D. Wilkinson, William S. York, Christian M. Zmasek, Kiyoshi Asai, Toshihisa Takagi
Software Mentions: 4
Published: over 14 years ago

10.3389/fpls.2021.635784

Transcriptomic Analysis of Changes in Gene Expression During Flowering Induction in Sugarcane Under Controlled Photoperiodic Conditions
Cited by: 13
Author(s): João Ricardo Vieira Manechini, Paulo Henrique da Silva Santos, Elisson Romanel, Michael dos Santos Brito, Maximiliano Salles Scarpari, Stephen D. Jackson, Luciana Rossini Pinto, Renato Vicentini
Software Mentions: 4
Published: almost 3 years ago

10.1371/journal.pone.0198191

Early responses to dehydration in contrasting wild Arachis species
Cited by: 21
Author(s): C. C. Vinson, Ana Paula Zotta Mota, Thais Nicolini Oliveira, Larissa Arrais Guimarães, Soraya C. M. Leal‐Bertioli, Thomas Christopher Rhys Williams, Alexandre Lima Nepomuceno, Mario Alfredo Passos Saraiva, Ana Cláudia Guerra Araújo, P. M. Guimarães, Ana Cristina Miranda Brasileiro
Software Mentions: 4
Published: almost 6 years ago

10.3389/fphar.2019.00747

Bioinformatic Study of Transcriptome Changes in the Mice Lumbar Spinal Cord After the 30-Day Spaceflight and Subsequent 7-Day Readaptation on Earth: New Insights Into Molecular Mechanisms of the Hypogravity Motor Syndrome
Cited by: 8
Author(s): M. S. Kuznetsov, Artur Nicolaevich Lisukov, Albert A. Rizvanov, O. V. Tyapkina, Oleg Gusev, P. N. Rezvyakov, I. B. Kozlovskaya, E. E. Nikolskiy, Р. Р. Исламов
Software Mentions: 4
Published: almost 5 years ago

10.1186/s13059-019-1758-4

Cytoscape Automation: empowering workflow-based network analysis
Cited by: 753
Author(s): David Otasek, John H. Morris, Jorge Bouças, Alexander Pico, Barry Demchak
Software Mentions: 4
Published: over 4 years ago

10.1038/s41598-017-06200-4

Associating transcription factors and conserved RNA structures with gene regulation in the human brain
Cited by: 12
Author(s): Nikolai Hecker, Stefan E. Seemann, Asli Silahtaroglu, Walter L. Ruzzo, Jan Gorodkin
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijerph10116106

IAServ: An Intelligent Home Care Web Services Platform in a Cloud for Aging-in-Place
Cited by: 27
Author(s): Chuan‐Jun Su, Chang-Yu Chiang
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.04235

Polycomb- and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
Cited by: 43
Author(s): James C. McGann, Jon A. Oyer, Saurabh Garg, Huilan Yao, Jun Li, Xin Feng, Lujian Liao, John R. Yates, Gail Mandel
Software Mentions: 4
Published: over 9 years ago

10.3390/ijms20143425

Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network
Cited by: 17
Author(s): Lan Gongqiang, Jiyun Zhou, Ruifeng Xu, Qin Lu, Hongpeng Wang
Software Mentions: 4
Published: almost 5 years ago

10.3389/fmicb.2018.01339

Arbuscular Mycorrhizal Symbiosis Leads to Differential Regulation of Drought-Responsive Genes in Tissue-Specific Root Cells of Common Bean
Cited by: 29
Author(s): Gustavo Henrique Recchia, Enéas Ricardo Konzen, Fernanda Cassieri, Danielle Gregório Gomes Caldas, Siu Mui Tsai
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41396-017-0043-3

Energy limitation of cyanophage development: implications for marine carbon cycling
Cited by: 54
Author(s): Richard John Puxty, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 4
Published: over 6 years ago

10.3389/fnins.2020.00545

MVPANI: A Toolkit With Friendly Graphical User Interface for Multivariate Pattern Analysis of Neuroimaging Data
Cited by: 25
Author(s): Yanmin Peng, Xi Zhang, Yifan Li, Qian Su, Sijia Wang, Feng Liu, Chunshui Yu, Meng Liang
Software Mentions: 3
Published: almost 4 years ago

10.3389/fninf.2018.00052

BRANT: A Versatile and Extendable Resting-State fMRI Toolkit
Cited by: 49
Author(s): Kaibin Xu, Yong Liu, Yafeng Zhan, Jiaji Ren, Tianzi Jiang
Software Mentions: 3
Published: over 5 years ago

10.3389/fneur.2020.589125

The Medial Thalamus Plays an Important Role in the Cognitive and Emotional Modulation of Orofacial Pain: A Functional Magnetic Resonance Imaging-Based Study
Cited by: 10
Author(s): Jun Yu, Hong Yang, Feifei Zhang, Jue Wang, He Li, Xin Yang, Hu Long, Fēi Li, Qiyong Gong, Wenli Lai
Software Mentions: 3
Published: over 3 years ago

10.3390/ijms22073393

MIAT Is an Upstream Regulator of NMYC and the Disruption of the MIAT/NMYC Axis Induces Cell Death in NMYC Amplified Neuroblastoma Cell Lines
Cited by: 5
Author(s): Barbara Feriančiková, Tereza Feglarová, Lenka Krsková, Tomáš Eckschlager, Aleš Vícha, Jan Hraběta
Software Mentions: 3
Published: about 3 years ago

10.3389/fninf.2018.00059

A Novel, Fast, Reliable, and Data-Driven Method for Simultaneous Single-Trial Mining and Amplitude—Latency Estimation Based on Proximity Graphs and Network Analysis
Cited by: 0
Author(s): Stavros I. Dimitriadis, Lisa Brindley, Lisa Helen Evans, David Linden, Krish Devi Singh
Software Mentions: 3
Published: over 5 years ago

10.3389/fimmu.2019.01928

The Transcriptional and Protein Profile From Human Infected Neuroprogenitor Cells Is Strongly Correlated to Zika Virus Microcephaly Cytokines Phenotype Evidencing a Persistent Inflammation in the CNS
Cited by: 44
Author(s): Morganna Costa Lima, Leila Rodrigues de Mendonça, Antônio Mauro Rezende, Raquel Medialdea-Carrera, Conceição Elidianne Aníbal-Silva, Matthew Demers, Leonardo D’Aiuto, Joel Wood, Kodavali V. Chowdari, Michael J. Griffiths, Antonio R. Lucena-Araújo, Manoel Barral‐Netto, Elisa de Almeida Neves Azevedo, Renan Willian Alves, Pablo Cantalice Santos Farias, Ernesto T. A. Marques, Priscila M. S. Castanha, Claire L. Donald, Alain Kohl, Vishwajit L. Nimgaonkar, Rafael Freitas Oliveira Franca
Software Mentions: 3
Published: over 4 years ago

10.3389/fmolb.2016.00002

A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks
Cited by: 6
Author(s): Benjamin Merlet, Nils Paulhe, Florence Vinson, Clément Frainay, Maxime Chazalviel, Nathalie Poupin, Yoann Gloaguen, Franck Giacomoni, Fabien Jourdan
Software Mentions: 3
Published: about 8 years ago

10.1111/jipb.12862

Identification of plant genes putatively involved in the perception of fungal ergosterol‐squalene
Cited by: 15
Author(s): Laura Lindo, Rosa E. Cardoza, Alicia Lorenzana de la Varga, Pedro A. Casquero, Santiago Gutiérrez
Software Mentions: 3
Published: over 4 years ago

10.3389/fnins.2016.00515

A Hitchhiker's Guide to Functional Magnetic Resonance Imaging
Cited by: 132
Author(s): José Miguel Soares, Ricardo Magalhães, Pedro Silva Moreira, Alexandre Vieira de Sousa, Edward Ganz, Adriana Sampaio, Victor Alves, Paulo Marques, Nuno Sousa
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms22136674

Sub-Chronic Effects of Slight PAH- and PCB-Contaminated Mesocosms in Paracentrotus lividus Lmk: A Multi-Endpoint Approach and De Novo Transcriptomic
Cited by: 7
Author(s): Luisa Albarano, Valerio Zupo, Davide Caramiello, Maria Toscanesi, Marco Trifuoggi, Marco Guida, Giovanni Libralato, Maria Costantini
Software Mentions: 3
Published: almost 3 years ago

10.12688/f1000research.10750.2

General guidelines for biomedical software development
Cited by: 11
Author(s): Luís A. Bastião Silva, Rafael C. Jiménez, Niklas Blomberg, José Luís Oliveira
Software Mentions: 3
Published: almost 7 years ago

10.12688/f1000research.14612.2

eXamine: Visualizing annotated networks in Cytoscape
Cited by: 3
Author(s): Philipp Spohr, Kasper Dinkla, Gunnar W. Klau, Mohammed El-Kebir
Software Mentions: 3
Published: almost 6 years ago

10.1186/1741-7007-10-55

Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast
Cited by: 31
Author(s): João A. Paredes, Laura Carreto, João Simões, Ana R. Bezerra, Ana Catarina Gomes, Rodrigo Santamaría, Misha Kapushesky, Gabriela Moura, Manuel A. S. Santos
Software Mentions: 3
Published: almost 12 years ago

10.1007/s10664-019-09707-8

Search-based multi-vulnerability testing of XML injections in web applications
Cited by: 10
Author(s): Sadeeq Jan, Annibale Panichella, Andrea Arcuri, Lionel C. Briand
Software Mentions: 3
Published: about 5 years ago

10.3892/mmr.2015.3318

PUFA diets alter the microRNA expression profiles in an inflammation rat model
Cited by: 34
Author(s): Zheng Zhang, Yubin Ge, Jinyu Zhang, Meilan Xue, Quan Li, Dongliang Lin, Wenhui Ma
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2105-12-218

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript
Cited by: 36
Author(s): Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K. Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen Parkinson, Morris A. Swertz
Software Mentions: 3
Published: almost 13 years ago

10.1080/22221751.2019.1637072

Papillomavirus can be transmitted through the blood and produce infections in blood recipients: Evidence from two animal models
Cited by: 28
Author(s): Nancy M. Cladel, Pengfei Jiang, Jingwei J. Li, Xuwen Peng, Timothy K. Cooper, Vladimır Majerčiak, Karla K. Balogh, Thomas J. Meyer, Sarah A. Brendle, Lynn R. Budgeon, Debra Shearer, Regina Munden, Maggie Cam, Raghavan Vallur, Neil D. Christensen, Zhi-Ming Zheng, Jiafen Hu
Software Mentions: 3
Published: over 5 years ago

10.3390/cells9030525

Stress Reshapes the Physiological Response of Halophile Fungi to Salinity
Cited by: 23
Author(s): Yordanis Pérez-Llano, Eya Caridad Rodríguez-Pupo, Irina S. Druzhinina, Komal Chenthamara, Feng Cai, Nina Gunde‐Cimerman, Polona Zalar, Cene Gostinčar, Rok Kostanjšek, Jorge Luis Folch-Mallol, Ramón Alberto Batista-García, María del Rayo Sánchez-Carbente
Software Mentions: 3
Published: about 4 years ago

10.1371/journal.pone.0235575

Comparative gut transcriptome analysis of Diatraea saccharalis in response to the dietary source
Cited by: 4
Author(s): Daniel D. Noriega, Fabrício Barbosa Monteiro Arraes, José Dijair Antonino, Leonardo Lima Pepino Macedo, Fernando Fonseca, Roberto Coiti Togawa, Priscila Grynberg, Maria C. M. Silva, A. S. Negrisoli, Carolina Vianna Morgante, Maria Fátima Grossi-de-Sá
Software Mentions: 3
Published: almost 4 years ago

10.1186/s12864-018-4605-1

Genome-wide transcriptional analyses in Anopheles mosquitoes reveal an unexpected association between salivary gland gene expression and insecticide resistance
Cited by: 26
Author(s): Alison T. Isaacs, Henry Mawejje, Sean Tomlinson, Daniel J. Rigden, Martin J. Donnelly
Software Mentions: 3
Published: about 6 years ago

10.1111/j.1365-2958.2011.07760.x

Multimodal dynamic response of the Buchnera aphidicola pLeu plasmid to variations in leucine demand of its host, the pea aphid Acyrthosiphon pisum
Cited by: 20
Author(s): J. Viñuelas, Gérard Febvay, G. Duport, Stefano Colella, Jean‐Michel Fayard, Hubert Charles, Yvan Rahbé, Federica Calevro
Software Mentions: 3
Published: almost 13 years ago

10.1089/biores.2014.0053

Biological Effects Induced by Specific Advanced Glycation End Products in the Reconstructed Skin Model of Aging
Cited by: 31
Author(s): Hervé Piégay, Hélène Zucchi, Zhen Dai, David R. Sell, Christopher M. Strauch, Vincent M. Monnier, Daniel Asselineau
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0190292

Examining the short-term anxiolytic and antidepressant effect of Floatation-REST
Cited by: 34
Author(s): Justin S. Feinstein, Sahib S. Khalsa, Hung‐Wen Yeh, Colleen Wohlrab, W. Kyle Simmons, Murray B. Stein, Martin P. Paulus
Software Mentions: 3
Published: over 6 years ago

10.1242/dev.169367

Distal-less activates butterfly eyespots consistent with a reaction diffusion process
Cited by: 53
Author(s): Heidi Connahs, Sham Tlili, Jelle van Creij, Tricia Y. J. Loo, Tirtha Das Banerjee, Timothy E. Saunders, Antónia Monteiro
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0183526

Transcriptomic profile of cystic fibrosis patients identifies type I interferon response and ribosomal stalk proteins as potential modifiers of disease severity
Cited by: 23
Author(s): Michael Kormann, Alexander Dewerth, Felizitas A. Eichner, Praveen Baskaran, Andreas Hector, Nicolas Regamey, Dominik Hartl, Rupert Handgretinger, Justin S. Antony
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-11-344

Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays
Cited by: 18
Author(s): Cyril Dégletagne, Céline Keime, Benjamin Rey, Marc de Dinechin, Fabien Forcheron, Paul Chuchana, Pierre Jouventin, Christian Gautier, Claude Duchamp
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0248054

Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes
Cited by: 5
Author(s): Jaqueline Raquel de Almeida, Diego Mauricio Riaño-Pachón, Lívia Maria Franceschini, Isaneli Batista dos Santos, Jessica Aparecida Ferrarezi, Pedro Avelino Maia de Andrade, Cláudia Barros Monteiro-Vitorello, Carlos Alberto Labate, Maria Carolina Quecine
Software Mentions: 3
Published: about 3 years ago