Ecosyste.ms: Papers

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: over 12 years ago

10.1186/1471-2164-15-754

Transcriptome profiling of natural dichromatism in the annual fishes Nothobranchius furzeri and Nothobranchius kadleci
Cited by: 21
Author(s): Enoch Ng’oma, Marco Groth, Roberto Ripa, Matthias Platzer, Alessandro Cellerino
Software Mentions: 3
Published: about 10 years ago

10.3389/fgene.2021.662843

Effect of the Expression of ELOVL5 and IGFBP6 Genes on the Metastatic Potential of Breast Cancer Cells
Cited by: 5
Author(s): С. В. Никулин, Г. С. Захарова, Andrey Poloznikov, M. P. Raigorodskaya, Daniel Wicklein, Udo Schumacher, Stepan Nersisyan, Jonas Bergquist, Georgy Bakalkin, Л. В. Астахова, Alexander G. Tonevitsky
Software Mentions: 3
Published: over 3 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: almost 9 years ago

10.3389/fgene.2021.630187

CoExp: A Web Tool for the Exploitation of Co-expression Networks
Cited by: 13
Author(s): Sonia García-Ruiz, Ana Luisa Gil-Martínez, Alejandro Cisterna, Federico Jurado-Ruiz, Regina H. Reynolds, Nabec, Mark Cookson, John Hardy, Mina Ryten, Juan A. Botía
Software Mentions: 3
Published: over 3 years ago

10.1186/2041-1480-3-11

COEUS: “semantic web in a box” for biomedical applications
Cited by: 37
Author(s): Pedro Lopes, José Luís Oliveira
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12864-019-5795-x

Transcriptional analysis of renal dopamine-mediated Na+ homeostasis response to environmental salinity stress in Scatophagus argus
Cited by: 10
Author(s): Maoliang Su, Jia Zhou, Zhengyu Duan, Junbin Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2797-9

The biorepository portal toolkit: an honest brokered, modular service oriented software tool set for biospecimen-driven translational research
Cited by: 16
Author(s): Alex Felmeister, Aaron J. Masino, Tyler J. Rivera, Adam Resnick, Jeffrey W. Pennington
Software Mentions: 3
Published: over 8 years ago

10.1155/2020/3041498

SCALEUS-FD: A FAIR Data Tool for Biomedical Applications
Cited by: 5
Author(s): Arnaldo Pereira, Rui Pedro Lopes, José Luís Oliveira
Software Mentions: 3
Published: about 4 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: over 7 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: over 6 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 5 years ago

10.3389/fnbeh.2014.00388

Addiction and reward-related genes show altered expression in the postpartum nucleus accumbens
Cited by: 31
Author(s): Changjiu Zhao, Brian E. Eisinger, Terri M. Driessen, Stephen C. Gammie
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0229513

The RNA-seq transcriptomic analysis reveals genes mediating salt tolerance through rapid triggering of ion transporters in a mutant barley
Cited by: 24
Author(s): Sareh Yousefirad, Hassan Soltanloo, Seyedeh Sanaz Ramezanpour, Khalil Zaynali Nezhad, Vahid Shariati
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0147727

Transcriptomic Determinants of Scrapie Prion Propagation in Cultured Ovine Microglia
Cited by: 12
Author(s): Juan F. Muñoz-Gutiérrez, Sebastián Aguilar Pierlé, David A. Schneider, Timothy V. Baszler, James B. Stanton
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pcbi.1006542

Eleven quick tips to build a usable REST API for life sciences
Cited by: 17
Author(s): Aleksandra Tarkowska, Denise Carvalho-Silva, Charles E. Cook, E. B. Turner, Alex Bateman, Andy Yates
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.0010016

Glucocorticoid Receptor-Dependent Gene Regulatory Networks
Cited by: 194
Author(s): Panin Le, Joshua R. Friedman, Jonathan Schug, John Brestelli, J. Brandon Parker, Irina M. Bochkis, Klaus H. Kaestner
Software Mentions: 3
Published: over 19 years ago

10.1371/journal.pone.0221170

Inter-genus gene expression analysis in livestock fibroblasts using reference gene validation based upon a multi-species primer set
Cited by: 4
Author(s): Marcelo Tigre Moura, Roberta L. O. Silva, Pábola Santos Nascimento, José Carlos Ferreira-Silva, Ludymila Furtado Cantanhêde, Éderson Akio Kido, Ana Maria Benko‐Iseppon, Marcos Antônio Lemos Oliveira
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0080467

Runx3-mediated Transcriptional Program in Cytotoxic Lymphocytes
Cited by: 56
Author(s): Joseph Lotem, Ditsa Levanon, Varda Negreanu, Dena Leshkowitz, Gérard Friedlander, Yoram Groner
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pcbi.1004008

A RESTful API for Accessing Microbial Community Data for MG-RAST
Cited by: 62
Author(s): Andreas Wilke, Jared Bischof, Travis Harrison, Tom Brettin, Mark D’Souza, Wolfgang Gerlach, Hunter Matthews, Tobias Paczian, Jared Wilkening, Elizabeth M. Glass, Narayan Desai, Folker Meyer
Software Mentions: 3
Published: almost 10 years ago

10.7717/peerj-cs.376

On automated RBAC assessment by constructing a centralized perspective for microservice mesh
Cited by: 4
Author(s): Dipta Das, Andrew Walker, Vincent Bushong, Jan Svacina, Tomáš Černý, Václav Matyáš
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pgen.0030145

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

10.1186/1471-2202-15-11

Genes showing altered expression in the medial preoptic area in the highly social maternal phenotype are related to autism and other disorders with social deficits
Cited by: 33
Author(s): Terri M. Driessen, Brian E. Eisinger, Changjiu Zhao, Sharon A. Stevenson, Michael C. Saul, Stephen C. Gammie
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0206583

Test-retest reliability of task-based and resting-state blood oxygen level dependence and cerebral blood flow measures
Cited by: 46
Author(s): Štefan Holiga, Fabio Sambataro, Cécile Luzy, Gérard Greig, Neena Sarkar, Remco Renken, Jan-Bernard C Marsman, Scott Schobel, Alessandro Bertolino, Juergen Dukart
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pcbi.1008977

Swarm: A federated cloud framework for large-scale variant analysis
Cited by: 2
Author(s): Amir Bahmani, Kyle Ferriter, Vandhana Krishnan, Arash Alavi, Amir Alavi, Philip S. Tsao, M Snyder, Cuiping Pan
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2202-14-69

Abnormal activity of default mode network in GERD patients
Cited by: 4
Author(s): Huihui Sun, Ying Chen, Xiaofeng Zhao, Xiang-Bin Wang, Yilin Jiang, Peng Wu, Yinhan Tang, Qiang Meng, Shuchang Xu
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pgen.1008649

Non-lethal exposure to H2O2 boosts bacterial survival and evolvability against oxidative stress
Cited by: 49
Author(s): Alexandro Rodríguez‐Rojas, Joshua Jay Kim, Paul R. Johnston, Olga Makarova, Murat Eravci, Christoph Weise, Regine Hengge, Jens Rolff
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0105707

Changes in Cecal Microbiota and Mucosal Gene Expression Revealed New Aspects of Epizootic Rabbit Enteropathy
Cited by: 50
Author(s): Christine Bäuerl, María Carmen Collado, Manuel Zúñiga, E. Blas, Gaspar Pérez‐Martínez
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1009129

A novel role for kynurenine 3-monooxygenase in mitochondrial dynamics
Cited by: 11
Author(s): Daniel C. Maddison, Mónica Alfonso-Núñez, Aisha M. Swaih, Carlo Breda, Susanna Campesan, Natalie Allcock, Anna Straatman-Iwanowska, Charalambos P. Kyriacou, Flaviano Giorgini
Software Mentions: 3
Published: about 4 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: about 7 years ago

10.1002/1878-0261.12903

REST promotes ETS1‐dependent vascular growth in medulloblastoma
Cited by: 9
Author(s): Shavali Shaik, Satoru Maegawa, Amanda R. Haltom, Feng Wang, Xue Xiao, Tara Dobson, Ajay Sharma, Yanwen Yang, Jyothishmathi Swaminathan, Vikas Kundra, Xiao Nan Li, Keri Schadler, Arif Harmanci, Lin Xu, Vidya Gopalakrishnan
Software Mentions: 3
Published: almost 4 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: over 3 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: almost 10 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: over 13 years ago

10.1371/journal.pone.0077490

Transcriptional Reprogramming of CD11b+Esamhi Dendritic Cell Identity and Function by Loss of Runx3
Cited by: 29
Author(s): Joseph Dicken, Alexander Mildner, Dena Leshkowitz, Ivo P. Touw, Shay Hantisteanu, Steffen Jung, Yoram Groner
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0104136

Twitter in the Cross Fire—The Use of Social Media in the Westgate Mall Terror Attack in Kenya
Cited by: 117
Author(s): Tomer Simon, Avishay Goldberg, Limor Aharonson‐Daniel, Dmitry Leykin, Bruria Adini
Software Mentions: 3
Published: about 10 years ago

10.1186/s12916-021-01962-1

Functional connectivity changes in cerebral small vessel disease - a systematic review of the resting-state MRI literature
Cited by: 22
Author(s): Maximilian Schulz, Caroline Malherbe, Bastian Cheng, Götz Thomalla, Eckhard Schlemm
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: over 3 years ago

10.1038/s41598-017-10245-w

REST, a master regulator of neurogenesis, evolved under strong positive selection in humans and in non human primates
Cited by: 21
Author(s): Alessandra Mozzi, Franca Rosa Guerini, Diego Forni, Andrea Saul Costa, Raffaello Nemni, Francesca Baglio, Monia Cabinio, Stefania Riva, Chiara Pontremoli, Mario Clerici, Manuela Sironi, Rachele Cagliani
Software Mentions: 3
Published: about 7 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: almost 5 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: over 3 years ago

10.1371/journal.pone.0093489

The Mechanisms Underlying α-Amanitin Resistance in Drosophila melanogaster: A Microarray Analysis
Cited by: 17
Author(s): Chelsea L. Mitchell, Michael C. Saul, Liang Liu, Hairong Wei, Thomas Werner
Software Mentions: 3
Published: over 10 years ago

10.3390/jcm8111966

Connectome Analysis of Brain Functional Network Alterations in Depressive Patients with Suicidal Attempt
Cited by: 19
Author(s): Jun‐Cheng Weng, Yu-Syuan Chou, Yuan-Hsiung Tsai, Chun-Te Lee, Ming‐Hong Hsieh, Vincent Chin‐Hung Chen
Software Mentions: 3
Published: about 5 years ago

10.1186/1758-2946-3-18

AMBIT RESTful web services: an implementation of the OpenTox application programming interface
Cited by: 58
Author(s): Nina Jeliazkova, Vedrin Jeliazkov
Software Mentions: 3
Published: over 13 years ago

10.1093/jxb/ert234

Nitrogen metabolism of two contrasting poplar species during acclimation to limiting nitrogen availability
Cited by: 172
Author(s): Jie Luo, Hong Li, Tong‐Xian Liu, Andrea Polle, Changhui Peng, Zhibin Luo
Software Mentions: 3
Published: over 11 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: about 8 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: almost 4 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: over 4 years ago

10.1038/srep11148

Disrupted resting-state attentional networks in T2DM patients
Cited by: 47
Author(s): Wenqing Xia, Shaohua Wang, Hengyi Rao, Andrea M. Spaeth, Pin Wang, Yue Yang, Rong Huang, Rongrong Cai, Hao Sun
Software Mentions: 3
Published: over 9 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: almost 9 years ago

10.1186/s12885-016-2936-3

Global DNA methylation profiling uncovers distinct methylation patterns of protocadherin alpha4 in metastatic and non-metastatic rhabdomyosarcoma
Cited by: 11
Author(s): Lucia Tombolan, Elena Poli, Paolo Martini, Angelica Zin, Caterina Millino, Beniamina Pacchioni, Barbara Celegato, Gianni Bisogno, Chiara Romualdi, Angelo Rosolen, Gerolamo Lanfranchi
Software Mentions: 3
Published: about 8 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: about 6 years ago

10.1371/journal.pone.0038602

Gene Expression Changes in the Septum: Possible Implications for MicroRNAs in Sculpting the Maternal Brain
Cited by: 19
Author(s): Changjiu Zhao, Michael C. Saul, Terri M. Driessen, Stephen C. Gammie
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2229-14-185

Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacaoL., the chocolate tree
Cited by: 25
Author(s): Siela N. Maximova, Sergio Florez, Xiangling Shen, Nicolas Niemenak, Yufan Zhang, Wayne R. Curtis, Mark J. Guiltinan
Software Mentions: 3
Published: over 10 years ago

10.1186/s12864-018-4439-x

mORCA: ubiquitous access to life science web services
Cited by: 1
Author(s): Sergio Díaz-del-Pino, Oswaldo Trelles, Juan Falgueras
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: over 6 years ago

10.1093/bioinformatics/bty742

MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians
Cited by: 41
Author(s): K. Joeri van der Velde, Floris Imhann, Bart Charbon, Chao Pang, David van Enckevort, Mariska Slofstra, Ruggero Barbieri, Rudi Alberts, Dennis Hendriksen, Fleur D.L. Kelpin, Mark de Haan, Tommy de Boer, Sido Haakma, Connor Stroomberg, Salome Scholtens, Gert-Jan van de Geijn, Eleonora A. M. Festen, Rinse K. Weersma, Morris A. Swertz
Software Mentions: 3
Published: about 6 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: about 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: over 14 years ago

10.1186/s12870-018-1373-7

Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance
Cited by: 24
Author(s): Ana Paula Zotta Mota, Bruna Vidigal, Étienne Danchin, Roberto Coiti Togawa, Soraya C. M. Leal‐Bertioli, David J. Bertioli, Ana Cláudia Guerra Araújo, Ana Cristina Miranda Brasileiro, P. M. Guimarães
Software Mentions: 3
Published: over 6 years ago

10.3389/fnhum.2015.00386

GRETNA: a graph theoretical network analysis toolbox for imaging connectomics
Cited by: 544
Author(s): Jinhui Wang, Xindi Wang, Mingrui Xia, Xuhong Liao, Alan C. Evans, Yong He
Software Mentions: 2
Published: over 9 years ago

10.3389/fnhum.2015.00074

Differential cerebral response to somatosensory stimulation of an acupuncture point vs. two non-acupuncture points measured with EEG and fMRI
Cited by: 27
Author(s): Till Nierhaus, Daniel Pach, Weixin Huang, Xiangyu Long, Vitaly Napadow, Stephanie Roll, Fanrong Liang, Burkhard Pleger, Arno Villringer, Claudia M. Witt
Software Mentions: 2
Published: almost 10 years ago

10.3389/fnhum.2014.00409

Network complexity as a measure of information processing across resting-state networks: evidence from the Human Connectome Project
Cited by: 101
Author(s): Ian M. McDonough, Kaoru Nashiro
Software Mentions: 2
Published: over 10 years ago

10.3389/fnhum.2018.00279

Effects of the 2-Repeat Allele of the DRD4 Gene on Neural Networks Associated With the Prefrontal Cortex in Children With ADHD
Cited by: 9
Author(s): Andan Qian, Jiejie Tao, Xin Wang, Huiru Liu, Ling-Xiao Ji, Chuang Yang, Qiong Ye, Chengchun Chen, Jiance Li, Jingliang Cheng, Meihao Wang, Ke Zhao
Software Mentions: 2
Published: over 6 years ago

10.3389/fcell.2017.00012

The Importance of REST for Development and Function of Beta Cells
Cited by: 21
Author(s): David Martín, Anne Grapin-Botton
Software Mentions: 2
Published: over 7 years ago

10.1186/s12885-016-2274-5

Snail-induced epithelial-to-mesenchymal transition of MCF-7 breast cancer cells: systems analysis of molecular changes and their effect on radiation and drug sensitivity
Cited by: 36
Author(s): Roman Mezencev, Lilya V. Matyunina, Neda Jabbari, John F. McDonald
Software Mentions: 2
Published: over 8 years ago

10.3389/fnhum.2018.00322

Mapping the Spatiotemporal Evolution of Emotional Processing: An MEG Study Across Arousal and Valence Dimensions
Cited by: 11
Author(s): Charis Styliadis, Andreas A. Ioannides, Panagiotis D. Bamidis, Christos Papadelis
Software Mentions: 2
Published: over 6 years ago

10.3389/fnhum.2020.574148

Brain Responses to Food Odors Associated With BMI Change at 2-Year Follow-Up
Cited by: 6
Author(s): Pengfei Han, Hong Chen, Thomas Hummel
Software Mentions: 2
Published: about 4 years ago

10.3389/fnhum.2019.00365

Stereoscopic Rendering via Goggles Elicits Higher Functional Connectivity During Virtual Reality Gaming
Cited by: 9
Author(s): Caroline Garcia Forlim, Lukas Bittner, Fariba Mostajeran, Frank Steinicke, Jürgen Gallinat, Simone Kühn
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-12-423

Testing the importance of jasmonate signalling in induction of plant defences upon cabbage aphid (Brevicoryne brassicae) attack
Cited by: 57
Author(s): Anna Kuśnierczyk, Diem Hong Tran, Per Winge, Tommy S Jørstad, John C. Reese, Joanna Troczyńska, Atle M. Bones
Software Mentions: 2
Published: over 13 years ago

10.3389/fnagi.2014.00075

Deciphering the Molecular Profile of Plaques, Memory Decline and Neuron Loss in Two Mouse Models for Alzheimer’s Disease by Deep Sequencing
Cited by: 71
Author(s): Yvonne Bouter, Tim Kacprowski, Robert Weißmann, Katharina Dietrich, Henning Borgers, Andreas Brauß, Christian Sperling, Oliver Wirths, Mario Albrecht, Lars Riff Jensen, Andreas W. Kuß, Thomas A. Bayer
Software Mentions: 2
Published: over 10 years ago

10.18632/aging.102846

Baicalin ameliorates neuropathology in repeated cerebral ischemia-reperfusion injury model mice by remodeling the gut microbiota
Cited by: 42
Author(s): Jianfeng Liu, Tianhua Zhang, Yingying Wang, Chengqing Si, Xudong Wang, Ruitao Wang, Zhonghua Lv
Software Mentions: 2
Published: over 4 years ago

10.3390/antiox9080662

Neuroprotective Effect of HIF Prolyl Hydroxylase Inhibition in an In Vitro Hypoxia Model
Cited by: 18
Author(s): Maria Savyuk, Mikhail Krivonosov, Tatiana A. Mishchenko, Irina G. Gazaryan, Mikhail Ivanchenko, A. Yu. Khristichenko, Andrey Poloznikov, Dmitry M. Hushpulian, С. В. Никулин, E. A. Tonevitsky, Guzal Abuzarova, Еlena V. Mitroshina, Maria V. Vedunova
Software Mentions: 2
Published: over 4 years ago

10.1186/s12864-017-3989-7

A genome-wide transcriptome map of pistachio (Pistacia vera L.) provides novel insights into salinity-related genes and marker discovery
Cited by: 30
Author(s): Maryam Moazzzam Jazi, Seyed Mahdi Seyedi, Esmaeil Ebrahimie, Mansour Ebrahimi, Gianluca De Moro, Christopher Botanga
Software Mentions: 2
Published: over 7 years ago

10.3389/fbioe.2019.00106

Cyberbiosecurity Challenges of Pathogen Genome Databases
Cited by: 15
Author(s): Boris A. Vinatzer, Lenwood S. Heath, Hussain M. J. Almohri, Michael J. Stulberg, Christopher J. Lowe, Song Li
Software Mentions: 2
Published: over 5 years ago

10.3389/fnhum.2020.585664

Increased Amygdala-Paracentral Lobule/Precuneus Functional Connectivity Associated With Patients With Mood Disorder and Suicidal Behavior
Cited by: 14
Author(s): Ran Zhang, Luheng Zhang, Shengnan Wei, Pengshuo Wang, Xiaowei Jiang, Yanqing Tang, Fei Wang
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0148451

Identification and Validation of Reference Genes and Their Impact on Normalized Gene Expression Studies across Cultivated and Wild Cicer Species
Cited by: 37
Author(s): D. Srinivas Reddy, Pooja Bhatnagar‐Mathur, Palakolanu Sudhakar Reddy, Katamreddy Sri Cindhuri, Adusumalli Sivaji Ganesh, Kiran K. Sharma
Software Mentions: 2
Published: almost 9 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

10.1186/s12864-016-2693-3

Theobroma cacao L. pathogenesis-related gene tandem array members show diverse expression dynamics in response to pathogen colonization
Cited by: 36
Author(s): Andrew S. Fister, Luis C. Mejía, Yufan Zhang, Edward Allen Herre, Siela N. Maximova, Mark J. Guiltinan
Software Mentions: 2
Published: over 8 years ago

10.1016/j.exer.2019.03.024

Mutation in the mouse histone gene Hist2h3c1 leads to degeneration of the lens vesicle and severe microphthalmia
Cited by: 4
Author(s): Sharmilee Vetrivel, Natascia Tiso, Andrea Kügler, Martin Irmler, Marion Horsch, Johannes Beckers, Daniela Hladik, Florian Giesert, Valérie Gailus‐Durner, Helmut Fuchs, Sibylle Sabrautzki, Martin Hrabé de Angelis, Jochen Graw
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-14-607

RNA-seq analyses of gene expression in the microsclerotia of Verticillium dahliae
Cited by: 69
Author(s): Dechassa Duressa, Amy Anchieta, Dongquan Chen, Anna Klimes, Maria D. García-Pedrajas, Katherine F. Dobinson, Steven J. Klosterman
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0159563

Glutathione S-Transferase Regulation in Calanus finmarchicus Feeding on the Toxic Dinoflagellate Alexandrium fundyense
Cited by: 9
Author(s): Vittoria Roncalli, Michelle J. Jungbluth, Petra H. Lenz
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0173289

Comparing resting state fMRI de-noising approaches using multi- and single-echo acquisitions
Cited by: 68
Author(s): Ottavia Dipasquale, Arjun Sethi, Maria Marcella Laganà, Francesca Baglio, Giuseppe Baselli, Prantik Kundu, Neil A. Harrison, Mara Cercignani
Software Mentions: 2
Published: over 7 years ago

10.3390/antiox9020180

Pharmacological Targets of Kaempferol Within Inflammatory Pathways—A Hint Towards the Central Role of Tryptophan Metabolism
Cited by: 15
Author(s): Stefanie Hofer, Simon Geisler, Rebecca Lisandrelli, Huu Tung Nguyen, Markus Ganzera, Harald Schennach, Dietmar Fuchs, Julian E. Fuchs, Johanna M. Gostner, Katharina Kurz
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0050064

Differential Deactivation during Mentalizing and Classification of Autism Based on Default Mode Network Connectivity
Cited by: 92
Author(s): Donna L. Murdaugh, Svetlana V. Shinkareva, Hrishikesh R. Deshpande, Jing Wang, Mark R. Pennick, Rajesh K. Kana
Software Mentions: 2
Published: about 12 years ago

10.1186/s12859-020-03952-1

DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks
Cited by: 33
Author(s): Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A. Birchler
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12859-018-2016-6

BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways
Cited by: 18
Author(s): In-Young Kim, Saemi Choi, Sun Kim
Software Mentions: 2
Published: almost 7 years ago

10.18632/aging.202763

Gut microbiota from mice with cerebral ischemia-reperfusion injury affects the brain in healthy mice
Cited by: 10
Author(s): Wang Hong-ru, Shangjun Ren, Hailing Lv, Lili Cao
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0076234

NR4A2 Is Regulated by Gastrin and Influences Cellular Responses of Gastric Adenocarcinoma Cells
Cited by: 13
Author(s): Kristine Misund, Linn-Karina M. Selvik, Shalini Rao, Kristin G. Nørsett, Ingrid Bakke, Arne K. Sandvik, Astrid Lægreid, Torunn Bruland, Wenche S. Prestvik, Liv Thommesen
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0120345

Default Mode Network, Motor Network, Dorsal and Ventral Basal Ganglia Networks in the Rat Brain: Comparison to Human Networks Using Resting State-fMRI
Cited by: 53
Author(s): Adam Sierakowiak, Cyril Monnot, Sahar Nikkhou Aski, Martin Uppman, Tie‐Qiang Li, Peter Damberg, Stefan Brené
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-11-582

Differential gene expression during the moult cycle of Antarctic krill (Euphausia superba)
Cited by: 43
Author(s): Paul J. Seear, Geraint A. Tarling, Gavin Burns, William P. Goodall‐Copestake, E. Gaten, Özge Özkaya, Ezio Rosato
Software Mentions: 2
Published: about 14 years ago

10.1186/s12859-015-0797-4

Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data
Cited by: 34
Author(s): Ralf Eggeling, Teemu Roos, Petri Myllymäki, Ivo Große
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0115867

Identification of Genes Associated with Reproduction in the Mud Crab (Scylla olivacea) and Their Differential Expression following Serotonin Stimulation
Cited by: 19
Author(s): Napamanee Kornthong, Scott F. Cummins, Charoonroj Chotwiwatthanakun, Kanjana Khornchatri, Attakorn Engsusophon, Peter Hanna, Prasert Sobhon
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12991-018-0217-z

Resting-state brain activity in Chinese boys with low functioning autism spectrum disorder
Cited by: 13
Author(s): Gaizhi Li, Kathryn Rossbach, Wenqing Jiang, Yasong Du
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0098346

Structural and Functional Brain Alterations in End Stage Renal Disease Patients on Routine Hemodialysis: A Voxel-Based Morphometry and Resting State Functional Connectivity Study
Cited by: 51
Author(s): Yingwei Qiu, Xiaofei Lv, Huanhuan Su, Guihua Jiang, Cheng Li, Tian Jian-guo
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0028949

Proteome Changes Driven by Phosphorus Deficiency and Recovery in the Brown Tide-Forming Alga Aureococcus anophagefferens
Cited by: 60
Author(s): Louie L. Wurch, Erin M. Bertrand, Mak A. Saito, Benjamin A. S. Van Mooy, Sonya T. Dyhrman
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0212089

In vitro evaluation of the protective effects of plant extracts against amyloid-beta peptide-induced toxicity in human neuroblastoma SH-SY5Y cells
Cited by: 23
Author(s): Ana Luiza Sereia, Marcelo Tempesta de Oliveira, Adrivânio Baranoski, Leila Larisa Medeiros Marques, Fabianne Martins Ribeiro, Raquel Garcia Isolani, Daniela Cristina de Medeiros Araújo, Danielly Chierrito, Danielle Lazarin-Bidóia, Acácio Antônio Ferreira Zielinski, Cláudio Roberto Novello, Celso Vataru Nakamura, Mário Mantovani, João Carlos Palazzo de Mello
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0243869

Evaluation of the impact of surgical aortic valve replacement on short-term cardiovascular and cerebrovascular controls through spontaneous variability analysis
Cited by: 6
Author(s): Alberto Porta, Angela Fantinato, Vlasta Bari, Francesca Gelpi, Beatrice Cairo, Beatrice De Maria, Enrico Giuseppe Bertoldo, Valentina Fiolo, Edward Callus, Carlo De Vincentiis, Marianna Volpe, Raffaella Molfetta, Marco Ranucci
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0215729

Reference genes selection for Calotropis procera under different salt stress conditions
Cited by: 6
Author(s): Maria Reis Valois Coêlho, Rebeca Rivas, José Ribamar Costa Ferreira‐Neto, Valesca Pandolfi, João Pacífico Bezerra-Neto, Ana Maria Benko‐Iseppon, Mariana Santos
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0228680

Comparative transcriptome provides molecular insight into defense-associated mechanisms against spider mite in resistant and susceptible common bean cultivars
Cited by: 13
Author(s): Abdul Hadi Hoseinzadeh, Aboozar Soorni, Marie Shoorooei, Masoud Torkzadeh Mahani, R Maali Amiri, Hossein Allahyari, Reza Mohammadi
Software Mentions: 2
Published: almost 5 years ago