cran: gProfileR | Projects | Ecosyste.ms: Papers

10.3389/fgene.2019.01079

HiCeekR: A Novel Shiny App for Hi-C Data Analysis
Cited by: 13
Author(s): Lucio Di Filippo, Dario Righelli, Miriam Gagliardi, Maria R. Matarazzo, Claudia Angelini
Software Mentions: 12
Published: over 4 years ago

10.3389/fcimb.2021.687607

Early Leukocyte Responses in Ex-Vivo Models of Healing and Non-Healing Human Leishmania (Viannia) panamensis Infections
Cited by: 1
Author(s): María Adelaida Gómez, Ashton T. Belew, Adriana Navas, Mariana Rosales-Chilama, Julieth Murillo, Laura A. L. Dillon, Theresa A Alexander, Álvaro José Martínez-Valencia, Najib M. El-Sayed
Software Mentions: 12
Published: over 2 years ago

10.3390/ijms21124217

Transcriptome, Spliceosome and Editome Expression Patterns of the Porcine Endometrium in Response to a Single Subclinical Dose of Salmonella Enteritidis Lipopolysaccharide
Cited by: 6
Author(s): Łukasz Paukszto, Anita Mikołajczyk, J Jastrzebski, Marta Majewska, Kamil Dobrzyń, Marta Kieżun, Tadeusz Kamiński
Software Mentions: 11
Published: almost 4 years ago

10.12688/f1000research.13925.3

BED: a Biological Entity Dictionary based on a graph data model
Cited by: 1
Author(s): Patrice Godard, Jonathan van Eyll
Software Mentions: 10
Published: almost 6 years ago

10.1186/s13229-019-0262-8

Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer
Cited by: 25
Author(s): Jaume Forés-Martos, Ferrán Catalá-López, Jon Sánchez-Valle, Kristina Ibáñez, Héctor Tejero, Helena Palma-Gudiel, Joan Climent, Véra Pancaldi, Lourdes Fañanás, Celso Arango, Mara Parellada, Anaı̈s Baudot, Daniel Vogt, John L.R. Rubenstein, Alfonso Valencia, Rafael Tabarés‐Seisdedos
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pgen.1009259

Loss of endocytosis-associated RabGEF1 causes aberrant morphogenesis and altered autophagy in photoreceptors leading to retinal degeneration
Cited by: 9
Author(s): Passley Hargrove-Grimes, Anupam Mondal, Jessica Gumerson, Jacob Nellissery, Angel Aponte, Linn Gieser, Haohua Qian, Robert N Fariss, Juan S. Bonifacino, Tiansen Li, Anand Swaroop
Software Mentions: 9
Published: over 3 years ago

10.7554/eLife.53278

GATA6 mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm
Cited by: 25
Author(s): Arun Sharma, Lauren Wasson, Jon A. L. Willcox, Sarah U. Morton, Joshua M. Gorham, Daniel M. DeLaughter, Meraj Neyazi, Manuel Schmid, Radhika Agarwal, Min Young Jang, Christopher N. Toepfer, Tarsha Ward, Yuri Kim, Alexandre C. Pereira, Steven R. DePalma, Angela Tai, Seongwon Kim, David A. Conner, Daniel Bernstein, Bruce D. Gelb, Wendy K. Chung, Elizabeth Goldmuntz, George A. Porter, Martin Tristani‐Firouzi, Deepak Srivastava, Jonathan G. Seidman, Christine E. Seidman
Software Mentions: 9
Published: over 3 years ago

10.3390/cells10071576

Transcriptomic Profiling of Femoral Veins in Deep Vein Thrombosis in a Porcine Model
Cited by: 7
Author(s): Leszek Gromadziński, Łukasz Paukszto, Agnieszka Skowrońska, Piotr Holak, Michał Smoliński, Elżbieta Łopieńska–Biernat, Ewa Lepiarczyk, Aleksandra Lipka, J Jastrzebski, Marta Majewska
Software Mentions: 7
Published: almost 3 years ago

10.3389/fimmu.2021.729217

Timing of Transcriptomic Peripheral Blood Mononuclear Cell Responses of Sheep to Fasciola hepatica Infection Differs From Those of Cattle, Reflecting Different Disease Phenotypes
Cited by: 4
Author(s): Dagmara A. Niedziela, Amalia Naranjo‐Lucena, Verónica Molina-Hernández, John A. Browne, Á. Martínez-Moreno, J. Pérez, David E. MacHugh, Grace Mulcahy
Software Mentions: 6
Published: over 2 years ago

10.1093/bioinformatics/bty646

Automated workflow composition in mass spectrometry-based proteomics
Cited by: 37
Author(s): Magnus Palmblad, Anna‐Lena Lamprecht, Jon C. Ison, Veit Schwämmle
Software Mentions: 6
Published: almost 6 years ago

10.1038/s41598-021-82429-4

Molecular characterization of atherosclerosis in HIV positive persons
Cited by: 5
Author(s): Adam Cornwell, Rohith Palli, Meera V. Singh, Lauren Benoodt, Alicia Tyrell, Jun Abe, Giovanni Schifitto, Sanjay B. Maggirwar, Juilee Thakar
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-018-33276-3

Mutation pattern analysis reveals polygenic mini-drivers associated with relapse after surgery in lung adenocarcinoma
Cited by: 5
Author(s): Laura Bennett, Mary Howell, Danish Memon, Chris Smowton, Cong Zhou, Crispin Miller
Software Mentions: 5
Published: over 5 years ago

10.1242/dev.183855

Aging induces aberrant state transition kinetics in murine muscle stem cells
Cited by: 50
Author(s): Jacob C. Kimmel, Ara B. Hwang, Annarita Scaramozza, Wallace F. Marshall, Andrew S. Brack
Software Mentions: 5
Published: over 4 years ago

10.1186/s12870-018-1329-y

Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
Cited by: 39
Author(s): Ji Huang, Jue-Fei Zheng, Hui Yuan, Karen M. McGinnis
Software Mentions: 5
Published: almost 6 years ago

10.7717/peerj.229

Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures
Cited by: 43
Author(s): Amir Foroushani, Fiona S. L. Brinkman, David J. Lynn
Software Mentions: 5
Published: over 10 years ago

10.1186/s12885-019-6249-1

Comprehensive transcriptomic analyses of tissue, serum, and serum exosomes from hepatocellular carcinoma patients
Cited by: 38
Author(s): Robin Mjelle, Simona Dima, Nicolae Bacalbaşa, Konika Chawla, Andrei Sorop, Dana Cucu, Vlad Herlea, Pål Sætrom, Irinel Popescu
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-020-74705-6

Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method
Cited by: 5
Author(s): Marta Lucchetta, Marco Pellegrini
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.61894

Epigenetic reprogramming rewires transcription during the alternation of generations in Arabidopsis
Cited by: 45
Author(s): Michael Borg, Ranjith Papareddy, Rodolphe Dombey, Elin Axelsson, Michael D. Nodine, David Twell, Frédéric Berger
Software Mentions: 5
Published: over 3 years ago

10.1111/acel.13012

The conserved histone chaperone LIN‐53 is required for normal lifespan and maintenance of muscle integrity in <i>Caenorhabditis elegans</i>
Cited by: 11
Author(s): Stefanie Müthel, Bora Uyar, Ming He, Anne Krause, Burcu Vitrinel, Selman Bulut, Djordje Vasiljevic, Iris Marchal, Stefan Kempa, Altuna Akalin, Baris Tursun
Software Mentions: 4
Published: almost 5 years ago

10.3389/fnmol.2020.00057

Sequences of Reverse Transcribed Brain DNA Are Modified by Learning
Cited by: 2
Author(s): Antonio Giuditta, Joyce Casalino
Software Mentions: 4
Published: about 4 years ago

10.1038/s41598-017-04070-4

A GPU-accelerated algorithm for biclustering analysis and detection of condition-dependent coexpression network modules
Cited by: 21
Author(s): Anindya Bhattacharya, Yan Cui
Software Mentions: 4
Published: almost 7 years ago

10.1038/srep33736

MBD3 expression and DNA binding patterns are altered in a rat model of temporal lobe epilepsy
Cited by: 4
Author(s): Joanna Bednarczyk, Konrad J. Dębski, Anna Bot, Katarzyna Łukasiuk
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-14-882

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)
Cited by: 55
Author(s): D. Wong, Crystal Sweetman, Damian Paul Drew, Christopher M. Ford
Software Mentions: 4
Published: over 10 years ago

10.1038/celldisc.2017.13

Genome-wide profiling of DNA 5-hydroxymethylcytosine during rat Sertoli cell maturation
Cited by: 7
Author(s): Miriam Landfors, Jostein Johansen, Jan Magnus Aronsen, Cathrine Broberg Vågbø, Louis C. Doré, Chuan He, Ivar Sjaastad, Pål Sætrom, Péter Fedorcsák, John Arne Dahl, Håvard Aanes, Markus Fußer, Arne Klungland
Software Mentions: 4
Published: about 7 years ago

10.4049/jimmunol.2000450

Exhausted CD4+ T Cells during Malaria Exhibit Reduced mTORc1 Activity Correlated with Loss of T-bet Expression
Cited by: 9
Author(s): Ana Villegas-Méndez, Garima Khandelwal, Lucy M McGowan, Rebecca S Dookie, Michael Haley, Charlotte George, David Sims, Graham Lord, Linda V. Sinclair, Richard G. Jenner, Kevin N. Couper
Software Mentions: 4
Published: over 3 years ago

10.12688/f1000research.6925.1

GOsummaries: an R Package for Visual Functional Annotation of Experimental Data
Cited by: 71
Author(s): Raivo Kolde, Jaak Vilo
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-021-97909-w

Joint changes in RNA, RNA polymerase II, and promoter activity through the cell cycle identify non-coding RNAs involved in proliferation
Cited by: 7
Author(s): Siv Anita Hegre, Helle Samdal, Antonin Klima, Endre Bakken Stovner, Kristin G. Nørsett, Nina Beate Liabakk, Lene Christin Olsen, Konika Chawla, Per Arne, Pål Sætrom
Software Mentions: 4
Published: over 2 years ago

10.1093/bioinformatics/btab175

Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights
Cited by: 3
Author(s): Juan A. Sánchez, Ana Luisa Gil-Martínez, Alejandro Cisterna, Sonia García-Ruiz, Alicia Gómez-Pascual, Regina H. Reynolds, Mike A. Nalls, John Hardy, Mina Ryten, Juan A. Botía
Software Mentions: 3
Published: about 3 years ago

10.1186/s12870-015-0478-5

New insights into the evolutionary history of plant sorbitol dehydrogenase
Cited by: 22
Author(s): Yuping Jia, D. Wong, Crystal Sweetman, John B. Bruning, Christopher M. Ford
Software Mentions: 3
Published: about 9 years ago

10.1186/s12918-017-0420-6

An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks
Cited by: 196
Author(s): Juan A. Botía, Jana Vandrovcová, Paola Forabosco, Sebastian Guelfi, Karishma D’Sa, John Hardy, Cathryn M. Lewis, Mina Ryten, Michael E. Weale
Software Mentions: 3
Published: about 7 years ago

10.1007/s00429-017-1389-z

MicroRNAs contribute to postnatal development of laminar differences and neuronal subtypes in the rat medial entorhinal cortex
Cited by: 6
Author(s): Lene Christin Olsen, Kally C. O’Reilly, Nina‐Beate Liabakk, Menno P. Witter, Pål Sætrom
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pcbi.1006933

An integrative transcriptome analysis framework for drug efficacy and similarity reveals drug-specific signatures of anti-TNF treatment in a mouse model of inflammatory polyarthritis
Cited by: 12
Author(s): Niki Karagianni, Ksanthi Kranidioti, Nikolaos Fikas, Maria Tsochatzidou, Panagiotis Chouvardas, Maria C Denis, George Kollias, Christoforos Nikolaou
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0179385

RNA-Seq and CyTOF immuno-profiling of regenerating lacrimal glands identifies a novel subset of cells expressing muscle-related proteins
Cited by: 19
Author(s): Dillon Hawley, Jian Ding, Suharika Thotakura, Scott Haskett, Hema Aluri, Claire L. Kublin, Audrey M. Michel, Lisa Clapisson, Michaël Mingueneau, Driss Zoukhri
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0118551

Overexpression of the Transcription Factor Sp1 Activates the OAS-RNAse L-RIG-I Pathway
Cited by: 17
Author(s): Valéryane Dupuis-Maurin, Lilia Brinza, Joël Baguet, Émilie Plantamura, Stéphane Schicklin, Solène Chambion, Claire Macari, Martine Tomkowiak, Emmanuelle Deniaud, Yann Leverrier, Jacqueline Marvel, M Michallet
Software Mentions: 3
Published: about 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/s13059-017-1147-9

Discovery and functional prioritization of Parkinson’s disease candidate genes from large-scale whole exome sequencing
Cited by: 92
Author(s): Iris E. Jansen, Hui Ye, Sasja Heetveld, Marie C. Lechler, Helen Michels, Renée I. Seinstra, Steven Lubbe, Valérie Drouet, Suzanne Lesage, Elisa Majounie, J. Raphael Gibbs, Mike A. Nalls, Mina Ryten, Juan A. Botía, Jana Vandrovcová, Javier Simón‐Sánchez, Melissa Castillo-Lizardo, Patrizia Rizzu, Cornelis Blauwendraat, Amit K. Chouhan, Yarong Li, Puja Yogi, Najaf Amin, Cornelia M. van Duijn, Huw R. Morris, Alexis Brice, Andrew B. Singleton, Della David, Ellen A. A. Nollen, Sandeep Jain, Zhandong Liu, Peter Heutink
Software Mentions: 3
Published: over 7 years ago

10.1016/j.gpb.2018.01.001

Comparative Analysis of Human Genes Frequently and Occasionally Regulated by m 6 A Modification
Cited by: 3
Author(s): Yuan Zhou, Qinghua Cui
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-017-17322-0

Transcriptomic profiling of the human brain reveals that altered synaptic gene expression is associated with chronological aging
Cited by: 43
Author(s): Allissa Dillman, Elisa Majounie, Jinhui Ding, J. Raphael Gibbs, Dena G. Hernandez, Sampath Arepalli, Bryan J. Traynor, Andrew B. Singleton, Dagmar Galter, Mark Cookson
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-19100-4

Single-cell RNA-sequencing resolves self-antigen expression during mTEC development
Cited by: 28
Author(s): Ricardo J. Miragaia, Xiuwei Zhang, Tomás Gomes, Valentine Svensson, Tomislav Ilicic, Johan Henriksson, Gozde Kar, Tapio Lönnberg
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-020-74944-7

Interleukin-11 is important for vascular smooth muscle phenotypic switching and aortic inflammation, fibrosis and remodeling in mouse models
Cited by: 35
Author(s): Wei‐Wen Lim, Ben Corden, Benjamin Ng, Konstantinos Vanezis, G. D’Agostino, Anissa A. Widjaja, Weihua Song, Chen Xie, Liping Su, Xiu-Yi Kwek, Nicole Tee, Jinqiao Dong, Nicole S. J. Ko, Mao Wang, Chee Jian Pua, Muhammad Hasan Jamal, Beeyong Soh, V. Sivakumar, Sebastian Schäfer, Stuart A. Cook
Software Mentions: 3
Published: over 3 years ago

10.7554/eLife.37344

Chromatin accessibility dynamics across C. elegans development and ageing
Cited by: 66
Author(s): Jürgen Jänes, Dong Yan, Michael Schoof, Jacques Serizay, Alex Appert, Chiara Cerrato, Carson Woodbury, Chen Ron, Carolina Gemma, Ni Huang, Djem U. Kissiov, Przemyslaw Stempor, Annette Steward, Eva Zeiser, Sascha Sauer, Julie Ahringer
Software Mentions: 3
Published: over 5 years ago

10.1016/j.stem.2020.10.001

SARS-CoV-2 Infects the Brain Choroid Plexus and Disrupts the Blood-CSF Barrier in Human Brain Organoids
Cited by: 352
Author(s): Laura Pellegrini, Anna Albecka, Donna L. Mallery, Max J. Kellner, David Paul, Andrew P. Carter, Leo C. James, Madeline A. Lancaster
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-020-69695-4

Identification of differentially expressed genes profiles in a combined mouse model of Parkinsonism and colitis
Cited by: 7
Author(s): Ana-Luisa Gil-Martínez, Lorena Cuenca‐Bermejo, Ana González-Cuello, Consuelo Sánchez-Rodrigo, Antonio Parrado, Sheela Vyas, Emiliano Fernández-Villalba, María Teófila Vicente Herrero
Software Mentions: 2
Published: almost 4 years ago

10.3390/genes11060681

Novel Insights into the Protective Properties of ACTH(4-7)PGP (Semax) Peptide at the Transcriptome Level Following Cerebral Ischaemia–Reperfusion in Rats
Cited by: 15
Author(s): Ivan B. Filippenkov, Vasily V. Stavchansky, Alina E. Denisova, Vadim V. Yuzhakov, L.E. Sevankaeva, Olga Yu. Sudarkina, В. Г. Дмитриева, Leonid V. Gubsky, N. F. Myasoedov, Svetlana A. Limborska, Lyudmila V. Dergunova
Software Mentions: 2
Published: almost 4 years ago

10.1093/jxb/ery020

The GARP/MYB-related grape transcription factor AQUILO improves cold tolerance and promotes the accumulation of raffinose family oligosaccharides
Cited by: 57
Author(s): Xiaoming Sun, José Tomás Matus, Darren Chern Jan Wong, Zemin Wang, Fengmei Chai, Langlang Zhang, Ting Fang, Li Zhao, Yi Wang, Yuepeng Han, Qingfeng Wang, Shaohua Li, Zhenchang Liang, H. P. Xin
Software Mentions: 2
Published: over 6 years ago

10.18632/oncotarget.15310

Transcriptome analysis reveals non-identical microRNA profiles between arterial and venous plasma
Cited by: 19
Author(s): Wenjing Xu, Yuan Zhou, Xu Gao, Bin Geng, Qinghua Cui
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0160577

Diurnal Variations of Human Circulating Cell-Free Micro-RNA
Cited by: 42
Author(s): Niels H. H. Heegaard, Anting Liu Carlsen, Berit Lilje, Kim Lee Ng, Birte Svensson, Henrik L. Jørgensen, Henriette P Sennels, Jan Fahrenkrug
Software Mentions: 2
Published: almost 8 years ago

10.3390/cancers13164025

Antithetic hTERT Regulation by Androgens in Prostate Cancer Cells: hTERT Inhibition Is Mediated by the ING1 and ING2 Tumor Suppressors
Cited by: 7
Author(s): Sophie Bartsch, Kimia Mirzakhani, Lavinia Neubert, Alexander T Stenzel, Marzieh Ehsani, Mohsen Esmaeili, Thanakorn Pungsrinont, Merve Kacal, Seyed Mohammad Mahdi Rasa, Julia Kallenbach, D. Damodaran, Federico Ribaudo, Marc‐Oliver Grimm, Francesco Neri, Aria Baniahmad
Software Mentions: 2
Published: almost 3 years ago

10.3390/genes12081260

Extensive Changes in Transcription Dynamics Reflected on Alternative Splicing Events in Systemic Lupus Erythematosus Patients
Cited by: 3
Author(s): Sofia Papanikolaou, George Βertsias, Christoforos Nikolaou
Software Mentions: 2
Published: almost 3 years ago

10.1093/hmg/ddy232

Proteomic analysis reveals co-ordinated alterations in protein synthesis and degradation pathways in LRRK2 knockout mice
Cited by: 48
Author(s): Laura Pellegrini, David N. Hauser, Yan Li, Adamantios Mamais, Alexandra Beilina, R. Ileng Kumaran, Andrea Wetzel, Jonathon Nixon‐Abell, George R. Heaton, Iakov N. Rudenko, Mor R. Alkaslasi, Natalie Ivanina, Heather L. Melrose, Mark Cookson, Kirsten Harvey
Software Mentions: 2
Published: almost 6 years ago

10.1038/s12276-021-00639-2

YAP inactivation in estrogen receptor alpha-positive hepatocellular carcinoma with less aggressive behavior
Cited by: 5
Author(s): Youngsic Jeon, Jeong Eun Yoo, Hyungjin Rhee, Young-Joo Kim, Gwang Il Kim, Taek Chung, Sarah Yoon, Boram Shin, Hyun Goo Woo, Young Nyun Park
Software Mentions: 2
Published: about 3 years ago

10.1038/s41598-017-04400-6

A molecular hypothesis to explain direct and inverse co-morbidities between Alzheimer’s Disease, Glioblastoma and Lung cancer
Cited by: 69
Author(s): Jon Sánchez-Valle, Héctor Tejero, Kristina Ibáñez, José Luis Portero, Martin Krallinger, Fátima Al‐Shahrour, Rafael Tabarés‐Seisdedos, Anaı̈s Baudot, Alfonso Valencia
Software Mentions: 1
Published: almost 7 years ago

10.1534/g3.119.400775

Genetic Interactions Affect Lung Function in Patients with Systemic Sclerosis
Cited by: 8
Author(s): Anna L. Tyler, James Mahoney, Gregory W. Carter
Software Mentions: 1
Published: over 4 years ago

10.3389/fcell.2020.582255

Coding Variants Coupled With Rapid Modeling in Zebrafish Implicate Dynein Genes, dnaaf1 and zmynd10, as Adolescent Idiopathic Scoliosis Candidate Genes
Cited by: 11
Author(s): Yunjia Wang, Zhenhao Liu, Guanteng Yang, Qile Gao, Lairong Xiao, Jiong Li, Chaofeng Guo, Benjamin R Troutwine, Ryan S. Gray, Lu Xie, Hongqi Zhang
Software Mentions: 1
Published: over 3 years ago

10.1186/s12931-018-0744-9

Integrative genomics identifies new genes associated with severe COPD and emphysema
Cited by: 18
Author(s): Phuwanat Sakornsakolpat, Jarrett Morrow, Peter J. Castaldi, Craig P. Hersh, Yohan Bossé, Edwin K. Silverman, Ani Manichaikul, Michael H. Cho
Software Mentions: 1
Published: about 6 years ago

10.1038/srep39719

Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis
Cited by: 15
Author(s): Lynsey K. Whitacre, Jesse L. Hoff, Robert D. Schnabel, Sara Albarella, Francesca Ciotola, V. Peretti, Francesco Strozzi, Chiara Ferrandi, L. Ramunno, Tad S. Sonstegard, J. L. Williams, Jeremy F. Taylor, Jared E. Decker
Software Mentions: 1
Published: over 7 years ago

Projects: cran: gProfileR

Papers Mentioning gProfileR 56