Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: bioconductor: ArrayExpress

https://packages.ecosyste.ms/registries/bioconductor.org/packages/ArrayExpress

Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
1 version
Latest release: about 1 year ago
1 dependent package
124,798 downloads total

Papers Mentioning ArrayExpress 1,962

10.7554/eLife.45051
The long non-coding RNA Cerox1 is a post transcriptional regulator of mitochondrial complex I catalytic activity
Cited by: 36
Author(s): Tamara Sirey, Kenny Roberts, Wilfried Haerty, Oscar C. Bedoya-Reina, Sebastian Rogatti-Granados, Jennifer Y. Tan, Nick Li, Lisa C. Heather, Roderick N. Carter, Sarah Cooper, Andrew J. Finch, Jimi Wills, Nicholas M. Morton, Ana C. Marques, Chris P. Ponting
Software Mentions: 1
Published: over 5 years ago
10.7554/eLife.69160
GIV/Girdin, a non-receptor modulator for Gαi/s, regulates spatiotemporal signaling during sperm capacitation and is required for male fertility
Cited by: 5
Author(s): Sequoyah Reynoso, Vanessa Castillo, Gajanan D. Katkar, Inmaculada López-Sánchez, Sahar Taheri, Celia R. Espinoza, Cristina C. Rohena, Debashis Sahoo, Pascal Gagneux, Pradipta Ghosh
Software Mentions: 1
Published: over 3 years ago
10.7554/eLife.58374
SOX11 promotes epithelial/mesenchymal hybrid state and alters tropism of invasive breast cancer cells
Cited by: 24
Author(s): Erik Oliemuller, Richard Newman, Siu Man Tsang, Shane Foo, Gareth Muirhead, Farzana Noor, Syed Haider, Iskander Aurrekoetxea-Rodríguez, María dM Vivanco, Beatrice A. Howard
Software Mentions: 1
Published: about 4 years ago
10.7554/eLife.66865
Metabolic flexibility via mitochondrial BCAA carrier SLC25A44 is required for optimal fever
Cited by: 10
Author(s): Takeshi Yoneshiro, Nobuhiko Kataoka, Jacquelyn M. Walejko, Kenji Ikeda, Zachary D. Brown, Momoko Yoneshiro, Scott B. Crown, Tsuyoshi Osawa, Juro Sakai, Robert W. McGarrah, Phillip J. White, Kazuhiro Nakamura, Shingo Kajimura
Software Mentions: 1
Published: over 3 years ago
10.7554/eLife.03743
The transcription factor Pitx2 positions the embryonic axis and regulates twinning
Cited by: 33
Author(s): Angela Torlopp, Mohsin A.F. Khan, Nidia M M Oliveira, Ingrid Lekk, Luz Mayela Soto‐Jiménez, Alona Sosinsky, Claudio D. Stern
Software Mentions: 1
Published: almost 10 years ago
10.7554/eLife.09886
Protein kinase C coordinates histone H3 phosphorylation and acetylation
Cited by: 13
Author(s): Zoulfia Darieva, Aaron Webber, Stacey Warwood, Andrew D. Sharrocks
Software Mentions: 1
Published: about 9 years ago
10.3390/ijms10083658
Co-Expression of Neighboring Genes in the Zebrafish (Danio rerio) Genome
Cited by: 15
Author(s): Huai-Kuang Tsai, Peiying Huang, Cheng−Yan Kao, Daryi Wang
Software Mentions: 1
Published: over 15 years ago
10.3390/ijms11093397
Practical Application of Toxicogenomics for Profiling Toxicant-Induced Biological Perturbations
Cited by: 21
Author(s): Naoki Kiyosawa, Sunao Manabe, Takashi Yamoto, Atsushi Sanbuissho
Software Mentions: 1
Published: about 14 years ago
10.3390/ijms140611444
Silicon Era of Carbon-Based Life: Application of Genomics and Bioinformatics in Crop Stress Research
Cited by: 6
Author(s): Man-Wah Li, Xiaofeng Qi, Meng Ni, Hon‐Ming Lam
Software Mentions: 1
Published: over 11 years ago
10.3390/ijms151019037
ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates
Cited by: 7
Author(s): Michael Roemer, Linus Backert, Johannes Eichner, Andreas Zell
Software Mentions: 1
Published: about 10 years ago
10.3390/ijms19051369
Meta-Analysis and Experimental Validation Identified FREM2 and SPRY1 as New Glioblastoma Marker Candidates
Cited by: 11
Author(s): Marko Vidak, Ivana Jovčevska, Neja Šamec, Alja Zottel, Mirjana Liović, Damjana Rozman, Sašo Džeroski, Peter Juvan, Radovan Komel
Software Mentions: 1
Published: over 6 years ago
10.3390/ijms19071967
miR-196a Is Able to Restore the Aggressive Phenotype of Annexin A1 Knock-Out in Pancreatic Cancer Cells by CRISPR/Cas9 Genome Editing
Cited by: 26
Author(s): Raffaella Belvedere, Pasquale Saggese, Emanuela Pessolano, Domenico Memoli, Valentina Bizzarro, Francesca Rizzo, Luca Parente, Alessandro Weisz, Antonello Petrella
Software Mentions: 1
Published: over 6 years ago
10.3390/ijms20133173
Meta-Analysis of Microarray Expression Studies on Metformin in Cancer Cell Lines
Cited by: 8
Author(s): Hans-Juergen Schulten, Sherin Bakhashab
Software Mentions: 1
Published: over 5 years ago
10.3390/ijms20215274
The CCR4–NOT Deadenylase Complex Maintains Adipocyte Identity
Cited by: 11
Author(s): Akinori Takahashi, Shohei Takaoka, Shungo Kobori, Tomokazu Yamaguchi, Sara Ferwati, Keiji Kuba, Tadashi Yamamoto, Toru Suzuki
Software Mentions: 1
Published: about 5 years ago
10.3390/ijms20225783
Genome-Wide Identification and Characterization of ABC Transporters in Nine Rosaceae Species Identifying MdABCG28 as a Possible Cytokinin Transporter linked to Dwarfing
Cited by: 19
Author(s): Yi Feng, Qiran Sun, Guifen Zhang, Ting Wu, Xinzhong Zhang, Xuefeng Xu, Zhenhai Han, Yi Wang
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.pone.0176353
Intracellular signaling entropy can be a biomarker for predicting the development of cervical intraepithelial neoplasia
Cited by: 4
Author(s): Masakazu Sato, Kei Kawana, Katsuyuki Adachi, Asaha Fujimoto, Midori Yoshida, Hitomi Nakamura, Hidetoshi Nishida, Tatsuo Inoue, Ayumi Taguchi, Juri Ogishima, Shuichiro Eguchi, Aki Yamashita, Kensuke Tomio, Osamu Wada-Hiraike, Katsutoshi Oda, Takeshi Nagamatsu, Yutaka Osuga, Tomoyuki Fujii
Software Mentions: 1
Published: over 7 years ago
10.3389/fninf.2014.00051
Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool
Cited by: 11
Author(s): Andrew Zaldivar, Jeffrey L. Krichmar
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0088089
Phenotypic Modulation of Primary Vascular Smooth Muscle Cells by Short-Term Culture on Micropatterned Substrate
Cited by: 66
Author(s): Sea‐Jin Chang, Sang Yun Song, Jungsul Lee, Jonghee Yoon, Junseong Park, Sungyoung Choi, Je‐Kyun Park, Kyunghee Choi, Chulhee Choi
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0014207
Transcriptional Analysis Implicates Endoplasmic Reticulum Stress in Bovine Spongiform Encephalopathy
Cited by: 24
Author(s): Yue Tang, Wei Xiang, Linda A. Terry, Hans A. Kretzschmar, Otto Windl
Software Mentions: 1
Published: almost 14 years ago
10.1371/journal.pone.0031867
Human Cryptochrome-1 Confers Light Independent Biological Activity in Transgenic Drosophila Correlated with Flavin Radical Stability
Cited by: 26
Author(s): Jacqueline Vieira, Alex R. Jones, Antoine Danon, Michiyo Sakuma, Nathalie Hoang, David Robles, Shirley Tait, Derren J. Heyes, Marie Christine Picot, Taishi Yoshii, Charlotte Helfrich‐Förster, Guillaume Soubigou, Jean Yves Coppée, André Klarsfeld, François Rouyer, Nigel S. Scrutton, Margaret Ahmad
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0110288
Integrated Analysis of Microarray Data of Atherosclerotic Plaques: Modulation of the Ubiquitin-Proteasome System
Cited by: 11
Author(s): Zhe Wang, Dong Guo, Bin Yang, Jian Wang, Rong Wang, Xiaowei Wang, Qunye Zhang
Software Mentions: 1
Published: about 10 years ago
10.3389/fonc.2019.01515
CXCL1 as an Unfavorable Prognosis Factor Negatively Regulated by DACH1 in Non-small Cell Lung Cancer
Cited by: 24
Author(s): Shengnan Yu, Ming Yi, Lei Xu, Shuang Qin, An‐Ping Li, Kongming Wu
Software Mentions: 1
Published: almost 5 years ago
10.3389/fonc.2017.00332
Human Epididymis Protein 4 Promotes Events Associated with Metastatic Ovarian Cancer via Regulation of the Extracelluar Matrix
Cited by: 19
Author(s): Jennifer Ribeiro, Hilary Gaudet, Mehreen Ali Khan, Christoph Schorl, Nicole James, M. Oliver, Paul DiSilvestro, Richard G. Moore, Naohiro Yano
Software Mentions: 1
Published: almost 7 years ago
10.3389/fonc.2019.00026
EYA2 Correlates With Clinico-Pathological Features of Breast Cancer, Promotes Tumor Proliferation, and Predicts Poor Survival
Cited by: 16
Author(s): Hanxiao Xu, Yanmei Jiao, Ming Yi, Wei Zhao, Zeyu Wu
Software Mentions: 1
Published: almost 6 years ago
10.1371/journal.pone.0009426
The Genome of Streptococcus mitis B6 - What Is a Commensal?
Cited by: 105
Author(s): Dalia Denapaite, Reinhold Brückner, Michael Nuhn, Peter Reichmann, Bernhard Henrich, Patrick Maurer, Yvonne Schähle, Peter Selbmann, Wolfgang Zimmermann, R. Wambutt, Regine Hakenbeck
Software Mentions: 1
Published: over 14 years ago
10.1371/journal.pone.0089297
Meta-Analysis of Pathway Enrichment: Combining Independent and Dependent Omics Data Sets
Cited by: 43
Author(s): Alexander Kaever, Manuel Landesfeind, Kirstin Feussner, Burkhard Morgenstern, Ivo Feußner, Peter Meinicke
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0004344
The Staphylococcus aureus Response to Unsaturated Long Chain Free Fatty Acids: Survival Mechanisms and Virulence Implications
Cited by: 157
Author(s): John Kenny, Deborah Ward, Elisabet Josefsson, Ing-Marie Jonsson, Jason Hinds, Huw H. Rees, Jodi A. Lindsay, Andrej Tarkowski, Malcolm J. Horsburgh
Software Mentions: 1
Published: almost 16 years ago
10.1371/journal.pone.0100178
Chondroitin Sulfate Proteoglycan CSPG4 as a Novel Hypoxia-Sensitive Marker in Pancreatic Tumors
Cited by: 21
Author(s): Shereen Keleg, Titov Alexandr, Anette Heller, Thomas Giese, Christine Tjaden, Sufian S. Ahmad, Matthias M. Gaida, Andrea S. Bauer, Jens Werner, Nathalia A. Giese
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0010692
Skeletal Site-Related Variation in Human Trabecular Bone Transcriptome and Signaling
Cited by: 33
Author(s): Satya S. Varanasi, Ole Kristoffer Olstad, Daniel Swan, P. L. Sanderson, Vigdis T. Gautvik, Sjur Reppe, Roger M. Francis, Kaare M. Gautvik, Harish K. Datta
Software Mentions: 1
Published: over 14 years ago
10.3389/fonc.2021.605884
Exosomal LncRNA LBX1-AS1 Derived From RBPJ Overexpressed-Macrophages Inhibits Oral Squamous Cell Carcinoma Progress via miR-182-5p/FOXO3
Cited by: 17
Author(s): Yilong Ai, Haigang Wei, Si-Pei Wu, Zhe Tang, Xia Li, Chen Zou
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pone.0084187
High Expression of CD109 Antigen Regulates the Phenotype of Cancer Stem-Like Cells/Cancer-Initiating Cells in the Novel Epithelioid Sarcoma Cell Line ESX and Is Related to Poor Prognosis of Soft Tissue Sarcoma
Cited by: 53
Author(s): Makoto Emori, Tomohide Tsukahara, Masaki Murase, Masanobu Kano, Kenji Murata, Akiko Takahashi, Terufumi Kubo, Hiroko Asanuma, Kazuyo Yasuda, Vitaly Kochin, Mitsunori Kaya, Satoshi Nagoya, Jun Nishio, Hiroshi Iwasaki, Tomoko Sonoda, Tadashi Hasegawa, Toshihiko Torigoe, Takuro Wada, Toshihiko Yamashita, Noriyuki Sato
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0018796
Stroma Regulates Increased Epithelial Lateral Cell Adhesion in 3D Culture: A Role for Actin/Cadherin Dynamics
Cited by: 31
Author(s): Karen Chambers, Joanna Pearson, Naveed Aziz, Peter O’Toole, David R. Garrod, Shona Lang
Software Mentions: 1
Published: over 13 years ago
10.1098/rsob.120091
Systems analysis of transcription factor activities in environments with stable and dynamic oxygen concentrations
Cited by: 27
Author(s): Matthew D. Rolfe, Andrea Ocone, Melanie R. Stapleton, Simon T.E. Hall, Eleanor W. Trotter, Robert K. Poole, Guido Sanguinetti, Jeffrey Green
Software Mentions: 1
Published: over 12 years ago
10.3389/fonc.2020.00044
Clinical Significance of Circulating miR-1273g-3p and miR-122-5p in Pancreatic Cancer
Cited by: 19
Author(s): Tommaso Mazza, Domenica Gioffreda, Andrea Fontana, Tommaso Biagini, Massimo Carella, Orazio Palumbo, Evaristo Maiello, Francesca Bazzocchi, Angelo Andriulli, Francesca Tavano
Software Mentions: 1
Published: almost 5 years ago
10.3389/fonc.2020.00068
Comprehensive Review of Web Servers and Bioinformatics Tools for Cancer Prognosis Analysis
Cited by: 70
Author(s): Hong Zheng, Guosen Zhang, Lu Zhang, Qiang Wang, Huimin Li, Yali Han, Longxiang Xie, Zhongyi Yan, Yongqiang Li, Yang An, H. Dong, Wan Zhu, Xiangqian Guo
Software Mentions: 1
Published: almost 5 years ago
10.3389/fonc.2019.00145
Spheroid-Induced Epithelial-Mesenchymal Transition Provokes Global Alterations of Breast Cancer Lipidome: A Multi-Layered Omics Analysis
Cited by: 29
Author(s): Yun Pyo Kang, Jung-ho Yoon, Nguyen Phuoc Long, Gi‐Bang Koo, Hyunjin Noh, Seung-Jae Oh, Sae Bom Lee, Hyung Min Kim, Ji Yeon Hong, Wonjun Lee, Seul Ji Lee, Soon‐Sun Hong, Sung Won Kwon, You‐Sun Kim
Software Mentions: 1
Published: over 5 years ago
10.3389/fphar.2018.00847
UBE2C Is a Potential Biomarker of Intestinal-Type Gastric Cancer With Chromosomal Instability
Cited by: 43
Author(s): Jun Zhang, Xinyu Liu, Guanzhen Yu, Lei Liu, Jiejun Wang, Xiaoyu Chen, Yuhai Bian, Yuan Ji, Xiaoyan Zhou, Yinan Chen, Jun Ji, Zhen Xiang, Li Guo, Jing‐Yuan Fang, Yihong Sun, Hui Cao, Zhenggang Zhu, Yingyan Yu
Software Mentions: 1
Published: over 6 years ago
10.1371/journal.pone.0028552
The Discovery of Putative Urine Markers for the Specific Detection of Prostate Tumor by Integrative Mining of Public Genomic Profiles
Cited by: 15
Author(s): Min Chen, Kai Wang, Liang Zhang, Cheng Li, Yongliang Yang
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.pone.0040900
Distinct Genes Related to Drug Response Identified in ER Positive and ER Negative Breast Cancer Cell Lines
Cited by: 18
Author(s): Kui Shen, Shara D. Rice, David A. Gingrich, Dakun Wang, Mi Zhang, Chunqiao Tian, Zhenyu Ding, Stacey L. Brower, Paul R. Ervin, Michael J. Gabrin, George C. Tseng, Nan Song
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0001791
Transcriptomic Analyses Reveal Novel Genes with Sexually Dimorphic Expression in the Zebrafish Gonad and Brain
Cited by: 109
Author(s): Rajini Sreenivasan, Minnie Cai, Richárd Bártfai, Xingang Wang, Alan Christoffels, László Orbán
Software Mentions: 1
Published: over 16 years ago
10.3389/fphar.2017.00563
Transcriptome Profiling in Systems Vascular Medicine
Cited by: 22
Author(s): Suowen Xu
Software Mentions: 1
Published: about 7 years ago
10.3389/fphar.2020.00533
Cyclooxygenase 2-Regulated Genes an Alternative Avenue to the Development of New Therapeutic Drugs for Colorectal Cancer
Cited by: 17
Author(s): Alicia M. Hidalgo-Estévez, Konstantinos Stamatakis, Marta Jiménez-Martínez, Ricardo López‐Pérez, Manuel Fresno
Software Mentions: 1
Published: over 4 years ago
10.3389/fphys.2018.00937
Blood Gene Expression and Vascular Function Biomarkers in Professional Saturation Diving
Cited by: 15
Author(s): Fatima Zohra Kiboub, Andreas Møllerløkken, Astrid Hjelde, Arnar Flatberg, Øyvind Loennechen, Ingrid Eftedal
Software Mentions: 1
Published: over 6 years ago
10.3389/fphys.2019.00474
Mitochondrial Adaptations in Elderly and Young Men Skeletal Muscle Following 2 Weeks of Bed Rest and Rehabilitation
Cited by: 30
Author(s): Alessia Buso, Marina Comelli, Raffaella Picco, Miriam Isola, Benedetta Magnesa, Rado Pišot, Jörn Rittweger, Desy Salvadego, Boštjan Šimunič, Bruno Grassi, Irene Mavelli
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0230313
A 3-gene biomarker signature to predict response to taxane-based neoadjuvant chemotherapy in breast cancer
Cited by: 5
Author(s): Jim Kallarackal, Florian Bürger, S. Del Bianco, Alessandro Romualdi, Martina Schad
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0006880
Nuclear Receptor SHP Activates miR-206 Expression via a Cascade Dual Inhibitory Mechanism
Cited by: 44
Author(s): Guisheng Song, Lili Wang
Software Mentions: 1
Published: about 15 years ago
10.1371/journal.pone.0228408
GLIPR1 expression is reduced in multiple myeloma but is not a tumour suppressor in mice
Cited by: 2
Author(s): Natasha Friend, Jacqueline E. Noll, Khatora S. Opperman, Kimberley C. Clark, Krzysztof M. Mrozik, Kate Vandyke, Duncan R. Hewett, Andrew C.W. Zannettino
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pone.0075882
microRNA-22 Promotes Heart Failure through Coordinate Suppression of PPAR/ERR-Nuclear Hormone Receptor Transcription
Cited by: 72
Author(s): Priyatansh Gurha, Tiannan Wang, Ashley H. Larimore, Yassine Sassi, Cei Abreu‐Goodger, Maricela Ramirez, Anilkumar K. Reddy, Stefan Engelhardt, George E. Taffet, Xander H.T. Wehrens, Mark L. Entman, Antony Rodríguez
Software Mentions: 1
Published: about 11 years ago
10.3390/ijms21103480
The GOLIATH Project: Towards an Internationally Harmonised Approach for Testing Metabolism Disrupting Compounds
Cited by: 33
Author(s): Juliette Legler, Daniel Zalko, Fabien Jourdan, Miriam N. Jacobs, Bernard Fromenty, Patrick Balaguer, William Bourguet, Vesna Munić Kos, Ángel Nadal, Claire Beausoleil, Susana Cristóbal, Sylvie Remy, Sibylle Ermler, Luigi Margiotta-Casaluci, Julian L. Griffin, Bruce Blumberg, Christophe Chesné, Sebastian Hoffmann, Patrik L. Andersson, Jorke H. Kamstra
Software Mentions: 1
Published: over 4 years ago
10.3389/fpls.2021.640324
Identification and Characterization of Perennial Ryegrass (Lolium perenne) Vernalization Genes
Cited by: 2
Author(s): Rowan P. Herridge, * Samarth, Lynette Brownfield, Richard C. Macknight
Software Mentions: 1
Published: over 3 years ago
10.3389/fpls.2020.00753
Light Regulation of Chlorophyll and Glycoalkaloid Biosynthesis During Tuber Greening of Potato S. tuberosum
Cited by: 12
Author(s): Haruko Okamoto, Laurence J. M. Ducreux, J. William Allwood, Pete E. Hedley, Alison J. Wright, Vidyanath Gururajan, Matthew J. Terry, Mark A. Taylor
Software Mentions: 1
Published: over 4 years ago
10.3389/fpls.2016.01836
An LRR/Malectin Receptor-Like Kinase Mediates Resistance to Non-adapted and Adapted Powdery Mildew Fungi in Barley and Wheat
Cited by: 39
Author(s): Jeyaraman Rajaraman, Dimitar Douchkov, Goetz Hensel, Francesca L. Stefanato, Anna Gordon, Nelzo C. Ereful, Octav Caldararu, Andrei-José Petrescu, Jochen Kumlehn, Lesley A. Boyd, Patrick Schweizer
Software Mentions: 1
Published: almost 8 years ago
10.3389/fpls.2017.00445
Altered Expression of Genes Implicated in Xylan Biosynthesis Affects Penetration Resistance against Powdery Mildew
Cited by: 22
Author(s): Jamil Chowdhury, Stefanie Lück, Jeyaraman Rajaraman, Dimitar Douchkov, Neil J. Shirley, Julian G. Schwerdt, Patrick Schweizer, Geoffrey B. Fincher, Rachel A. Burton, Alan Little
Software Mentions: 1
Published: over 7 years ago
10.3390/ijms21113749
17-Aminogeldanamycin Inhibits Constitutive Nuclear Factor-Kappa B (NF-κB) Activity in Patient-Derived Melanoma Cell Lines
Cited by: 7
Author(s): Mariusz L. Hartman, Magdalena Rogut, Aleksandra Mielczarek-Lewandowska, Michal Wozniak, Małgorzata Czyż
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0006759
Butyrate-Induced Transcriptional Changes in Human Colonic Mucosa
Cited by: 143
Author(s): Steven Vanhoutvin, Freddy J. Troost, Henrike M. Hamer, Patrick Lindsey, Ger H. Koek, Daisy Jonkers, Andrea Kodde, Koen Venema, Robert Jan Brummer
Software Mentions: 1
Published: about 15 years ago
10.3389/fpls.2017.02158
Biology in the Dry Seed: Transcriptome Changes Associated with Dry Seed Dormancy and Dormancy Loss in the Arabidopsis GA-Insensitive sleepy1-2 Mutant
Cited by: 25
Author(s): Sven K. Nelson, Tohru Ariizumi, Camille M. Steber
Software Mentions: 1
Published: almost 7 years ago
10.3389/fpls.2020.00098
BarleyNet: A Network-Based Functional Omics Analysis Server for Cultivated Barley, Hordeum vulgare L.
Cited by: 15
Author(s): Sungho Lee, Tak H. Lee, Sunmo Yang, Insuk Lee
Software Mentions: 1
Published: almost 5 years ago
10.3389/fpls.2016.00903
Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach
Cited by: 11
Author(s): Jun Li, Patrick Xuechun Zhao
Software Mentions: 1
Published: over 8 years ago
10.3389/fpls.2012.00294
Reverse Engineering: A Key Component of Systems Biology to Unravel Global Abiotic Stress Cross-Talk
Cited by: 34
Author(s): Swetlana Friedel, Björn Usadel, Nicolaus von Wirén, Nese Sreenivasulu
Software Mentions: 1
Published: almost 13 years ago
10.1371/journal.pone.0020938
COLOMBOS: Access Port for Cross-Platform Bacterial Expression Compendia
Cited by: 24
Author(s): Kristof Engelen, Qiang Fu, Pieter Meysman, Aminael Sánchez-Rodríguez, Riet De Smet, Kim Lemmens, Ana Carolina Fierro, Kathleen Marchal
Software Mentions: 1
Published: over 13 years ago
10.1371/journal.pone.0019844
Extracellular Matrix Formation Enhances the Ability of Streptococcus pneumoniae to Cause Invasive Disease
Cited by: 60
Author(s): Claudia Trappetti, Abiodun D. Ogunniyi, Marco R. Oggioni, James C. Paton
Software Mentions: 1
Published: over 13 years ago
10.3389/fpls.2019.00315
ABA-Induced Vegetative Diaspore Formation in Physcomitrella patens
Cited by: 27
Author(s): Muhammad Arif, Manuel Hiß, Marta Tomek, Hauke Busch, Rabea Meyberg, Stefanie Tintelnot, Ralf Reski, Stefan A. Rensing, Wolfgang Frank
Software Mentions: 1
Published: over 5 years ago
10.3390/ijms21124442
Functional Heterogeneity of Protein Kinase A Activation in Multipotent Stromal Cells
Cited by: 11
Author(s): Pyotr A. Tyurin‐Kuzmin, Maxim Karagyaur, Konstantin Kulebyakin, Daniyar T. Dyikanov, Vadim Chechekhin, Anastasiya M Ivanova, Mariya Skryabina, Mikhail Arbatskiy, Veronika Sysoeva, Kalinina Ni, В. А. Ткачук
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pone.0009894
Functional Clustering of Periodic Transcriptional Profiles through ARMA(p,q)
Cited by: 32
Author(s): Ning Li, Timothy L. McMurry, Arthur Berg, Zhong Wang, Scott A. Berceli, Rongling Wu
Software Mentions: 1
Published: over 14 years ago
10.1371/journal.pone.0112655
Identification of Modulators of the Nuclear Receptor Peroxisome Proliferator-Activated Receptor α (PPARα) in a Mouse Liver Gene Expression Compendium
Cited by: 58
Author(s): Keiyu Oshida, Naresh Vasani, Russell S. Thomas, Dawn Applegate, Mitchell B. Rosen, Barbara D. Abbott, Christopher Lau, Grace L. Guo, Lauren M. Aleksunes, Curtis D. Klaassen, J. Christopher Corton
Software Mentions: 1
Published: almost 10 years ago
10.1534/g3.117.300225
A Deconvolution Protocol for ChIP-Seq Reveals Analogous Enhancer Structures on the Mouse and Human Ribosomal RNA Genes
Cited by: 30
Author(s): Jean-Clément Mars, Marianne Sabourin-Felix, Michel G. Tremblay, Tom Moss
Software Mentions: 1
Published: almost 7 years ago
10.3390/ijms21207437
Targeting SRC Kinase Signaling in Pancreatic Cancer Stem Cells
Cited by: 17
Author(s): Sonia Alcalá, Víctor Mayoral-Varo, Laura Ruiz-Cañas, Juan Carlos López-Gil, Christopher Heeschen, Jorge Martı́n-Pérez, Bruno Sáinz
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pone.0138889
Adipose Tissue Dysfunction and Altered Systemic Amino Acid Metabolism Are Associated with Non-Alcoholic Fatty Liver Disease
Cited by: 63
Author(s): Sulin Cheng, Reija Autio, Ronald Borra, Xiaowei Ojanen, Leiting Xu, Timo Törmäkangas, Markku Alén
Software Mentions: 1
Published: about 9 years ago
10.3390/genes5030726
Enterococcus faecalis Infection and Reactive Oxygen Species Down-Regulates the miR-17-92 Cluster in Gastric Adenocarcinoma Cell Culture
Cited by: 22
Author(s): Jesper A.B. Strickertsson, Lene Juel Rasmussen, Lennart Friis‐Hansen
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0041683
Identification of Novel Markers of Mouse Fetal Ovary Development
Cited by: 43
Author(s): Huijun Chen, Jodie Palmer, Rathi D Thiagarajan, Marcel E. Dinger, Emmanuelle Lesieur, Hansheng Sheng Chiu, Alexandra Schulz, Cassy M. Spiller, Sean M. Grimmond, Melissa H. Little, Peter Koopman, Dagmar Wilhelm
Software Mentions: 1
Published: over 12 years ago
10.1371/journal.pone.0075290
Coordinated and Interactive Expression of Genes of Lipid Metabolism and Inflammation in Adipose Tissue and Liver during Metabolic Overload
Cited by: 22
Author(s): Wen Miin Liang, Giulia Tonini, Petra Mulder, Thomas Kelder, Marjan van Erk, Anita M. van den Hoek, Rob Mariman, Peter Y. Wielinga, Michela Baccini, Teake Kooistra, Annibale Biggeri, Robert Kleemann
Software Mentions: 1
Published: about 11 years ago
10.1371/journal.pone.0023944
A Stratified Transcriptomics Analysis of Polygenic Fat and Lean Mouse Adipose Tissues Identifies Novel Candidate Obesity Genes
Cited by: 45
Author(s): Nicholas M. Morton, Yvonne B. Nelson, Zoi Michailidou, Emma M. Di Rollo, Lynne Ramage, Patrick W. F. Hadoke, Jonathan R. Seckl, L. Bünger, Simon Horvat, Christopher J. Kenyon, Donald R. Dunbar
Software Mentions: 1
Published: about 13 years ago
10.1371/journal.pone.0021463
E-Cadherin Acts as a Regulator of Transcripts Associated with a Wide Range of Cellular Processes in Mouse Embryonic Stem Cells
Cited by: 29
Author(s): Francesca Soncin, Lisa Mohamet, Sarah Ritson, Kate Hawkins, Nicoletta Bobola, Leo Zeef, Catherine L.R. Merry, Christopher M. Ward
Software Mentions: 1
Published: over 13 years ago
10.1111/jcmm.13023
Reduced angiogenic gene expression in morbillivirus‐triggered oncolysis in a translational model for histiocytic sarcoma
Cited by: 24
Author(s): Vanessa Maria Pfankuche, Ingo Spitzbarth, Stefanie Lapp, Reiner Ulrich, Ulrich Deschl, Arno Kalkuhl, Wolfgang Baumgärtner, Christina Puff
Software Mentions: 1
Published: about 8 years ago
10.1111/jcmm.13051
Acquired TET 2 mutation in one patient with familial platelet disorder with predisposition to AML led to the development of pre‐leukaemic clone resulting in T2‐ ALL and AML ‐M0
Cited by: 10
Author(s): Vladimir T. Manchev, Hind Bouzid, Iléana Antony-Debré, Betty Leite, Guillaume Meurice, Nathalie Droin, Thomas Prébet, Régis Costello, William Vainchenker, Isabelle Plo, M’Boyba Diop, Elizabeth Macintyre, Vahid Asnafi, Rémi Favier, Véronique Baccini, Hana Raslová
Software Mentions: 1
Published: almost 8 years ago
10.3390/ijms21218069
Intra-Individual Behavioural Variability: A Trait under Genetic Control
Cited by: 12
Author(s): Rie Henriksen, Andrey Höglund, Jesper Fogelholm, Robin N. Abbey-Lee, Martin Johnsson, Niels Jeroen Dingemanse, Dominic Wright
Software Mentions: 1
Published: about 4 years ago
10.1371/journal.pone.0184317
Differential expression of tetraspanin superfamily members in dendritic cell subsets
Cited by: 19
Author(s): Malou Zuidscherwoude, Kuntal Worah, Alie van der Schaaf, Sonja I. Buschow, Annemiek B. van Spriel
Software Mentions: 1
Published: about 7 years ago
10.1186/s13023-014-0160-2
Molecular characterization of subcutaneous panniculitis-like T-cell lymphoma reveals upregulation of immunosuppression- and autoimmunity-associated genes
Cited by: 15
Author(s): Pilvi Maliniemi, Sonja Hahtola, Kristian Ovaska, Leila Jeskanen, Liisa Väkevä, Kirsi Jäntti, Rudolf Stadler, David Michonneau, Sylvie Fraïtag, Sampsa Hautaniemi, Annamari Ranki
Software Mentions: 1
Published: about 10 years ago
10.1371/journal.pone.0016419
Genetic Variation in Spatio-Temporal Confined USA300 Community-Associated MRSA Isolates: A Shift from Clonal Dispersion to Genetic Evolution?
Cited by: 15
Author(s): Neeltje Carpaij, Rob J. L. Willems, Thomas W. Rice, Robert A. Weinstein, Jason Hinds, Adam A. Witney, Jodi A. Lindsay, Marc J. M. Bonten, Ad C. Fluit
Software Mentions: 1
Published: almost 14 years ago
10.1172/JCI129115
Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia
Cited by: 29
Author(s): Alhomidi Almotiri, Hamed Ahmad A. Alzahrani, Juan Bautista Menendez-Gonzalez, Ali Abdelfattah, Badi Alotaibi, Lubaid Saleh, Adelle Greene, Mia R. F. Georgiou, Alex Gibbs, Amani Salem Alsayari, Sarab Taha, Leigh-anne Thomas, Dhruv Shah, Sarah Edkins, Peter Giles, Marc P. Stemmler, Simone Brabletz, Thomas Brabletz, Ashleigh S. Boyd, Florian A. Siebzehnrübl, Neil P. Rodrigues
Software Mentions: 1
Published: almost 4 years ago
10.1371/journal.pone.0030269
Angiogenic mRNA and microRNA Gene Expression Signature Predicts a Novel Subtype of Serous Ovarian Cancer
Cited by: 99
Author(s): Stefan Bentink, Benjamin Haibe‐Kains, Thomas S. Risch, Jian–Bing Fan, Michelle S. Hirsch, Kristina M. Holton, Renee Rubio, Craig April, Jing Chen, Eliza Wickham-Garcia, Joyce F. Liu, Aedín C. Culhane, Ronny Drapkin, John Quackenbush, Ursula A. Matulonis
Software Mentions: 1
Published: almost 13 years ago
10.1093/jxb/ert337
Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
Cited by: 109
Author(s): Selahattin Danisman, Aalt D. J. van Dijk, Andrea Bimbó, Froukje van der Wal, Lars Hennig, Stefan de Folter, Gerco C. Angenent, Richard G. H. Immink
Software Mentions: 1
Published: about 11 years ago
10.1093/jxb/ert397
Overexpression of<i>PYL5</i>in rice enhances drought tolerance, inhibits growth, and modulates gene expression
Cited by: 178
Author(s): Hyun-Mi Kim, Kyeyoon Lee, Hyunsik Hwang, Nikita Bhatnagar, Dool Yi Kim, In Sun Yoon, Myung-Ok Byun, Sun Tae Kim, Ki‐Hong Jung, Beom-Gi Kim
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pone.0065034
Cholecalciferol (Vitamin D3) Improves Myelination and Recovery after Nerve Injury
Cited by: 102
Author(s): Jean-François Chabas, Delphine Stephan, Tanguy Marqueste, Stéphane García, Marie‐Noëlle Lavaut, Catherine Nguyen, R. Legré, Michel Khrestchatisky, Patrick Decherchi, François Féron
Software Mentions: 1
Published: over 11 years ago
10.1016/j.kint.2018.11.040
Lrig2 and Hpse2, mutated in urofacial syndrome, pattern nerves in the urinary bladder
Cited by: 25
Author(s): Neil Roberts, Emma Hilton, Filipa Lopes, Subir Singh, Michael J. Randles, Natalie J. Gardiner, Karl Chopra, Riccardo Coletta, Zunera Bajwa, Robert J. Hall, Wyatt W. Yue, Franz Schaefer, Stefanie Weber, Roger Henriksson, Helen M. Stuart, Håkan Hedman, William G. Newman, Adrian S. Woolf
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0080625
MicroRNA-99 Family Members Suppress Homeobox A1 Expression in Epithelial Cells
Cited by: 33
Author(s): Dan Chen, Zujian Chen, Y. Jin, Dragan Dragas, Leitao Zhang, Barima S. Adjei, Anxun Wang, Yang Dai, Xiaofeng Zhou
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.ppat.1000066
The Uptake of Apoptotic Cells Drives Coxiella burnetii Replication and Macrophage Polarization: A Model for Q Fever Endocarditis
Cited by: 49
Author(s): Marie Benoit, Éric Ghigo, Christian Capo, Didier Raoult, Jean‐Louis Mège
Software Mentions: 1
Published: over 16 years ago
10.3390/ijms22126505
Screen Key Genes Associated with Distraction-Induced Osteogenesis of Stem Cells Using Bioinformatics Methods
Cited by: 2
Author(s): Jishizhan Chen, Jia Hua, Wenhui Song
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.ppat.1000529
Comprehensive Identification of Salmonella enterica Serovar Typhimurium Genes Required for Infection of BALB/c Mice
Cited by: 74
Author(s): Roy R. Chaudhuri, Sarah Peters, Stephen J. Pleasance, Helen Northen, Chrissie Willers, Gavin K. Paterson, Danielle B. Cone, Andrew G. Allen, Paul Owen, Gil Shalom, Dov J. Stekel, Ian G. Charles, Duncan J. Maskell
Software Mentions: 1
Published: over 15 years ago
10.1371/journal.ppat.1000813
Innate Killing of Leishmania donovani by Macrophages of the Splenic Marginal Zone Requires IRF-7
Cited by: 60
Author(s): Rebecca A. Phillips, Mattias Svensson, Naveed Aziz, Asher Maroof, Najmeeyah Brown, Lynette Beattie, Nathalie Signoret, Paul M. Kaye
Software Mentions: 1
Published: over 14 years ago
10.1371/journal.pone.0181812
Reprogramming human gallbladder cells into insulin-producing β-like cells
Cited by: 33
Author(s): Feorillo Galivo, Eric Benedetti, Yuhan Wang, Carl Pelz, Jonathan Schug, Klaus H. Kaestner, Markus Grompe
Software Mentions: 1
Published: over 7 years ago
10.1155/2019/1697913
Plasticity of Drug-Naïve and Vemurafenib- or Trametinib-Resistant Melanoma Cells in Execution of Differentiation/Pigmentation Program
Cited by: 24
Author(s): Małgorzata Czyż, Małgorzata Sztiller-Sikorska, Anna Gajos-Michniewicz, Marta Osrodek, Mariusz L. Hartman
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.pone.0218934
Ticagrelor induces paraoxonase-1 (PON1) and better protects hypercholesterolemic mice against atherosclerosis compared to clopidogrel
Cited by: 10
Author(s): Hasseri Halim, Decha Pinkaew, Preedakorn Chunhacha, Patuma Sinthujaroen, Perumal Thiagarajan, Kenichi Fujise
Software Mentions: 1
Published: over 5 years ago
10.1371/journal.ppat.1003083
A Strong Immune Response in Young Adult Honeybees Masks Their Increased Susceptibility to Infection Compared to Older Bees
Cited by: 70
Author(s): James C. Bull, Eugene V. Ryabov, Gill Prince, Andrew Mead, Cunjin Zhang, Laura Baxter, J. K. Pell, Juliet L. Osborne, Dave Chandler
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pone.0051129
Identification of Putative Rhamnogalacturonan-II Specific Glycosyltransferases in Arabidopsis Using a Combination of Bioinformatics Approaches
Cited by: 16
Author(s): Aline Voxeur, Aurélie André, C. Breton, Patrice Lerouge
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.ppat.1005469
In Vivo Molecular Dissection of the Effects of HIV-1 in Active Tuberculosis
Cited by: 44
Author(s): Lucy Bell, Gabriele Pollara, Pascoe Mellissa, Gillian S. Tomlinson, Rannakoe Lehloenya, Jennifer Roe, Richard Meldau, R F Miller, Alan D. Ramsay, Benjamin M. Chain, Keertan Dheda, Mahdad Noursadeghi
Software Mentions: 1
Published: over 8 years ago
10.1371/journal.ppat.1007315
The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing
Cited by: 47
Author(s): Daniela Begolo, Isabel M. Vincent, Federica Giordani, Ina Pöhner, Michael Witty, T.G. Rowan, Zakaria Bengaly, Kirsten Gillingwater, Yvonne R. Freund, Rebecca C. Wade, Michael P. Barrett, Christine Clayton
Software Mentions: 1
Published: about 6 years ago
10.1371/journal.pone.0042228
Loss of Abdominal Muscle in Pitx2 Mutants Associated with Altered Axial Specification of Lateral Plate Mesoderm
Cited by: 14
Author(s): Diana G. Eng, Hsiao-Yen Ma, Jun Xu, Hung-Ping Shih, Michael Groß, Chrissa Kiouss
Software Mentions: 1
Published: over 12 years ago
10.1371/annotation/121b04a1-0cbb-4e24-8a63-fc9cdd31ec76
Correction: Klf4 Is a Transcriptional Regulator of Genes Critical for EMT, Including Jnk1 (Mapk8)
Cited by: 24
Author(s): Neha Tiwari, Nathalie Meyer-Schaller, Phil Arnold, Helena Antoniadis, Mikhail Pachkov, Erik van Nimwegen, Gerhard Christofori
Software Mentions: 1
Published: about 11 years ago
10.1073/pnas.1912109117
The circadian clock protein REVERBα inhibits pulmonary fibrosis development
Cited by: 50
Author(s): Peter Cunningham, P. J. J. De Meijer, Alicja Nazgiewicz, Simon Anderson, Lee A. Borthwick, James Bagnall, Gareth Kitchen, Monika Lodyga, Nicola Begley, Rajamiyer Venkateswaran, Rajesh Shah, Paul F. Mercer, Hannah J. Durrington, Neil C. Henderson, Karen Piper Hanley, Andrew J. Fisher, Rachel C. Chambers, David A. Bechtold, Julie Gibbs, A. S. I. Loudon, Martin K. Rutter, Boris Hinz, David Ray, John Blaikley
Software Mentions: 1
Published: almost 5 years ago