bioconductor: limma | Projects | Ecosyste.ms: Papers

10.7554/eLife.14926

Polycomb enables primitive endoderm lineage priming in embryonic stem cells
Cited by: 27
Author(s): Robert S. Illingworth, Jurriaan Hölzenspies, Fabian V Roske, Wendy A. Bickmore, Joshua M. Brickman
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0194225

Combined use of protein biomarkers and network analysis unveils deregulated regulatory circuits in Duchenne muscular dystrophy
Cited by: 22
Author(s): Silvia Parolo, Luca Marchetti, Mario Lauria, Karla Misselbeck, Marie‐Pier Scott‐Boyer, Laura Caberlotto, Corrado Priami
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0056632

Using Weakly Conserved Motifs Hidden in Secretion Signals to Identify Type-III Effectors from Bacterial Pathogen Genomes
Cited by: 34
Author(s): Xiaobao Dong, Yongjun Zhang, Ziding Zhang
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0220894

System analysis of cross-talk between nuclear receptors reveals an opposite regulation of the cell cycle by LXR and FXR in human HepaRG liver cells
Cited by: 12
Author(s): Leonore Wigger, Cristina Casals-Casas, Michaël Baruchet, Bao Khanh Trang, Sylvain Pradervand, Aurélien Naldi, Béatrice Desvergne
Software Mentions: 1
Published: about 7 years ago

10.1242/dev.122952

Two Forkhead transcription factors regulate cardiac progenitor specification by controlling the expression of receptors of the fibroblast growth factor and Wnt signaling pathways
Cited by: 10
Author(s): Shaad M. Ahmad, P. Bhattacharyya, Neal Jeffries, Stephen S. Gisselbrecht, Alan M. Michelson
Software Mentions: 1
Published: almost 12 years ago

10.1242/dev.100487

A single allele of Hdac2 but not Hdac1 is sufficient for normal mouse brain development in the absence of its paralog
Cited by: 71
Author(s): Astrid Hagelkrüys, Sabine Lagger, Julia Krahmer, Alexandra Leopoldi, Matthias Artaker, Oliver Pusch, Jürgen Zezula, Simon Weissmann, Yunyun Xie, Christian Schöfer, Michaela Schlederer, Gerald Brosch, Patrick Matthias, Jim Selfridge, Hans Lassmann, Juergen A. Knoblich, Christian Seiser
Software Mentions: 1
Published: over 12 years ago

10.1242/dev.136465

RBOH-mediated ROS production facilitates lateral root emergence in Arabidopsis
Cited by: 134
Author(s): Beata Orman-Ligeza, Boris Parizot, Riet De Rycke, Ana Fernandez, Ellie Himschoot, Frank Van Breusegem, Malcolm J. Bennett, Claire Périlleux, Tom Beeckman, Xavier Draye
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0046243

Transcriptional Profiling of a Yeast Colony Provides New Insight into the Heterogeneity of Multicellular Fungal Communities
Cited by: 30
Author(s): Ana Traven, Amrei Jänicke, Paul F. Harrison, Angavai Swaminathan, Torsten Seemann, Traude H. Beilharz
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0188177

Long 3'UTR of Nurr1 mRNAs is targeted by miRNAs in mesencephalic dopamine neurons
Cited by: 12
Author(s): Luis Alberto Pereira, Roberto Munita, Mauricio González, Marı́a Estela Andrés
Software Mentions: 1
Published: almost 9 years ago

10.1242/dev.168161

Transcriptionally dynamic progenitor populations organised around a stable niche drive axial patterning
Cited by: 43
Author(s): Filip J. Wymeersch, Stavroula Skylaki, Yali Huang, Julia A. Watson, Constantinos Economou, Carylyn Marek-Johnston, Simon R. Tomlinson, Valerie Wilson
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0155191

Maternal Whole Blood Gene Expression at 18 and 28 Weeks of Gestation Associated with Spontaneous Preterm Birth in Asymptomatic Women
Cited by: 47
Author(s): Yujing J. Heng, Craig E. Pennell, Sheila McDonald, Angela Vinturache, Jingxiong Xu, Mary W. F. Lee, Laurent Briollais, Andrew W. Lyon, Donna M. Slater, Alan D. Bocking, Lawrence de Koning, David M. Olson, Siobhan M. Dolan, Suzanne Tough, Stephen J. Lye
Software Mentions: 1
Published: over 10 years ago

10.18632/oncotarget.26370

Limitations of current in vitro models for testing the clinical potential of epigenetic inhibitors for treatment of pediatric ependymoma
Cited by: 7
Author(s): Hazel A. Rogers, Rebecca Chapman, Holly Kings, Julie Allard, Jodie Barron-Hastings, Kristian W. Pajtler, Martin Sill, Stefan M. Pfister, Richard G. Grundy
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12872-020-01701-z

Investigation of the underlying genes and mechanism of familial hypercholesterolemia through bioinformatics analysis
Cited by: 7
Author(s): Dinghui Wang, Bin Liu, Tianhua Xiong, Wenlong Yu, Sheng Qiang
Software Mentions: 1
Published: about 6 years ago

10.1007/s00125-021-05427-1

IGFBP-1 expression is reduced in human type 2 diabetic glomeruli and modulates β1-integrin/FAK signalling in human podocytes
Cited by: 15
Author(s): Abigail C Lay, Lorna J Hale, Holly Stowell-Connolly, Robert J P Pope, Viji Nair, Wenjun Ju, Eva Márquez, Ruth Rollason, Jennifer A. Hurcombe, Bryony Hayes, Timothy Roberts, Lawrence Gillam, Jonathan Allington, Robert G. Nelson, Matthias Kretzler, Jeff M.P. Holly, Claire M Perks, Craig A. McArdle, Gavin I. Welsh, Richard J M Coward
Software Mentions: 1
Published: over 5 years ago

10.1186/s12885-019-5927-3

Estimation of immune cell content in tumor using single-cell RNA-seq reference data
Cited by: 28
Author(s): Xiaoqing Yu, Yian Ann Chen, José R. Conejo-Garcia, Christine H. Chung, Xuefeng Wang
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0176139

Hypomethylating agents synergize with irinotecan to improve response to chemotherapy in colorectal cancer cells
Cited by: 28
Author(s): Anup Sharma, Rajita Vatapalli, Eihab Abdelfatah, K. Wyatt McMahon, Zachary Kerner, Angela A. Guzzetta, Jasvinder Singh, Cynthia A. Zahnow, Stephen B. Baylin, Sashidhar R. Yerram, Yue Hu, Nilofer S. Azad, Nita Ahuja
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0135520

Pharmacokinetics and Pharmacodynamics with Extended Dosing of CC-486 in Patients with Hematologic Malignancies
Cited by: 52
Author(s): Eric Laille, Tao Shi, Guillermo Garcia‐Manero, Christopher R. Cogle, Steven D. Gore, Joel Hetzer, Keshava Kumar, Barry S. Skikne, Kyle J. MacBeth
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0228195

GPCR-induced YAP activation sensitizes fibroblasts to profibrotic activity of TGFβ1
Cited by: 19
Author(s): Katarina Zmajkovicova, Yasmina Bauer, Katalin Menyhart, Marie Schnoebelen, Diego Freti, Maxime Boucher, Bérengère Renault, R. O. Studer, Magdalena Birker‐Robaczewska, Axel Klenk, Oliver Nayler, John Gatfield
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0101802

Differences in miRNA Expression in Early Stage Lung Adenocarcinomas that Did and Did Not Relapse
Cited by: 27
Author(s): Mick D. Edmonds, Christine M. Eischen
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0046673

Dynamics of Membrane Potential Variation and Gene Expression Induced by Spodoptera littoralis, Myzus persicae, and Pseudomonas syringae in Arabidopsis
Cited by: 45
Author(s): Irene Bricchi, Cinzia M. Bertea, Andrea Occhipinti, Ivan A. Paponov, Massimo E. Maffei
Software Mentions: 1
Published: almost 14 years ago

10.1371/journal.pone.0001398

Molecular Characterization of Spontaneous Mesenchymal Stem Cell Transformation
Cited by: 148
Author(s): Daniel Rubio, Sílvia García, Maria F. Paz, Teresa de la Cueva, Luis A. López-Fernández, Alison C. Lloyd, Javier García‐Castro, António Bernad
Software Mentions: 1
Published: almost 19 years ago

10.3390/diagnostics10030177

Predictive Analyses of Prognostic-Related Immune Genes and Immune Infiltrates for Glioblastoma
Cited by: 15
Author(s): Ping Liang, Yi Chai, He Zhao, Guihuai Wang
Software Mentions: 1
Published: over 6 years ago

10.18632/aging.101319

Towards natural mimetics of metformin and rapamycin
Cited by: 67
Author(s): Alexander Aliper, Leslie C. Jellen, Filomeno Cortese, Artemov Av, Darla Karpinsky-Semper, Alexey Moskalev, Andrew G. Swick, Alex Zhavoronkov
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12885-018-4852-1

Development of acquired resistance to lapatinib may sensitise HER2-positive breast cancer cells to apoptosis induction by obatoclax and TRAIL
Cited by: 17
Author(s): Alex J. Eustace, Neil T. Conlon, Martina S.J. McDermott, Brigid C. Browne, Patrick C. O’Leary, Frankie A. Holmes, Virginia Espina, Lance A. Liotta, Joyce O’Shaughnessy, Clair Gallagher, Lorraine O’Driscoll, Sweta Rani, Stephen F. Madden, Neil A. O’Brien, Charles Ginther, Dennis J. Slamon, Naomi Walsh, William M. Gallagher, Radosław Zagożdżon, R. William G. Watson, Norma O’Donovan, John Crown
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0017840

Adjunctive Dexamethasone Affects the Expression of Genes Related to Inflammation, Neurogenesis and Apoptosis in Infant Rat Pneumococcal Meningitis
Cited by: 22
Author(s): C. Blaser, Matthias Wittwer, Denis Grandgirard, Stephen L. Leib
Software Mentions: 1
Published: over 15 years ago

10.1155/2021/7253633

Expression of Four Autophagy-Related Genes Accurately Predicts the Prognosis of Gastrointestinal Cancer in Asian Patients
Cited by: 3
Author(s): Hua Tang, Yan Liang, Shanshan Xu, Rong Xia, Jiacheng Shen, Yuxin Zhang, Xing Gong, Yang Gi Min, Di Zhang, Tai-Yun Zhao, Shoulin Wang, Yi Zhang, Chao Wang
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0061580

Transcriptional and Metabolic Changes Associated to the Infection by Fusarium verticillioides in Maize Inbreds with Contrasting Ear Rot Resistance
Cited by: 49
Author(s): Valeria A. Campos-Bermudez, Carolina M. Fauguel, Marcos A. Tronconi, Paula Casati, Daniel A. Presello, Carlos S. Andreo
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0023682

Comprehensive Assessment of Host Responses to Ionizing Radiation by Nuclear Factor-κB Bioluminescence Imaging-Guided Transcriptomic Analysis
Cited by: 22
Author(s): Chung‐Ta Chang, Lin H, Tin Yun Ho, Chia-Cheng Li, Hsin Yi Lo, Shih-Lu Wu, Yi Huang, Ji An Liang, Chien Yun Hsiang
Software Mentions: 1
Published: about 15 years ago

10.1155/2016/3650909

Toward Noninvasive Diagnosis of IgA Nephropathy: A Pilot Urinary Metabolomic and Proteomic Study
Cited by: 19
Author(s): Michaela Neprašová, Dita Maixnerová, Jan Novák, Colin Reily, Bruce A. Julian, Jan Boron, Petr Novotný, Miloslav Suchánek, Vladimı́r Tesař, Petr Kačer
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0050596

Identification of a Transcription Factor Controlling pH-Dependent Organic Acid Response in Aspergillus niger
Cited by: 22
Author(s): Lars Poulsen, Mikael Rørdam Andersen, Anna Eliasson Lantz, Jette Thykær
Software Mentions: 1
Published: almost 14 years ago

10.1155/2021/4129993

Network Pharmacology Reveals That Resveratrol Can Alleviate COVID-19-Related Hyperinflammation
Cited by: 16
Author(s): Zijian Xiao, Qing Ye, Xiaoling Duan, Tao Xiang
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0013615

Functional Genomics of 5- to 8-Cell Stage Human Embryos by Blastomere Single-Cell cDNA Analysis
Cited by: 67
Author(s): Amparo Galán, David Montaner, Maria E. Póo, Diana Valbuena, Verónica Ruiz, Cristóbal Aguilar-Gallardo, Joaquı́n Dopazo, Carlos Simón
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0117164

Differential Adipose Tissue Gene Expression Profiles in Abacavir Treated Patients That May Contribute to the Understanding of Cardiovascular Risk: A Microarray Study
Cited by: 5
Author(s): Maryam Shahmanesh, Kenneth L. Phillips, Meg Boothby, Jeremy W. Tomlinson
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0206608

Regularization and grouping -omics data by GCA method: A transcriptomic case
Cited by: 3
Author(s): Monika Piwowar, Kinga A. Kocemba‐Pilarczyk, Piotr Piwowar
Software Mentions: 1
Published: almost 8 years ago

10.1155/2020/8847635

A Novel Gene Signature to Predict Survival Time and Incident Ventricular Arrhythmias in Patients with Dilated Cardiomyopathy.
Cited by: 1
Author(s): Chenliang Ge, Yan He
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0089596

Highly Immunoreactive IgG Antibodies Directed against a Set of Twenty Human Proteins in the Sera of Patients with Amyotrophic Lateral Sclerosis Identified by Protein Array
Cited by: 33
Author(s): Caroline May, Eckhard Nordhoff, Swaantje Casjens, Michael Turewicz, Martin Eisenacher, Ralf Gold, Thomas Brüning, Beate Pesch, Christian Stephan, Dirk Woitalla, Botond Penke, Tamás Janáky, Dezső Virók, László Szabó, J. Engelhardt, Helmut E. Meyer
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0097162

Changes in Gene Expression Associated with FTO Overexpression in Mice
Cited by: 32
Author(s): Myrte Merkestein, James S. McTaggart, Sheena Lee, Holger Kramer, Fiona McMurray, Mathilde Lafond, Lily Boutens, Roger D. Cox, Frances M. Ashcroft
Software Mentions: 1
Published: over 12 years ago

10.1155/2018/9369358

Expression of Pentose Phosphate Pathway-Related Proteins in Breast Cancer
Cited by: 30
Author(s): Jong Myung Choi, Eun Sol Kim, Ja Seung Koo
Software Mentions: 1
Published: almost 9 years ago

10.1155/2019/2407067

ELL2 Is Downregulated and Associated with Galactose-Deficient IgA1 in IgA Nephropathy
Cited by: 1
Author(s): Youxia Liu, Jie Zheng, Na Zhao, Junya Jia, Tiekun Yan
Software Mentions: 1
Published: over 7 years ago

10.1186/s12885-020-07184-7

Low dose environmental radon exposure and breast tumor gene expression
Cited by: 5
Author(s): Cheng Peng, Natalie DuPré, Trang VoPham, Yujing J. Heng, Gabrielle M. Baker, Christopher A. Rubadue, Kimberly Glass, Abhijeet R. Sonawane, Oana A. Zeleznik, Peter Kraft, Susan E. Hankinson, A. Heather Eliassen, Jaime E. Hart, Francine Laden, Rulla M. Tamimi
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0073024

IKKα/CHUK Regulates Extracellular Matrix Remodeling Independent of Its Kinase Activity to Facilitate Articular Chondrocyte Differentiation
Cited by: 38
Author(s): Eleonora Olivotto, Miguel Otero, Annalisa Astolfi, Daniela Platano, Angelo Facchini, Stefania Pagani, Flavio Flamigni, Andrea Facchini, Mary B. Goldring, Rosa Maria Borzı̀, Kenneth B. Marcu
Software Mentions: 1
Published: about 13 years ago

10.18632/aging.202320

Identification of the ceRNA networks in α-MSH-induced melanogenesis of melanocytes
Cited by: 12
Author(s): Ling Jiang, Jinhua Huang, Yibo Hu, Lei Li, Yujie Ouyang, Yan Liu, Hui Li, Si Li, Lun Yang, Yan Yang, Lihua Huang, Hong Xiang, Rong Xiao, Jing Chen, Qinghai Zeng
Software Mentions: 1
Published: almost 6 years ago

10.1155/2021/8889569

Differentially Expressed Circular RNA Profile in an Intracranial Aneurysm Group Compared with a Healthy Control Group
Cited by: 8
Author(s): Yonggang Ma, Baoqing Zhang, Dong Zhang, Shuo Wang, Maogui Li, Jizong Zhao
Software Mentions: 1
Published: over 5 years ago

10.1242/dmm.027953

Characterization of Drosophila saposin-related mutants as a model for lysosomal sphingolipid storage diseases
Cited by: 11
Author(s): Julia Sellin, Heike Schulze, Marie Paradis, Dominic Gosejacob, Cyrus Papan, Andrej Shevchenko, Olympia Psathaki, Achim Paululat, Melanie Thielisch, Konrad Sandhoff, Michael Hoch
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0018640

Identification of Prognostic Molecular Features in the Reactive Stroma of Human Breast and Prostate Cancer
Cited by: 137
Author(s): Anne Planche, Marina Bacac, Paolo Provero, Carlo Fusco, Mauro Delorenzi, Jean-Christophe Stehle, Ivan Stamenkovic
Software Mentions: 1
Published: over 15 years ago

10.1242/dmm.029678

Pumilio2 deficient mice show a predisposition for epilepsy
Cited by: 39
Author(s): Philipp Follwaczny, Rico Schieweck, Therese Riedemann, Antonia Demleitner, Tobias Straub, Anna H. Klemm, Martin Bilban, Bernd Sutor, Bastian Popper, Michael Kiebler
Software Mentions: 1
Published: almost 10 years ago

10.1242/dmm.022277

Urine-sample-derived human induced pluripotent stem cells as a model to study PCSK9-mediated autosomal dominant hypercholesterolemia
Cited by: 30
Author(s): Karim Si‐Tayeb, Salam Idriss, Benoite Champon, Amandine Caillaud, Matthieu Pichelin, Lucie Arnaud, Patricia Lemarchand, Cédric Le May, Kazem Zibara, Bertrand Cariou
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0104650

A Novel Glycated Hemoglobin A1c-Lowering Traditional Chinese Medicinal Formula, Identified by Translational Medicine Study
Cited by: 10
Author(s): Hsin Yi Lo, Chien Yun Hsiang, Tsai‐Chung Li, Hui Huang, Jaw Chyun Chen, Tin Yun Ho
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0006952

Gene Expression Profiling in Cells with Enhanced γ-Secretase Activity
Cited by: 6
Author(s): Alexandra I. Magold, Matthias Cacquevel, Patrick C. Fraering
Software Mentions: 1
Published: about 17 years ago

10.1371/journal.pone.0125013

Characterization of Differentially Expressed Genes Involved in Pathways Associated with Gastric Cancer
Cited by: 54
Author(s): Hao Li, Beiqin Yu, Jianfang Li, Liping Su, Min Yan, Jun Zhang, Chen Li, Zhenggang Zhu, Bingya Liu
Software Mentions: 1
Published: over 11 years ago

10.1186/s12885-018-4251-7

Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups
Cited by: 15
Author(s): Chris Lauber, Barbara Klink, Michael Seifert
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0002548

Novel MicroRNA Candidates and miRNA-mRNA Pairs in Embryonic Stem (ES) Cells
Cited by: 48
Author(s): Peili Gu, Jeffrey G. Reid, Xiaolian Gao, Chad A. Shaw, Chad J. Creighton, Peter L. Tran, Xiaochuan Zhou, Rafal Drabek, David L. Steffen, David M. Hoang, Michelle K. Weiss, A.O. Naghavi, Jad El-daye, Mahjabeen F. Khan, Glen B. Legge, David A. Wheeler, Richard A. Gibbs, Jonathan Miller, Austin J. Cooney, Preethi H. Gunaratne
Software Mentions: 1
Published: over 18 years ago

10.1186/s12885-016-2355-5

Progesterone receptor blockade in human breast cancer cells decreases cell cycle progression through G2/M by repressing G2/M genes
Cited by: 12
Author(s): Susan E. Clare, Akash Gupta, Mi Ran Choi, Manish Ranjan, Oukseub Lee, Jun Wang, David Ivancic, Julie Kim, Seema A. Khan
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0222513

PBMCs transcriptome profiles identified breed-specific transcriptome signatures for PRRSV vaccination in German Landrace and Pietrain pigs
Cited by: 9
Author(s): M. S. Islam, Christiane Neuhoff, Sharmin Aqter Rony, Christine Große‐Brinkhaus, Muhammad Jasim Uddin, Michael Hölker, Dawit Tesfaye, Ernst Tholen, K. Schellander, Maren Julia Pröll‐Cornelissen
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0193335

Molecular adaptations to phosphorus deprivation and comparison with nitrogen deprivation responses in the diatom Phaeodactylum tricornutum
Cited by: 68
Author(s): Leila Alipanah, Per Winge, Jens Rohloff, Javad Najafi, Tore Brembu, Atle M. Bones
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0013606

Yeast Biological Networks Unfold the Interplay of Antioxidants, Genome and Phenotype, and Reveal a Novel Regulator of the Oxidative Stress Response
Cited by: 15
Author(s): José M. Otero, Manos A. Papadakis, D.B.R.K. Gupta Udatha, Jens Nielsen, Gianni Panagiotou
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0032875

Skin Regeneration in Adult Axolotls: A Blueprint for Scar-Free Healing in Vertebrates
Cited by: 199
Author(s): Ashley W. Seifert, James R. Monaghan, S. Randal Voss, Malcolm Maden
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0128230

Genome-Wide Transcriptome Directed Pathway Analysis of Maternal Pre-Eclampsia Susceptibility Genes
Cited by: 52
Author(s): Hannah Ee Juen Yong, Phillip E. Melton, Matthew P. Johnson, Katy A. Freed, Bill Kalionis, Padma Murthi, Shaun P. Brennecke, Rosemary Keogh, Eric K. Moses
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0149263

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis
Cited by: 18
Author(s): Michael Roemer, Johannes Eichner, Andreas Dräger, Clemens Wrzodek, Finja Wrzodek, Andreas Zell
Software Mentions: 1
Published: over 10 years ago

10.1186/s12885-019-5838-3

Novel significant stage-specific differentially expressed genes in hepatocellular carcinoma
Cited by: 52
Author(s): Arjun Sarathi, Ashok Palaniappan
Software Mentions: 1
Published: over 7 years ago

10.1016/j.ebiom.2019.03.072

Identification of novel differentially methylated sites with potential as clinical predictors of impaired respiratory function and COPD
Cited by: 19
Author(s): Mairead Lesley Bermingham, Richard M Martin, Riccardo E. Marioni, Stewart W. Morris, Konrad Rawlik, Yanni Zeng, Archie Campbell, Paul Redmond, Heather C. Whalley, Mark Adams, Caroline Hayward, Ian J. Deary, David J. Porteous, Andrew M. McIntosh, Kathryn Evans
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0066278

Differentially Expressed Androgen-Regulated Genes in Androgen-Sensitive Tissues Reveal Potential Biomarkers of Early Prostate Cancer
Cited by: 28
Author(s): Dogus Murat Altintas, Nathalie Allioli, Myriam Decaussin, Simon Bernard, A. Ruffion, Jacques Samarut, Virginie Vlaeminck-Guillem
Software Mentions: 1
Published: over 13 years ago

10.1186/s12885-021-07959-6

Integrative genomic expression analysis reveals stable differences between lung cancer and systemic sclerosis
Cited by: 0
Author(s): Heng Li, Liping Ding, Xiaoping Hong, Yulan Chen, Rui Liao, Tingting Wang, Shuhui Meng, Zhuhua Jiang, Dongzhou Liu
Software Mentions: 1
Published: over 5 years ago

10.15252/embj.2020106272

Cellular stress promotes NOD1/2‐dependent inflammation via the endogenous metabolite sphingosine‐1‐phosphate
Cited by: 32
Author(s): Gang Pei, Joanna Żyła, Lichun He, Pedro Moura-Alves, Heidrun Steinle, Philippe Saikali, Laura Lozza, Natalie E. Nieuwenhuizen, January Weiner, Hans-Joachim Mollenkopf, Kornelia Ellwanger, Christine Arnold, Mojie Duan, Yulia A. Dagil, Мikhail Pashenkov, Ivo Gomperts Boneca, Thomas A. Kufer, Anca Dorhoi, Stefan H. E. Kaufmann
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0124340

Differentially Expressed MicroRNAs in Postpartum Breast Cancer in Hispanic Women
Cited by: 22
Author(s): J. Muñoz-Rodríguez, Lukáš Vrba, Bernard W. Futscher, Chengcheng Hu, Ian K. Komenaka, María Mercedes Meza-Montenegro, Luis Enrique Gutiérrez-Millán, Adrián Daneri‐Navarro, Patricia A. Thompson, Marı́a Elena Martı́nez
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0012882

Gene Expression Profiles of Colonic Mucosa in Healthy Young Adult and Senior Dogs
Cited by: 7
Author(s): Dong Yong Kil, Brittany M. Vester Boler, Carolyn J. Apanavicius, Lawrence B. Schook, Kelly S. Swanson
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pone.0133607

Transcriptional Response of Human Neurospheres to Helper-Dependent CAV-2 Vectors Involves the Modulation of DNA Damage Response, Microtubule and Centromere Gene Groups
Cited by: 9
Author(s): Stefania Piersanti, Romina Burla, Valerio Licursi, Catarina Brito, Mattia La Torre, Paula M. Alves, Daniel Simão, Carla Mottini, Sara Salinas, Rodolfo Negri, Enrico Tagliafico, Eric J. Kremer, Isabella Saggio
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0034659

Major Cellular and Physiological Impacts of Ocean Acidification on a Reef Building Coral
Cited by: 234
Author(s): Paulina Kaniewska, Paul Campbell, David I. Kline, Mauricio Rodríguez-Lanetty, David J. Miller, Sophie Dove, Ove Høegh-Guldberg
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0077627

PhysioSpace: Relating Gene Expression Experiments from Heterogeneous Sources Using Shared Physiological Processes
Cited by: 17
Author(s): Michael Lenz, Bernhard Schuldt, Franz‐Josef Müller, Andreas Schuppert
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0161129

COPD Exacerbation Biomarkers Validated Using Multiple Reaction Monitoring Mass Spectrometry
Cited by: 17
Author(s): Janice M. Leung, Virginia Chen, Zsuzsanna Hollander, Darlene Dai, Scott J. Tebbutt, Shawn D. Aaron, Kathy L. Vandemheen, Stephen I. Rennard, J. Mark FitzGerald, Prescott G. Woodruff, Stephen C. Lazarus, John E. Connett, Harvey O. Coxson, Bruce E. Miller, Christoph H. Borchers, Bruce M. McManus, Raymond T. Ng, Don D. Sin
Software Mentions: 1
Published: about 10 years ago

10.15252/embj.201695476

Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation
Cited by: 26
Author(s): Nicola Festuccia, Florian Halbritter, Andrea Corsinotti, Alessia Gagliardi, Douglas Colby, Simon R. Tomlinson, Ian Chambers
Software Mentions: 1
Published: about 8 years ago

10.15252/embj.201386874

Nuclear <scp>ARRB</scp> 1 induces pseudohypoxia and cellular metabolism reprogramming in prostate cancer
Cited by: 54
Author(s): Vincent Zecchini, Basetti Madhu, Roslin Russell, Nelma Pértega‐Gomes, Anne Y. Warren, Edoardo Gaude, Joana Borlido, Rory Stark, Heather Ireland-Zecchini, Roheet Bantval Rao, Helen E. Scott, Joan Boren, Charles E. Massie, Mohammad Asim, Kevin M. Brindle, John R. Griffiths, Christian Frezza, David E. Neal, Ian G. Mills
Software Mentions: 1
Published: over 12 years ago

10.18632/oncotarget.26776

The transcriptomic response to irinotecan in colon carcinoma bearing mice preconditioned by fasting
Cited by: 5
Author(s): F. Jongbloed, Sander A. Huisman, Harry van Steeg, Jeroen L. A. Pennings, Jan N.M. IJzermans, Martijn E.T. Dollé, Ron W. F. de Bruin
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0002141

Distinctive Patterns of MicroRNA Expression Associated with Karyotype in Acute Myeloid Leukaemia
Cited by: 250
Author(s): Amanda Dixon‐McIver, Philip East, Charles A. Mein, Jean‐Baptiste Cazier, Gael Molloy, Tracy Chaplin, T. Andrew Lister, Bryan D. Young, Silvana Debernardi
Software Mentions: 1
Published: over 18 years ago

10.7554/eLife.10592

TRAF2 regulates TNF and NF-κB signalling to suppress apoptosis and skin inflammation independently of Sphingosine kinase 1
Cited by: 70
Author(s): Nima Etemadi, Michaël Chopin, Holly Anderton, Maria C. Tanzer, James A Rickard, Waruni Abeysekera, Cathrine Hall, Sukhdeep K Spall, Bing Wang, Ye Xiong, Timothy Hla, Stuart M. Pitson, Claudine S. Bonder, Wendy Wei-Lynn Wong, Matthias Ernst, Gordon K. Smyth, David L. Vaux, Stephen L. Nutt, Ueli Nachbur, John Silke
Software Mentions: 1
Published: almost 11 years ago

10.18632/aging.103460

Comprehensive characterization of the tumor microenvironment for assessing immunotherapy outcome in patients with head and neck squamous cell carcinoma
Cited by: 6
Author(s): Jian Zhang, Xi Zhong, Huali Jiang, Hualong Jiang, Tao Xie, Yunhong Tian, Rong Li, Baiyao Wang, Jiexia Zhang, Yawei Yuan
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0068630

Methylation of the Claudin 1 Promoter Is Associated with Loss of Expression in Estrogen Receptor Positive Breast Cancer
Cited by: 42
Author(s): Francescopaolo Di Cello, Leslie Cope, Huili Li, Jana Jeschke, Wei Wang, Stephen B. Baylin, Cynthia A. Zahnow
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0066307

Gene Expression Profiling of Gliadin Effects on Intestinal Epithelial Cells Suggests Novel Non-Enzymatic Functions of Pepsin and Trypsin
Cited by: 11
Author(s): Amarjit Parmar, Dario Greco, Jarkko I. Venäläinen, Massimiliano Gentile, Emma Dukes, Päivi Saavalainen
Software Mentions: 1
Published: over 13 years ago

10.1002/emmm.201303123

Inhibition of phosphodiesterase‐4 promotes oligodendrocyte precursor cell differentiation and enhances <scp>CNS</scp> remyelination
Cited by: 45
Author(s): Yasir Ahmed Syed, Alexandra Baer, Matthias P. Hofer, Ginez A. González, Jon Rundle, Szymon Myrta, Jeffrey K. Huang, Chao Zhao, Moritz J. Rossner, Matthew Trotter, Gert Lubec, Robin J.M. Franklin, Mark R. Kotter
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0156151

Targeting Serglycin Prevents Metastasis in Murine Mammary Carcinoma
Cited by: 19
Author(s): Ananya Roy, Julia Femel, Elisabeth J. M. Huijbers, Dorothe Spillmann, Erik Larsson, Maria Ringvall, Anna-Karin Olsson, Magnus Åbrink
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0127498

Englerin A Agonizes the TRPC4/C5 Cation Channels to Inhibit Tumor Cell Line Proliferation
Cited by: 80
Author(s): Cheryl Carson, Pichai Raman, Jennifer Tullai, Lei Xu, Martin Hénault, Emily Thomas, Suresh Yeola, Jianmin Lao, Mark J. McPate, J. Martin Verkuyl, George Marsh, Jason Sarber, Adam Amaral, Scott Bailey, Danuta Lubicka, Helen Trinh Pham, Nicolette Miranda, Jian Ding, Hui Tang, Haisong Ju, Pamela Tranter, Nan Ji, Philipp Krastel, Rishi K. Jain, Andrew Schumacher, Joseph Loureiro, Elizabeth George, Giuliano Berellini, Nathan T. Ross, Simon M. Bushell, Gül Erdemli, Jonathan M. Solomon
Software Mentions: 1
Published: over 11 years ago

10.15252/emmm.201809960

Non‐canonical <scp>cM</scp> et regulation by vimentin mediates Plk1 inhibitor–induced apoptosis
Cited by: 16
Author(s): Ratnakar Singh, Shaohua Peng, Pavitra Viswanath, Vaishnavi Sambandam, Ли Шен, Xiayu Rao, Bingliang Fang, Jing Wang, Faye M. Johnson
Software Mentions: 1
Published: over 7 years ago

10.1080/21623945.2020.1795434

Integrative analyses of biomarkers and pathways for adipose tissue after bariatric surgery
Cited by: 17
Author(s): Yingshan Liu, Jing Jin, Yanshan Chen, Chuna Chen, Zhenguo Chen, Lingling Xu
Software Mentions: 1
Published: almost 7 years ago

10.18632/aging.102857

Adipose-derived mesenchymal stem cells-derived exosome-mediated microRNA-342-5p protects endothelial cells against atherosclerosis
Cited by: 52
Author(s): Xiaohui Xing, Zhongchen Li, Xin Yang, Mengyou Li, Chao Liu, Yingxin Pang, Zhang Liyong, Xueyuan Li, Guangcun Liu, Yi Xiao
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0029457

Convergent Differential Regulation of Parvalbumin in the Brains of Vocal Learners
Cited by: 42
Author(s): Erina Hara, Miriam V. Rivas, James M. Ward, Kazuo Okanoya, Erich D. Jarvis
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0020043

Differential Proteomics in Dequeened Honeybee Colonies Reveals Lower Viral Load in Hemolymph of Fertile Worker Bees
Cited by: 21
Author(s): Dries Cardoen, Ulrich Ernst, Matthias Van Vaerenbergh, Bart Boerjan, Dirk C. de Graaf, Tom Wenseleers, Liliane Schoofs, Peter Verleyen
Software Mentions: 1
Published: over 15 years ago

10.1002/emmm.201303581

HES6 drives a critical <scp>AR</scp> transcriptional programme to induce castration‐resistant prostate cancer through activation of an <scp>E</scp>2<scp>F</scp>1‐mediated cell cycle network
Cited by: 63
Author(s): Antonio Ramos-Montoya, Alastair Lamb, Roslin Russell, Thomas Carroll, Sarah Jurmeister, Núria Galeano-Dalmau, Charles E. Massie, Joan Boren, Hélène Bon, Vassiliki Théodorou, Maria Vias, Greg L. Shaw, Naomi L. Sharma, Helen Ross-Adams, Helen E. Scott, Sarah L. Vowler, William J. Howat, Anne Y. Warren, Richard Wooster, Ian G. Mills, David E. Neal
Software Mentions: 1
Published: over 12 years ago

10.1186/s12885-017-3100-4

The prognostic utility of the transcription factor SRF in docetaxel-resistant prostate cancer: in-vitro discovery and in-vivo validation
Cited by: 14
Author(s): Dara Lundon, Aidan Boland, Maria Prencipe, Grace Hurley, Amanda O’Neill, Elaine W. Kay, Sinéad Aherne, Padraig Doolan, Stephen F. Madden, Martin Clynes, Colm Morrissey, John M. Fitzpatrick, R. William G. Watson
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0064144

Generation and Characterization of an Nxf7 Knockout Mouse to Study NXF5 Deficiency in a Patient with Intellectual Disability
Cited by: 7
Author(s): Lieselot Vanmarsenille, Johan Verbeeck, Stefanie Belet, Anton Roebroek, Tom Van de Putte, Joke Nevelsteen, Zsuzsanna Callaerts-Végh, Rudi D’Hooge, Peter Marynen, Guy Froyen
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0082516

Epigenetic Regulation of Depot-Specific Gene Expression in Adipose Tissue
Cited by: 33
Author(s): Sandra Gehrke, Bodo Brueckner, Andreas Schepky, Johannes Klein, Alexander Iwen, Thomas C. G. Bosch, Horst Wenck, Marc Winnefeld, Sabine Hagemann
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0117471

Genome Wide Nucleosome Mapping for HSV-1 Shows Nucleosomes Are Deposited at Preferred Positions during Lytic Infection
Cited by: 20
Author(s): Jae-Wook Oh, Iryna Sanders, Eric Z. Chen, Hongzhe Li, John W. Tobias, R. Benjamin Isett, Sindura Penubarthi, Hao Sun, Don A. Baldwin, Nigel W. Fraser
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0005292

Short-Term Striatal Gene Expression Responses to Brain-Derived Neurotrophic Factor Are Dependent on MEK and ERK Activation
Cited by: 51
Author(s): Özgün Gökçe, Heike Runne, Aléxandre Kuhn, Ruth Lüthi-Carter
Software Mentions: 1
Published: over 17 years ago

10.1371/journal.pone.0030313

Mesenchymal Transition and PDGFRA Amplification/Mutation Are Key Distinct Oncogenic Events in Pediatric Diffuse Intrinsic Pontine Gliomas
Cited by: 205
Author(s): Stéphanie Puget, Cathy Philippe, Dorine A. Bax, Bastien Job, Pascale Varlet, Marie‐Pierre Junier, Felipe Andreiuolo, Dina Carvalho, Ricardo Reis, Léa Guerrini-Rousseau, Thomas Roujeau, Philippe Dessen, Catherine Richon, Vladimir Lazar, Gwénaël Le Teuff, Christian Sainte‐Rose, Birgit Geoerger, Gilles Vassal, Chris Jones, Jacques Grill
Software Mentions: 1
Published: over 14 years ago

10.15252/emmm.202012724

A novel P2X2‐dependent purinergic mechanism of enteric gliosis in intestinal inflammation
Cited by: 27
Author(s): Reiner Schneider, Patrick Leven, Tim R. Glowka, Ivan Kuzmanov, Mariola Lysson, Bianca Schneiker, Anna Miesen, Younis Baqi, Claudia Spanier, Iveta Grants, Elvio Mazzotta, Egina C. Villalobos-Hernández, Jörg C. Kalff, Christa E. Müller, Fedias L. Christofi, Sven Wehner
Software Mentions: 1
Published: almost 6 years ago

10.15252/emmm.201707814

Mutant <scp>CTNNB</scp> 1 and histological heterogeneity define metabolic subtypes of hepatoblastoma
Cited by: 35
Author(s): Stefania Crippa, Pierre‐Benoit Ancey, Jessica Vázquez, Paolo Angelino, Anne‐Laure Rougemont, Catherine Guettier, Vincent Zoete, Mauro Delorenzi, Olivier Michielin, Etienne Meylan
Software Mentions: 1
Published: about 9 years ago

10.7554/eLife.48625

PUMILIO, but not RBMX, binding is required for regulation of genomic stability by noncoding RNA NORAD
Cited by: 50
Author(s): Mahmoud M. Elguindy, Florian Kopp, Mohammad Goodarzi, Frederick Rehfeld, Anu Thomas, Tsung Cheng Chang, Joshua T. Mendell
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0168760

MicroRNA and Transcription Factor Gene Regulatory Network Analysis Reveals Key Regulatory Elements Associated with Prostate Cancer Progression
Cited by: 40
Author(s): Mehdi Sadeghi, Bijan Ranjbar, Mohamad Reza Ganjalikhany, Faiz M. Khan, Ulf Schmitz, Olaf Wolkenhauer, Satish Gupta
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0069660

Four Jointed Box 1 Promotes Angiogenesis and Is Associated with Poor Patient Survival in Colorectal Carcinoma
Cited by: 27
Author(s): Nicole T. Al-Greene, Anna L. Means, Pengcheng Lu, Aixiang Jiang, Carl Schmidt, A. Bapsi Chakravarthy, Nipun B. Merchant, Mary Kay Washington, Bing Zhang, Yu Shyr, Natasha G. Deane, R. Daniel Beauchamp
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0168899

Long-Term Transcriptomic Effects of Prebiotics and Synbiotics Delivered In Ovo in Broiler Chickens
Cited by: 39
Author(s): Anna Sławińska, Arkadiusz Płowiec, Maria Siwek, Marcin Jaroszewski, Marek Bednarczyk
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12885-020-07100-z

Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer
Cited by: 6
Author(s): Maryam Soleimani Dodaran, Simone Borgoni, Emre Sofyalı, Pernette J. Verschure, Stefan Wiemann, Perry D. Moerland, Antoine H. C. van Kampen
Software Mentions: 1
Published: about 6 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776