bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1000176

Somatic Pairing of Chromosome 19 in Renal Oncocytoma Is Associated with Deregulated ELGN2-Mediated Oxygen-Sensing Response
Cited by: 56
Author(s): Julie Koeman, Ryan C. Russell, Min‐Han Tan, David Petillo, Michael Westphal, Katherine Koelzer, Julie Metcalf, Zhongfa Zhang, Daisuke Matsuda, Karl Dykema, Heather L. Houseman, Eric J. Kort, Laura L. Furge, Richard J. Kahnoski, Stéphane Richard, Annick Vieillefond, Pamela J. Swiatek, Bin Tean Teh, Michael Ohh, Kyle A. Furge
Software Mentions: 1
Published: about 16 years ago

10.1371/journal.pgen.1002727

Regulating repression: roles for the sir4 N-terminus in linker DNA protection and stabilization of epigenetic states.
Cited by: 18
Author(s): Stephanie Kueng, Monika Tsai-Pflugfelder, Mariano Oppikofer, Helder Ferreira, Emma J. Roberts, Chinyen Tsai, Tim-Christoph Roloff, Ragna Sack, Susan M. Gasser
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pgen.1007484

GROWTH-REGULATING FACTOR 9 negatively regulates arabidopsis leaf growth by controlling ORG3 and restricting cell proliferation in leaf primordia
Cited by: 52
Author(s): Mohammad Amin Omidbakhshfard, Ushio Fujikura, Justyna Jadwiga Olas, Xue Gong, Salma Balazadeh, Bernd Mueller‐Roeber
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pgen.1002372

Heritable Epigenetic Variation among Maize Inbreds
Cited by: 140
Author(s): Steven R. Eichten, Ruth A. Swanson-Wagner, James C. Schnable, Amanda J. Waters, Peter J. Hermanson, Sanzhen Liu, Cheng‐Ting Yeh, Yi Jia, Karla C Gendler, Michael Freeling, Patrick S. Schnable, Matthew Vaughn, Nathan M. Springer
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pntd.0006863

A gene expression comparison of Trypanosoma brucei and Trypanosoma congolense in the bloodstream of the mammalian host reveals species-specific adaptations to density-dependent development
Cited by: 40
Author(s): Eleanor Silvester, Alasdair Ivens, Keith R. Matthews
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0025708

Effects of Hormone Agonists on Sf9 Cells, Proliferation and Cell Cycle Arrest
Cited by: 19
Author(s): Maeva Giraudo, Jérôme Califano, Frédérique Hilliou, Trang Tran, Nathalie Taquet, René Feyereisen, Gaëlle Le Goff
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0120337

MicroRNAs Are Part of the Regulatory Network that Controls EGF Induced Apoptosis, Including Elements of the JAK/STAT Pathway, in A431 Cells
Cited by: 22
Author(s): Ibrahim O. Alanazi, Peter Hoffmann, David L. Adelson
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0067057

Cystatin SN Upregulation in Patients with Seasonal Allergic Rhinitis
Cited by: 39
Author(s): Yoshimasa Imoto, Tohru Tokunaga, Yuri Matsumoto, Yuko Hamada, Manabu Ono, Tetsuji Yamada, Yatsuji Ito, Tadao Arinami, Mitsuhiro Okano, Emiko Noguchi, Shigeharu Fujieda
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0046961

Gene and Genome Parameters of Mammalian Liver Circadian Genes (LCGs)
Cited by: 10
Author(s): Gang Wu, Jiang Zhu, Fuhong He, Weiwei Wang, Songnian Hu, Jun Yu
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0004427

Detection of Gene Expression in an Individual Cell Type within a Cell Mixture Using Microarray Analysis
Cited by: 16
Author(s): Penelope A Bryant, Gordon K. Smyth, Roy M. Robins-Browne, Nigel Curtis
Software Mentions: 1
Published: almost 16 years ago

10.1371/journal.pone.0104379

Identification of Candidate Genes Associated with Leaf Senescence in Cultivated Sunflower (Helianthus annuus L.)
Cited by: 21
Author(s): Sebastián Moschen, Sofía A. Bengoa Luoni, Norma Paniego, H. Esteban Hopp, Guillermo A. A. Dosio, Paula Fernández, Ruth Amelia Heinz
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0172832

Genome-wide effects of MELK-inhibitor in triple-negative breast cancer cells indicate context-dependent response with p53 as a key determinant
Cited by: 24
Author(s): Marisa Simon, Fahmi Mesmar, Luísa A. Helguero, Cecilia Williams
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0175473

Molecular analysis of Culex quinquefasciatus larvae responses to Lysinibacillus sphaericus Bin toxin
Cited by: 9
Author(s): Chontida Tangsongcharoen, Natapong Jupatanakul, Boonhiang Promdonkoy, George Dimopoulos, Panadda Boonserm
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0137360

Small RNAs and Gene Network in a Durable Disease Resistance Gene—Mediated Defense Responses in Rice
Cited by: 19
Author(s): Hanming Hong, Yanyan Liu, Haitao Zhang, Jinghua Xiao, Xianghua Li, Shiping Wang
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0142646

Dynamic Bayesian Network Modeling of the Interplay between EGFR and Hedgehog Signaling
Cited by: 15
Author(s): Holger Fröhlich, Gloria Bahamondez, Frank Götschel, Ulrike Korf
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0149896

Prediction of Candidate Drugs for Treating Pancreatic Cancer by Using a Combined Approach
Cited by: 6
Author(s): Yanfen Ma, Jian Hu, Ning Zhang, Xinran Dong, Ying Liu, Bo Yang, Weidong Tian, Xiaoqin Wang
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0080741

Prognostic Value of PLAGL1-Specific CpG Site Methylation in Soft-Tissue Sarcomas
Cited by: 12
Author(s): Anne-Lise Peille, Véronique Brouste, Audrey Kauffmann, Pauline Lagarde, Valérie Le Morvan, Jean‐Michel Coindre, Frédéric Chibon, Lucie Bresson
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0066229

Transcriptional Analysis Reveals Gender-Specific Changes in the Aging of the Human Immune System
Cited by: 51
Author(s): Saara Marttila, Juulia Jylhävä, Tapio Nevalainen, Matti Nykter, Marja Jylhä, Antti Hervonen, Liina Tserel, Pärt Peterson, Mikko Hurme
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0118198

A Regression-Based Differential Expression Detection Algorithm for Microarray Studies with Ultra-Low Sample Size
Cited by: 7
Author(s): Daniel Vasiliu, Samuel Clamons, Molly J. McDonough, Brian Rabe, Margaret S. Saha
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0088844

Is Transcriptomic Regulation of Berry Development More Important at Night than During the Day?
Cited by: 38
Author(s): Markus Rienth, Laurent Torregrosa, Mary T. Kelly, Nathalie Luchaire, Anne Pellegrino, Jérôme Grimplet, Charles Romieu
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0050682

Genome-Wide Analysis of the Pho Regulon in a pstCA Mutant of Citrobacter rodentium
Cited by: 9
Author(s): Catherine Cheng, Matthew J. Wakefield, Jiyeon Yang, Marija Tauschek, Roy M. Robins-Browne
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0078931

Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes
Cited by: 30
Author(s): Fabrício Ramon Lopes, Daudi Jjingo, Carlos R. M. da Silva, Alan Carvalho Andrade, Pierre Marraccini, J. B. Teixeira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, Luiz Filipe Protásio Pereira, André Luís Laforga Vanzela, Lu Wang, King Jordan, Claudia M. A. Carareto
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0094621

Evaluation of Cancer Stem Cell Markers CD133, CD44, CD24: Association with AKT Isoforms and Radiation Resistance in Colon Cancer Cells
Cited by: 172
Author(s): Sara Häggblad Sahlberg, Diana Spiegelberg, Bengt Glimelius, Bo Stenerlöw, Marika Nestor
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0075556

Live Attenuated Rev-Independent Nef¯SIV Enhances Acquisition of Heterologous SIVsmE660 in Acutely Vaccinated Rhesus Macaques
Cited by: 7
Author(s): Nagadenahalli B. Siddappa, Mila Ayash-Rashkovsky, Victor G. Kramer, Sandra J. Lee, Mick Correll, Francis J. Novembre, François Villinger, Welkin E. Johnson, Agneta von Gegerfelt, Barbara K. Felber, Ruth M. Ruprecht
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0103744

IGF2 Promotes Growth of Adrenocortical Carcinoma Cells, but Its Overexpression Does Not Modify Phenotypic and Molecular Features of Adrenocortical Carcinoma
Cited by: 39
Author(s): Marine Guillaud‐Bataille, Bruno Ragazzon, Aurélien de Reyniès, Claire Chevalier, Isabelle Francillard, Olivia Barreau, Virginie Steunou, Johann Guillemot, Frédérique Tissier, Marthe Rizk-Rabin, Fernande René-Corail, Abir Al Ghuzlan, Guillaume Assié, Xavier Bertagna, Éric Baudin, Yves Le Bouc, Jérôme Bertherat, Éric Clauser
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0093713

Gonadotropin-Releasing Hormone Agonists Sensitize, and Resensitize, Prostate Cancer Cells to Docetaxel in a p53-Dependent Manner
Cited by: 12
Author(s): Roberta M. Moretti, Marina Montagnani Marelli, Deanne Taylor, Paolo G.V. Martini, Monica Marzagalli, Patrizia Limonta
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0171142

Identification of marginal causal relationships in gene networks from observational and interventional expression data
Cited by: 1
Author(s): Gilles Monneret, Florence Jaffrézic, Andrea Rau, Tatiana Zerjal, Grégory Nuel
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0205602

A genomic ruler to assess oncogenic transition between breast tumor and stroma
Cited by: 6
Author(s): Shubhada Dhage, Amanda Ernlund, Kelly V. Ruggles, Deborah Axelrod, Russell S. Berman, Daniel F. Roses, Robert J. Schneider
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0039088

Genome-Wide Profiling of Pluripotent Cells Reveals a Unique Molecular Signature of Human Embryonic Germ Cells
Cited by: 21
Author(s): Nikta Pashai, Haiping Hao, Angelo H. All, Siddharth Gupta, Raghothama Chaerkady, Alejandro De Los Angeles, John D. Gearhart, Candace L. Kerr
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0031081

Genome-Wide Analysis of the Complex Transcriptional Networks of Rice Developing Seeds
Cited by: 81
Author(s): Liang‐Jiao Xue, Jingjing Zhang, Xue Hou
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0060665

Transcriptomic Analysis of Streptomyces coelicolor Differentiation in Solid Sporulating Cultures: First Compartmentalized and Second Multinucleated Mycelia Have Different and Distinctive Transcriptomes
Cited by: 41
Author(s): Paula Yagüe, Antonio Rodríguez‐García, María Teresa López-García, Juan F. Martı́n, Beatriz Rioseras, Jesús Sánchez, Ángel Manteca
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0024004

Gene Expression and Biological Pathways in Tissue of Men with Prostate Cancer in a Randomized Clinical Trial of Lycopene and Fish Oil Supplementation
Cited by: 53
Author(s): Mark Jesus M. Magbanua, Ritu Roy, Eduardo V. Sosa, Vivian Weinberg, Scott Federman, Michael D. Mattie, Millie Hughes‐Fulford, Jeff Simko, Katsuto Shinohara, Christopher M. Haqq, Peter R. Carroll, June M. Chan
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0110065

AtRD22 and AtUSPL1, Members of the Plant-Specific BURP Domain Family Involved in Arabidopsis thaliana Drought Tolerance
Cited by: 66
Author(s): Vokkaliga T. Harshavardhan, Lê Văn Sơn, Christiane Seiler, Astrid Junker, Kathleen Weigelt‐Fischer, Christian Klukas, Thomas Altmann, Nese Sreenivasulu, Helmut Bäumlein, Markus Kuhlmann
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0050501

The Molecular Profiles of Neural Stem Cell Niche in the Adult Subventricular Zone
Cited by: 54
Author(s): Cheol Lee, Jiexiang Hu, Sherry Ralls, Toshio Kitamura, Y. Peng Loh, Yanqin Yang, Yoh‐suke Mukouyama, Sang‐Hyeon Ahn
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0024131

miR-143 Regulation of Prostaglandin-Endoperoxidase Synthase 2 in the Amnion: Implications for Human Parturition at Term
Cited by: 32
Author(s): Sun Young Kim, Roberto Romero, Adi L. Tarca, Gaurav Bhatti, Woo Jung Lee, Tinnakorn Chaiworapongsa, Sonia S. Hassan, Chong Jai Kim
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0105631

A Thirteen-Gene Expression Signature Predicts Survival of Patients with Pancreatic Cancer and Identifies New Genes of Interest
Cited by: 30
Author(s): Timothy E. Newhook, Edik M. Blais, James Lindberg, Sara J. Adair, Wenjun Xin, Jae K. Lee, Jason A. Papin, John T. Parsons, Todd W. Bauer
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0130300

Down Regulation of CLDND1 Induces Apoptosis in Breast Cancer Cells
Cited by: 14
Author(s): Chandrani Achari, Sofia Winslow, Christer Larsson
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0008182

Seasonal Differences of Gene Expression Profiles in Song Sparrow (Melospiza melodia) Hypothalamus in Relation to Territorial Aggression
Cited by: 83
Author(s): Motoko Mukai, Kirstin Replogle, Jenny Drnevich, Gang Wang, Douglas W. Wacker, Mark Band, David F. Clayton, John C. Wingfield
Software Mentions: 1
Published: almost 15 years ago

10.1371/journal.pone.0035191

Manipulation of Plant Defense Responses by the Tomato Psyllid (Bactericerca cockerelli) and Its Associated Endosymbiont Candidatus Liberibacter Psyllaurous
Cited by: 86
Author(s): Clare L. Casteel, Allison K. Hansen, Linda L. Walling, Timothy D. Paine
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0077232

High-Throughput 3D Screening Reveals Differences in Drug Sensitivities between Culture Models of JIMT1 Breast Cancer Cells
Cited by: 152
Author(s): Vesa Hongisto, Sandra Jernström, Vidal Fey, John-Patrick Mpindi, Kristine Kleivi Sahlberg, Olli Kallioniemi, Merja Perälä
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0048651

Py2T Murine Breast Cancer Cells, a Versatile Model of TGFβ-Induced EMT In Vitro and In Vivo
Cited by: 60
Author(s): Lorenz Waldmeier, Nathalie Meyer-Schaller, Maren Diepenbruck, Gerhard Christofori
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0056122

Differential Effects of Drug Interventions and Dietary Lifestyle in Developing Type 2 Diabetes and Complications: A Systems Biology Analysis in LDLr−/− Mice
Cited by: 21
Author(s): Marijana Radonjić, Peter Y. Wielinga, Suzan Wopereis, Thomas Kelder, Varshna Goelela, Lars Verschuren, Karin Toet, Wim van Duyvenvoorde, Bianca van der Werff van der Vat, Johanna H. M. Stroeve, N.H.P. Cnubben, Teake Kooistra, Ben van Ommen, Robert Kleemann
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0091728

Characterization of the Altered Gene Expression Profile in Early Porcine Embryos Generated from Parthenogenesis and Somatic Cell Chromatin Transfer
Cited by: 9
Author(s): Chi Zhou, J.R. Dobrinsky, Stephen Tsoi, G. R. Foxcroft, Walter T. Dixon, Paul Stothard, J. Verstegen, Michael K. Dyck
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0200652

Impact of congenital cytomegalovirus infection on transcriptomes from archived dried blood spots in relation to long-term clinical outcome
Cited by: 5
Author(s): Roberta Rovito, Hans-Jörg Warnatz, Szymon M. Kiełbasa, Hailiang Mei, Vyacheslav Amtislavskiy, Ramon Arens, Marie–Laure Yaspo, Hans Lehrach, Aloys C.M. Kroes, Jelle J. Goeman, Ann C.T.M. Vossen
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0047490

Hepatitis B Virus-Specific miRNAs and Argonaute2 Play a Role in the Viral Life Cycle
Cited by: 49
Author(s): C. Nelson Hayes, Sakura Akamatsu, Masataka Tsuge, Daiki Miki, Rie Akiyama, Hiromi Abe, Hidenori Ochi, Nobuhiko Hiraga, Michio Imamura, Shoichi Takahashi, Yoshiiku Kawakami, Waka Ohishi, Kazuaki Chayama
Software Mentions: 1
Published: about 12 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: over 11 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 8 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 12 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 15 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 9 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 11 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 11 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 13 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 13 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 9 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 8 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 11 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 11 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 16 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: over 8 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: 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 12 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: over 9 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 14 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 9 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 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: almost 9 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 9 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 12 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: about 14 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: almost 7 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 5 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 16 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 9 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 15 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: over 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 13 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 11 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 10 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 10 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: about 6 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: almost 10 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: about 14 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 12 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: over 13 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 11 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 13 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 17 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: about 12 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 10 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: almost 5 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: over 9 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 7 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 8 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: about 7 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 12 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: over 5 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: almost 12 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 6 years ago

10.3390/cancers12092554

Metformin Suppresses Cancer Stem Cells through AMPK Activation and Inhibition of Protein Prenylation of the Mevalonate Pathway in Colorectal Cancer
Cited by: 29
Author(s): Yoojeong Seo, Jang-Hyun Kim, Soo Jung Park, Sung Chul Park, Jae Hee Cheon, Won Ho Kim, Tae Il Kim
Software Mentions: 1
Published: about 4 years ago

Projects: bioconductor: limma

Papers Mentioning limma 7,776