bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1155/2020/4673153

Potential Prognostic Value and Mechanism of Stromal-Immune Signature in Tumor Microenvironment for Stomach Adenocarcinoma
Cited by: 8
Author(s): Xinying Zhu, Xing Xie, Qingchao Zhao, Lixian Zhang, Changjuan Li, Dongqiang Zhao
Software Mentions: 1
Published: over 4 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

10.3390/ijms21186660

The brlA Gene Deletion Reveals That Patulin Biosynthesis Is Not Related to Conidiation in Penicillium expansum
Cited by: 7
Author(s): Chrystian Zetina-Serrano, Ophélie Rocher, Claire Naylies, Yannick Lippi, Isabelle P. Oswald, Sophie Lorber, Olivier Puel
Software Mentions: 1
Published: about 4 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

10.1038/s41598-019-52682-9

The intrinsic circadian clock in podocytes controls glomerular filtration rate
Cited by: 22
Author(s): Camille Ansermet, Gabriel Centeno, Svetlana Nikolaeva, Marc Maillard, Sylvain Pradervand, Dmitri Firsov
Software Mentions: 1
Published: about 5 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

10.1038/s41598-019-52886-z

Identification of candidate cancer drivers by integrative Epi-DNA and Gene Expression (iEDGE) data analysis
Cited by: 4
Author(s): Amy Li, Bjoern Chapuy, Xaralabos Varelas, Paola Sebastiani, Stefano Monti
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-019-53482-x

Late recurrence of breast cancer is associated with pro-cancerous immune microenvironment in the primary tumor
Cited by: 43
Author(s): Takashi Terauchi, Li Yan, Mariko Asaoka, Omar M. Rashid, Kazuaki Takabe
Software Mentions: 1
Published: about 5 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.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

10.1038/s41598-019-54036-x

Bone marrow adipose tissue does not express UCP1 during development or adrenergic-induced remodeling
Cited by: 20
Author(s): Clarissa S. Craft, Hero Robles, Madelyn R. Lorenz, Eric D. Hilker, Kristann Magee, Thomas Levin Andersen, William P. Cawthorn, Ormond A. MacDougald, Charles Harris, Erica L. Scheller
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-53907-7

FGF Signalling in the Self-Renewal of Colon Cancer Organoids
Cited by: 28
Author(s): Jörg Otte, Levent Dizdar, Bianca Behrens, Wolfgang Goering, Wolfram Trudo Knoefel, Wasco Wruck, Nikolas H. Stoecklein, James Adjaye
Software Mentions: 1
Published: almost 5 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

10.3390/ijms21186858

Preventive Triple Gene Therapy Reduces the Negative Consequences of Ischemia-Induced Brain Injury after Modelling Stroke in a Rat
Cited by: 13
Author(s): Vage Markosyan, Zufar Z. Safiullov, Andrei Izmailov, Filip Fadeev, Mikhail Sokolov, M. S. Kuznetsov, Д. А. Трофимов, Evgeny Kim, Grayr Kundakchyan, Airat Gibadullin, И. И. Салафутдинов, Л. Ф. Нуруллин, Farid Vagizovich Bashirov, Р. Р. Исламов
Software Mentions: 1
Published: about 4 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

10.1038/s41598-019-54868-7

Novel Bead-Based Epitope Assay is a sensitive and reliable tool for profiling epitope-specific antibody repertoire in food allergy
Cited by: 35
Author(s): Maria Suprun, Robert C. Getts, Rohit Raghunathan, Galina Grishina, Marc Witmer, Gustavo Giménez, Hugh A. Sampson, Mayte Suárez‐Fariñas
Software Mentions: 1
Published: almost 5 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.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

10.1038/s41598-019-55287-4

TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome
Cited by: 8
Author(s): Shizuka Koshimizu, Yoshitomo Nakamura, Chikako Nishitani, Mariko Kobayashi, Hajime Ohyanagi, Takatsugu Yamamoto, Kentarô Yano
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-55645-2

Bacillus amyloliquefaciens MBI600 differentially induces tomato defense signaling pathways depending on plant part and dose of application
Cited by: 36
Author(s): Anastasia Dimopoulou, Ioannis Theologidis, Burghard Liebmann, Kriton Kalantidis, Nikon Vassilakos, Nicholas Skandalis
Software Mentions: 1
Published: almost 5 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.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

10.3390/ijms22158205

Identification of an IL-22-Dependent Gene Signature as a Pharmacodynamic Biomarker
Cited by: 1
Author(s): Julie Rae, Jason A. Hackney, Kevin Huang, Mary E. Keir, Ann Herman
Software Mentions: 1
Published: over 3 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.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.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

10.1038/s41598-019-57011-8

Regulation of Gdf5 expression in joint remodelling, repair and osteoarthritis
Cited by: 38
Author(s): Karolina Kania, Fabio Colella, Anna Helene Katrin Riemen, Hui Wang, Kenneth A. Howard, Thomas Aigner, Francesco Dell’Accio, Terence D. Capellini, Anke J. Roelofs, Cosimo De Bari
Software Mentions: 1
Published: almost 5 years ago

10.1155/2021/5545312

Identification and Validation of Potential Biomarkers and Pathways for Idiopathic Pulmonary Fibrosis by Comprehensive Bioinformatics Analysis
Cited by: 3
Author(s): Weibin Qian, Xinrui Cai, Qi Qian, Xinying Zhang
Software Mentions: 1
Published: over 3 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

10.1038/s41598-019-57293-y

CD40L membrane retention enhances the immunostimulatory effects of CD40 ligation
Cited by: 13
Author(s): Taha Elmetwali, Asmaa Salman, Wenbin Wei, Syed A. Hussain, Lawrence S. Young, Daniel H. Palmer
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2334-13-371

Nucleotide-binding oligomerization domain containing-like receptor family, caspase recruitment domain (CARD) containing 4 (NLRC4) regulates intrapulmonary replication of aerosolized Legionella pneumophila
Cited by: 9
Author(s): William R. Berrington, Kelly D. Smith, Shawn J. Skerrett, Thomas R. Hawn
Software Mentions: 1
Published: over 11 years ago

10.3390/ijms21196988

Proteomics Analysis of Plasma Membrane Fractions of the Root, Leaf, and Flower of Rice
Cited by: 2
Author(s): Yukimoto Iwasaki, Takafumi Itoh, Yusuke Hagi, Sakura Matsuta, Aki Nishiyama, Genki Chaya, Yuki Kobayashi, Kotaro Miura, Setsuko Komatsu
Software Mentions: 1
Published: about 4 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.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

10.1186/1471-2172-11-39

Changes in colon gene expression associated with increased colon inflammation in interleukin-10 gene-deficient mice inoculated with Enterococcus species
Cited by: 51
Author(s): Matthew P. G. Barnett, Warren C. McNabb, Adrian L. Cookson, Shuotun Zhu, Marcus Davy, Bianca Knoch, Kátia Nones, Alison J. Hodgkinson, Nicole C. Roy
Software Mentions: 1
Published: almost 15 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

10.1038/s41598-020-57698-0

Silencing of SENP2 in Multiple Myeloma Induces Bortezomib Resistance by Activating NF-κB Through the Modulation of IκBα Sumoylation
Cited by: 15
Author(s): Hong-Yi Xie, Yuanliang Gu, Wenjuan Wang, Xuyao Wang, Xiaojuan Ye, Chao Xin, Mengjiao Lü, B. Ashok Reddy, Peng Shu
Software Mentions: 1
Published: almost 5 years ago

10.1155/2021/8844261

Functional lncRNA-miRNA-mRNA Networks in Response to Baicalein Treatment in Hepatocellular Carcinoma
Cited by: 5
Author(s): Xin Zhao, Dongyang Tang, Xiaofei Chen, Shaoqing Chen, Cheng Wang
Software Mentions: 1
Published: almost 4 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

10.3390/ijms21217812

Circular RNAs and Their Linear Transcripts as Diagnostic and Prognostic Tissue Biomarkers in Prostate Cancer after Prostatectomy in Combination with Clinicopathological Factors
Cited by: 6
Author(s): Hannah Rochow, Monika Jung, Sabine Weickmann, Bernhard Ralla, Carsten Stephan, Sefer Elezkurtaj, Ergin Kilic, Zhao Zhi, Klaus Jung, Annika Fendler, Antonia Franz
Software Mentions: 1
Published: about 4 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.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

10.1038/s41598-020-58358-z

Stratifying cellular metabolism during weight loss: an interplay of metabolism, metabolic flexibility and inflammation
Cited by: 8
Author(s): Samar Tareen, Martina Kutmon, Theo M. de Kok, E.C.M. Mariman, Marleen A. van Baak, Chris T. Evelo, Michiel E. Adriaens, Ilja C. W. Arts
Software Mentions: 1
Published: almost 5 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.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

10.1186/1471-2172-12-41

Anti-inflammatory effects of tetradecylthioacetic acid (TTA) in macrophage-like cells from Atlantic salmon (Salmo salar L.)
Cited by: 3
Author(s): Fabian Grammes, Harald Takle
Software Mentions: 1
Published: over 13 years ago

10.3390/ijms21228479

Establishment of a Gene Signature to Predict Prognosis for Patients with Lung Adenocarcinoma
Cited by: 17
Author(s): Zhaodong Li, Fanghua Qi, Fan Li
Software Mentions: 1
Published: about 4 years ago

10.3390/ijms21228759

Phylostratic Shift of Whole-Genome Duplications in Normal Mammalian Tissues towards Unicellularity Is Driven by Developmental Bivalent Genes and Reveals a Link to Cancer
Cited by: 27
Author(s): Olga V. Anatskaya, Alexander E. Vinogradov, Ninel M. Vainshelbaum, Alessandro Giuliani, Jekaterina Ērenpreisa
Software Mentions: 1
Published: about 4 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

10.1155/2019/8308694

Bioinformatic Analysis of Circular RNA-Associated ceRNA Network Associated with Hepatocellular Carcinoma
Cited by: 25
Author(s): Jiacheng Wu, Lingling Shui, Yien Xiang, Xianzhi Qu, Ying Xie, Xuewen Zhang
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-59577-0

Deducing signaling pathways from parallel actions of arsenite and antimonite in human epidermal keratinocytes
Cited by: 3
Author(s): Marjorie A. Phillips, Ángela Cánovas, Miguel A. Rea, Alma Islas–Trejo, Juan F. Medrano, Blythe Durbin‐Johnson, David M. Rocke, Robert H. Rice
Software Mentions: 1
Published: almost 5 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.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.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.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

10.1155/2018/4283673

Derivation and Validation of the Potential Core Genes in Pancreatic Cancer for Tumor-Stroma Crosstalk
Cited by: 13
Author(s): Ran Xue, Lin Hua, Wenbin Xu, Yan Gao, Yanbo Pang, Jianyu Hao
Software Mentions: 1
Published: about 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

10.1038/s41598-020-60714-y

Identification of significant gene biomarkers of low back pain caused by changes in the osmotic pressure of nucleus pulposus cells
Cited by: 10
Author(s): Changsong Zhao, Xuemin Quan, Jie He, Rugang Zhao, Yao Zhang, Xin Li, Sheng Sun, Rui Ma, Qiang Zhang
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-60616-z

Integrated RNA and metabolite profiling of urine liquid biopsies for prostate cancer biomarker discovery
Cited by: 35
Author(s): Bongyong Lee, Iqbal Mahmud, John Marchica, Paweł Dereziński, Feng Qi, Fubo Wang, Piyush Joshi, Felipe Valerio, Inoel Rivera, Vipul Patel, Christian P. Pavlovich, Timothy J. Garrett, Gary P. Schroth, Yinghao Sun, Ranjan J. Perera
Software Mentions: 1
Published: over 4 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

10.3390/ijms21239051

Kisspeptin Influences the Reproductive Axis and Circulating Levels of microRNAs in Senegalese Sole
Cited by: 15
Author(s): Catarina C Oliveira, Elvira Fatsini, Ignacio Fernández, Catarina Anjos, François Chauvigné, Joan Cerdà, Robin Mjelle, Jorge M.O. Fernandes, Elsa Cabrita
Software Mentions: 1
Published: almost 4 years ago

10.1155/2019/4012590

Inhibition of LOXL2 Enhances the Radiosensitivity of Castration-Resistant Prostate Cancer Cells Associated with the Reversal of the EMT Process
Cited by: 20
Author(s): Peng Xie, Hongliang Yu, Feijiang Wang, Feng Yan, Xia He
Software Mentions: 1
Published: almost 6 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

10.1186/1471-2164-15-1018

Dissecting the organ specificity of insecticide resistance candidate genes in Anopheles gambiae: known and novel candidate genes
Cited by: 52
Author(s): Victoria A. Ingham, Christopher M. Jones, Pasquale Pignatelli, Vasileia Balabanidou, John Vontas, Simon C. Wagstaff, Jonathan D. Moore, Hilary Ranson
Software Mentions: 1
Published: almost 11 years ago

10.1186/1471-2164-12-437

A eukaryotic-type signalling system of Pseudomonas aeruginosa contributes to oxidative stress resistance, intracellular survival and virulence
Cited by: 42
Author(s): Jana Goldová, Aleš Ulrych, Kamil Hercík, Pavel Branný
Software Mentions: 1
Published: about 13 years ago

10.1155/2019/8340573

Network Analyses of Differentially Expressed Genes in Osteoarthritis to Identify Hub Genes
Cited by: 13
Author(s): Zhaoyan Li, Lei Zhong, Zhenwu Du, Gaoyang Chen, Jing Shang, Qiwei Yang, Qingyu Wang, Yang Song, Guizhen Zhang
Software Mentions: 1
Published: over 5 years ago

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

10.1038/s41598-020-60810-z

The role of semen and seminal plasma in inducing large-scale genomic changes in the female porcine peri-ovulatory tract
Cited by: 22
Author(s): Manuel Álvarez‐Rodríguez, Cristina A. Martínez, Dominic Wright, Heriberto Rodríguez-Martinez
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1003756

Genome-Wide Analysis of Cell Type-Specific Gene Transcription during Spore Formation in Clostridium difficile
Cited by: 132
Author(s): Laure Saujet, Fátima C. Pereira, Mónica Serrano, Olga Soutourina, Marc Monot, Pavel V. Shelyakin, Mikhail S. Gelfand, Bruno Dupuy, Adriano O. Henriques, Isabelle Martin‐Verstraete
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pgen.1004877

Antagonistic Cross-Regulation between Sox9 and Sox10 Controls an Anti-tumorigenic Program in Melanoma
Cited by: 84
Author(s): Olga Shakhova, Phil F. Cheng, Pravin J. Mishra, Daniel Zingg, Simon M. Schaefer, Julien Debbache, Jessica Häusel, Claudia Matter, Theresa Guo, Sean Davis, Paul S. Meltzer, Daniela Mihic‐Probst, Holger Moch, Michael Wegner, Glenn Merlino, Mitchell P. Levesque, Reinhard Dummer, Raffaella Santoro, Paolo Cinelli, Lukas Sommer
Software Mentions: 1
Published: almost 10 years ago

10.1038/s41598-020-62414-z

Transcriptomics in cancer revealed by Positron Emission Tomography radiomics
Cited by: 12
Author(s): Florent Tixier, Catherine Chèze-Le-Rest, Ulrike Schick, Brigitte Simon, Xavier Dufour, Stéphane Key, Olivier Pradier, Marc Aubry, Mathieu Hatt, Laurent Corcos, Dimitris Visvikis
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pgen.1004837

Global Analysis of Photosynthesis Transcriptional Regulatory Networks
Cited by: 30
Author(s): Saheed Imam, Daniel R. Noguera, Timothy J. Donohue
Software Mentions: 1
Published: almost 10 years ago

10.7717/peerj.5363

Profile and clinical implication of circular RNAs in human papillary thyroid carcinoma
Cited by: 22
Author(s): Huihui Ren, Zhelong Liu, Siyue Liu, Xinrong Zhou, Hong Wang, Jinchao Xu, Daowen Wang, Gang Yuan
Software Mentions: 1
Published: over 6 years ago

10.7717/peerj.9120

Identifying hub genes of papillary thyroid carcinoma in the TCGA and GEO database using bioinformatics analysis
Cited by: 15
Author(s): Ying Wang, Xiaolian Zhang, Huilin Leng, Yin Wang, Weizhong Zeng, Congling Zhang
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.9530

Analysis of prognostic genes in the tumor microenvironment of lung adenocarcinoma
Cited by: 19
Author(s): Zhanyu Xu, Mengli Zhao, Wenjie Chen, Kun Li, Fanglu Qin, Weiwei Xiang, Yu Sun, Jiangbo Wei, Liqiang Yuan, Shikang Li, Sheng-hua Lin
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-63840-9

Construction and analysis for differentially expressed long non-coding RNAs and mRNAs in acute myocardial infarction
Cited by: 10
Author(s): Ning Song, Xiangmei Li, Junyi Luo, Hua‐Jin Zhai, Qian Zhao, Xinrong Zhou, Fen Liu, Xue-He Zhang, Xiao‐Ming Gao
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-63904-w

Gene expression profiles for low-dose exposure to diethyl phthalate in rodents and humans: a translational study with implications for breast carcinogenesis
Cited by: 18
Author(s): Kalpana Gopalakrishnan, Vasily N. Aushev, Fabiana Manservisi, Laura Falcioni, Simona Panzacchi, Fiorella Belpoggi, Humberto Parada, Gail Garbowski, Hanina Hibshoosh, Regina M. Santella, Marilie D. Gammon, Susan L. Teitelbaum, Jia Chen
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.7831

Identification of a five-miRNA signature predicting survival in cutaneous melanoma cancer patients
Cited by: 18
Author(s): Tao Lu, Shuang Chen, Le Qu, Yunlin Wang, Hong‐Duo Chen, Chundi He
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-64356-y

Comprehensive analysis of the SLC16A gene family in pancreatic cancer via integrated bioinformatics
Cited by: 36
Author(s): Shan Yu, Yanshuang Wu, Chunlong Li, Zhipeng Qu, Ge Lou, Xiaorong Guo, Jingjing Ji, Nan Li, Mian Guo, Maomao Zhang, Lei Lei, Sheng Tai
Software Mentions: 1
Published: over 4 years ago

10.1186/1755-8794-7-35

A systems biology approach to understand the pathophysiological mechanisms of cardiac pathological hypertrophy associated with rosiglitazone
Cited by: 18
Author(s): Lars Verschuren, Peter Y. Wielinga, Thomas Kelder, Marijana Radonjić, Kanita Salic, Robert Kleemann, Ben van Ommen, Teake Kooistra
Software Mentions: 1
Published: over 10 years ago

10.7717/peerj.8021

Identification of key genes and long non-coding RNA associated ceRNA networks in hepatocellular carcinoma
Cited by: 15
Author(s): Jun Li, Wenli Li, Jian Zhang, Zhu Ma, Xiaoyan Wu, Lian Tang
Software Mentions: 1
Published: about 5 years ago

10.1038/s41598-020-64524-0

Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes
Cited by: 4
Author(s): Klev Diamanti, Robin Visvanathar, Maria J. Pereira, Marco Cavalli, Gang Pan, Chanchal Kumar, Stanko Skrtic, Ulf Risérus, Jan W. Eriksson, Joel Kullberg, Jan Komorowski, Claes Wadelius, Håkan Åhlström
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-65606-9

Bioinformatic analysis reveals the importance of epithelial-mesenchymal transition in the development of endometriosis
Cited by: 29
Author(s): Meihong Chen, Yilu Zhou, Hong Xu, Catherine M. Hill, Rob M. Ewing, Da He, Xiaoling Zhang, Yihua Wang
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-12-602

Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model
Cited by: 61
Author(s): Monica Llano‐Diez, Ann-Marie Gustafson, Carl A. Olsson, Hanna Göransson, Lars Larsson
Software Mentions: 1
Published: almost 13 years ago

10.7717/peerj.6495

Integrated bioinformatics analysis of As, Au, Cd, Pb and Cu heavy metal responsive marker genes through <i>Arabidopsis thaliana</i> GEO datasets
Cited by: 14
Author(s): Chao Niu, Min Jiang, Na Li, Ji Cao, Meifang Hou, Di-An Ni
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-66122-6

Anaesthetic-dependent changes in gene expression following acute and chronic exposure in the rodent brain
Cited by: 20
Author(s): Dannielle Upton, Kata Popovic, Roger Fulton, Michael Kassiou
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-66872-3

Identification of core genes in the progression of endometrial cancer and cancer cell-derived exosomes by an integrative analysis
Cited by: 25
Author(s): Shuang Shi, Qiang Tan, Fuqiang Feng, Heping Huang, Jingjie Liang, Dingren Cao, Zhengguang Wang
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.2470

Integrated analysis of ischemic stroke datasets revealed sex and age difference in anti-stroke targets
Cited by: 22
Author(s): Wen‐Xing Li, Shao‐Xing Dai, Qian Wang, Yicheng Guo, Yi Hong, Junrong Zheng, Jia‐Qian Liu, Dahai Liu, Gong‐Hua Li, Jing‐Fei Huang
Software Mentions: 1
Published: about 8 years ago

10.1038/s41598-020-66868-z

Distinct abdominal and gluteal adipose tissue transcriptome signatures are altered by exercise training in African women with obesity
Cited by: 14
Author(s): Pamela A. Nono Nankam, Matthias Blüher, Stephanie Kehr, Nora Klöting, Knut Krohn, Kevin Adams, Peter F. Stadler, Amy E. Mendham, Julia H. Goedecke
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-66221-4

Transcriptomic differences in MSA clinical variants
Cited by: 7
Author(s): Alexandra Pérez‐Soriano, Magdalena Arnal, Teresa Botta-Orfila, Darly M. Giraldo, Manel Fernández, Yaroslau Compta, Rubén Fernández‐Santiago, Mario Ezquerra, Gian Gaetano Tartaglia, Marı́a José Martı́, Esteban Muñoz, Javier Pagonabarraga, Francesc Valldeoriola, Jorge Hernández‐Vara, Serge Jauma Classen, Víctor Puente, Claustre Pont, Núria Caballol, Oriol de Fábregues, Asunción Ávila, Matilde Calopa, Carles Gaig, Pau Pástor, Montserrat Pujol, Joan Santamaría, Lluís Planellás, Ana Cámara
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-67550-0

A novel protective role for microRNA-3135b in Golgi apparatus fragmentation induced by chemotherapy via GOLPH3/AKT1/mTOR axis in colorectal cancer cells
Cited by: 21
Author(s): Stephanie I. Nuñez‐Olvera, Bibiana Chávez‐Munguía, María Cruz del Rocío Terrones-Gurrola, Laurence A. Marchat, Jonathan Puente-Rivera, Erika Ruiz‐García, Alma D. Campos‐Parra, Carlos Vázquez‐Calzada, Erik Lizárraga-Verdugo, Rosalío Ramos‐Payán, Yarely M. Salinas‐Vera, César López-Camarillo
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-67446-z

SnoRNA signatures in cartilage ageing and osteoarthritis
Cited by: 30
Author(s): Mandy J. Peffers, Alzbeta Chabronova, Panagiotis Balaskas, Yongxiang Fang, Philip Dyer, A. Cremers, Pieter J. Emans, Peter Z. Feczko, M.M. Caron, Tim J. M. Welting
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.11375

Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment
Cited by: 5
Author(s): Youzheng Xu, Yixin Xu, Chun Wang, Baoguo Xia, Qingling Mu, Shaohong Luan, Jun Fan
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.8096

Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma
Cited by: 12
Author(s): Haiping Zhang, Jian Zou, Ying Yin, Bo Zhang, Yaling Hu, Jingjing Wang, Hui‐Jun Mu
Software Mentions: 1
Published: almost 5 years ago

10.7717/peerj.6645

Identification of key genes, pathways and potential therapeutic agents for liver fibrosis using an integrated bioinformatics analysis
Cited by: 24
Author(s): Zhu Zhan, Yuhe Chen, Yuanqin Duan, Lin Li, Kenley Mew, Peng Hu, Hong Ren, Mingli Peng
Software Mentions: 1
Published: over 5 years ago

10.7717/peerj.6375

Identification of special key genes for alcohol-related hepatocellular carcinoma through bioinformatic analysis
Cited by: 16
Author(s): Xiuzhi Zhang, Chunyan Kang, Ningning Li, Xiaoli Liu, Jinzhong Zhang, Fenglan Gao, Liping Dai
Software Mentions: 1
Published: almost 6 years ago

10.7717/peerj.9086

Identification of key genes associated with progression and prognosis for lung squamous cell carcinoma
Cited by: 10
Author(s): Xu Ma, Hongyi Ren, Ruoyu Peng, Yi Li, Liang Ming
Software Mentions: 1
Published: over 4 years ago

10.7717/peerj.10830

The methylation level of TFAP2A is a potential diagnostic biomarker for retinoblastoma: an analytical validation study
Cited by: 4
Author(s): Qi Zeng, Sha Wang, Jia Tan, Lu Chen, Jinwei Wang
Software Mentions: 1
Published: over 3 years ago

10.7717/peerj.2839

Transcriptomic response of maize primary roots to low temperatures at seedling emergence
Cited by: 15
Author(s): Mauro Di Fenza, Bridget Hogg, Jim Grant, Susanne Barth
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-020-68890-7

Estrogens decrease osteoclast number by attenuating mitochondria oxidative phosphorylation and ATP production in early osteoclast precursors
Cited by: 41
Author(s): Ha‐Neui Kim, Filipa Ponte, Intawat Nookaew, Serra Ucer Ozgurel, Adriana Marques-Carvalho, Srividhya Iyer, Aaron Warren, Nùkhet Aykin-Burns, Kimberly J. Krager, Vilma A. Sardão, Li Han, Rafael de Cabo, Haibo Zhao, Robert L. Jilka, Stavros C. Manolagas, Maria Almeida
Software Mentions: 1
Published: over 4 years ago

Projects: bioconductor: limma

Papers Mentioning limma 7,776