10.1002/cam4.3900

A novel five‐gene signature predicts overall survival of patients with hepatocellular carcinoma
Cited by: 23
Author(s): Zhigang Wang, Leyu Pan, Deliang Guo, Xiaofeng Luo, Jie Tang, Weihua Yang, Yuxian Zhang, Anni Luo, Yang Gu, Yuxuan Pan
Software Mentions: 2
Published: over 5 years ago

10.1002/cam4.4095

Immunophenotype‐associated gene signature in ductal breast tumors varies by receptor subtype, but the expression of individual signature genes remains consistent
Cited by: 4
Author(s): Michael Behring, Yuanfan Ye, Amr Elkholy, Prachi Bajpai, Sumit Agarwal, Hyung‐Gyoon Kim, Akinyemi I. Ojesina, Howard W. Wiener, Upender Manne, Sadeep Shrestha, Ana I. Vázquez
Software Mentions: 2
Published: about 5 years ago

10.1002/cam4.3408

An immune‐related prognostic signature for predicting breast cancer recurrence
Cited by: 7
Author(s): Zelin Tian, Jianing Tang, Xing Liao, Qian Yang, Zeyu Wu
Software Mentions: 2
Published: about 6 years ago

10.1186/s12957-017-1190-8

Special role of JUN in papillary thyroid carcinoma based on bioinformatics analysis
Cited by: 9
Author(s): Wenzheng Chen, Qingfeng Li, Yunxia Lv, Debin Xu, Wanzhi Chen, Jichun Yu
Software Mentions: 2
Published: about 9 years ago

10.1186/s12957-017-1211-7

Identification of key lncRNAs in colorectal cancer progression based on associated protein–protein interaction analysis
Cited by: 23
Author(s): Haishan Zhu, Jiajing Yu, Haifeng Zhu, Yusheng Guo, Sheng-Ya Feng
Software Mentions: 2
Published: about 9 years ago

10.1186/s12957-017-1242-0

Integrated network analysis to explore the key genes regulated by parathyroid hormone receptor 1 in osteosarcoma
Cited by: 10
Author(s): Dong-Hui Guan, Honglai Tian
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12957-018-1380-z

Digital gene expression profiling analysis and its application in the identification of genes associated with improved response to neoadjuvant chemotherapy in breast cancer
Cited by: 7
Author(s): Xiaozhen Liu, Gan Jin, Jin Qian, Hongjian Yang, Hongchao Tang, Xiao Meng, Yongfeng Li
Software Mentions: 2
Published: over 8 years ago

10.1186/s12957-019-1587-7

Identification of co-expression modules and pathways correlated with osteosarcoma and its metastasis
Cited by: 11
Author(s): Jiansheng Wang, Yunguo Wang, Yongsheng Zhong, Xuedong Li, Shasha Du, Peng Xie, Guizhou Zheng, Jingming Han
Software Mentions: 2
Published: over 7 years ago

10.1186/s12957-020-02026-z

Prognostic biomarkers related to breast cancer recurrence identified based on Logit model analysis
Cited by: 15
Author(s): Xiaoying Zhou, Chuanguang Xiao, Tong Han, Shusheng Qiu, Meng Wang, Jun Chen, Weike Sun, Liang Li, Lili Lin
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12957-020-02116-y

Identification of a prognostic gene signature of colon cancer using integrated bioinformatics analysis
Cited by: 16
Author(s): Zhengyu Fang, Sumei Xu, Yiwen Xie, Weirong Yan
Software Mentions: 2
Published: over 5 years ago

10.1186/s12957-021-02124-6

Identification of differentially methylated genes as diagnostic and prognostic biomarkers of breast cancer
Cited by: 18
Author(s): Xiaohong Mao, Qiang Ye, Guobing Zhang, Jialiang Jiang, Hongying Zhao, Yanfei Shao, Ziqi Ye, Zixue Xuan, Ping Huang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12957-021-02137-1

Identification and validation of a miRNA-related expression signature for tumor mutational burden in colorectal cancer
Cited by: 9
Author(s): Li Xu, Qing Zheng
Software Mentions: 2
Published: over 5 years ago

10.1186/s12957-021-02384-2

Determination of a six-gene prognostic model for cervical cancer based on WGCNA combined with LASSO and Cox-PH analysis
Cited by: 17
Author(s): Shiyan Li, Fengjuan Han, Na Qi, Liyang Wen, Jia Li, Feng Cong, Qingling Wang
Software Mentions: 2
Published: about 5 years ago

10.1186/s13071-021-04996-9

Response to comments on our article (Yin YL et al., Parasit Vectors, 10.1186/s13071-021-04739-w) by Yuqing Wang and colleagues
Cited by: 1
Author(s): Yanling Yin, Xuefei Yang, Guanghui Zhao
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12989-014-0034-8

Oxidative stress and reduced responsiveness of challenged circulating leukocytes following pulmonary instillation of metal-rich particulate matter in rats
Cited by: 18
Author(s): Aaron Erdely, James M. Antonini, Shih‐Houng Young, Michael L. Kashon, Ja K. Gu, Tracy Hulderman, Rebecca Salmen, Terence Meighan, Jenny R. Roberts, Patti C. Zeidler-Erdely
Software Mentions: 2
Published: about 12 years ago

10.1186/s12989-014-0048-2

Inhalation of rod-like carbon nanotubes causes unconventional allergic airway inflammation
Cited by: 81
Author(s): Elina Rydman, Marit Ilves, Antti Joonas Koivisto, Pia Anneli Sofia Kinaret, Vittorio Fortino, Terhi Savinko, Maili Lehto, Ville Pulkkinen, Minnamari Vippola, Kaarle Hämeri, Sampsa Matikainen, Henrik Wolff, Kai Savolainen, Dario Greco, Harri Alenius
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12969-021-00556-8

The culture microenvironment of juvenile idiopathic arthritis synovial fibroblasts is favorable for endochondral bone formation through BMP4 and repressed by chondrocytes
Cited by: 3
Author(s): Megan M. Simonds, A. Schlefman, Suzanne M. McCahan, Kathleen E. Sullivan, Carlos D. Rosé, AnneMarie C. Brescia
Software Mentions: 2
Published: over 5 years ago

10.1186/s12969-020-00483-0

Juvenile idiopathic arthritis fibroblast-like synoviocytes influence chondrocytes to alter BMP antagonist expression demonstrating an interaction between the two prominent cell types involved in endochondral bone formation
Cited by: 2
Author(s): Megan M. Simonds, A. Schlefman, Suzanne M. McCahan, Kathleen E. Sullivan, Carlos D. Rosé, AnneMarie C. Brescia
Software Mentions: 2
Published: almost 6 years ago

10.7717/peerj.7782

Identification of hub genes and small-molecule compounds related to intracerebral hemorrhage with bioinformatics analysis
Cited by: 17
Author(s): Zhendong Liu, Ruotian Zhang, Xin Chen, Penglei Yao, Tao Yan, Wenwu Liu, Jiawei Yao, Andrei Sokhatskii, Ilgiz Gareev, Shen Zhao
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.11427

Identification of diagnostic genes and vital microRNAs involved in rheumatoid arthritis: based on data mining and experimental verification
Cited by: 6
Author(s): Conglin Ren, Mingshuang Li, Yang Zheng, Fengqing Wu, Weibin Du, Renfu Quan
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.6343

The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
Cited by: 4
Author(s): Keren Jia, Yingcheng Wu, Jingyi Ju, Liyang Wang, Lili Shi, Huiqun Wu, Kui Jiang, Jiancheng Dong
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.11320

Identification of a three-gene-based prognostic model in multiple myeloma using bioinformatics analysis
Cited by: 1
Author(s): Y. Albert Pan, Yijun Meng, Zhimin Zhai, Sheng Xiong
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.7872

Identification of potential biomarkers and pivotal biological pathways for prostate cancer using bioinformatics analysis methods
Cited by: 11
Author(s): Zihao He, Xiaolu Duan, Guohua Zeng
Software Mentions: 2
Published: almost 7 years ago

10.7717/peerj.7436

Identification of crucial genes based on expression profiles of hepatocellular carcinomas by bioinformatics analysis
Cited by: 21
Author(s): Ze-Kun Liu, Renyu Zhang, Yu‐Le Yong, Zhiyun Zhang, Can Li, Zhi‐Nan Chen, Huijie Bian
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.7024

Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis
Cited by: 9
Author(s): Pengfei Hu, Fangfang Sun, Jisheng Ran, Lidong Wu
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.9535

Diagnostic and prognostic values of upregulated SPC25 in patients with hepatocellular carcinoma
Cited by: 7
Author(s): Xunzhe Yang, Hongzhi Sun, Ying Song, Yang Li, Haibo Li
Software Mentions: 2
Published: about 6 years ago

10.7717/peerj.11986

Screening and identification of NOTCH1, CDKN2A, and NOS3 as differentially expressed autophagy-related genes in erectile dysfunction
Cited by: 1
Author(s): Chao Luo, Xiongcai Zhou, Li Wang, Qinyu Zeng, Junhong Fan, Shuhua He, Haibo Zhang, Anyang Wei
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.871

Proteomic responses to hypoxia at different temperatures in the great scallop (<i>Pecten maximus</i>)
Cited by: 16
Author(s): Sébastien Artigaud, Camille Lacroix, Joëlle Richard, Jonathan Flye-Sainte-Marie, Luca Bargelloni, Vianney Pichereau
Software Mentions: 2
Published: over 11 years ago

10.7717/peerj.10820

Abnormal expression of <i>HOXD11</i> promotes the malignant behavior of glioma cells and leads to poor prognosis of glioma patients
Cited by: 6
Author(s): Jialin Wang, Zhendong Liu, Cheng Zhang, Hongbo Wang, Ang Li, Binfeng Liu, Xiaoyu Lian, Zhishuai Ren, Wang Zhang, Yanbiao Wang, Bo Zhang, Bo Pang, Yanzheng Gao
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.7089

T cell receptor signaling pathway and cytokine-cytokine receptor interaction affect the rehabilitation process after respiratory syncytial virus infection
Cited by: 22
Author(s): Zuanhao Qian, Zhenglei Zhang, Yingying Wang
Software Mentions: 2
Published: over 7 years ago

10.7717/peerj.2775

Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis
Cited by: 46
Author(s): Nahid Safari-Alighiarloo, Mostafa Rezaei‐Tavirani, Mohammad Taghi Taghizadeh, Seyyed Mohammad Tabatabaei, Saeed Namaki
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.2516

Targeted genomic enrichment and sequencing of CyHV-3 from carp tissues confirms low nucleotide diversity and mixed genotype infections
Cited by: 27
Author(s): Saliha Hammoumi, Tatiana Vallaeys, Ayi Santika, Philippe Leleux, Ewa Borzym, Christophe Klopp, Jean‐Christophe Avarre
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pgen.1009186

Autocrine insulin pathway signaling regulates actin dynamics in cell wound repair
Cited by: 5
Author(s): Mitsutoshi Nakamura, Jeffrey M. Verboon, Tessa E. Allen, María Teresa Abreu-Blanco, Raymond Liu, Andrew N. M. Dominguez, Jeffrey J. Delrow, Susan M. Parkhurst
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1000142

Efficient Genetic Method for Establishing Drosophila Cell Lines Unlocks the Potential to Create Lines of Specific Genotypes
Cited by: 55
Author(s): Amanda Simcox, Srabani Mitra, Sharon L. Truesdell, Litty Paul, Ting Chen, Jonathan P. Butchar, Steven E. Justiniano
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pgen.1008455

The polyamine transporter Slc18b1(VPAT) is important for both short and long time memory and for regulation of polyamine content in the brain
Cited by: 16
Author(s): Robert Fredriksson, Smitha Sreedharan, Karin Nordenankar, Johan Alsiö, Frida A. Lindberg, A. Hutchinson, Anders Eriksson, Sahar Roshanbin, Diana M. Ciuculete, Anica Klockars, Aniruddha Todkar, Maria Hägglund, Sofie V. Hellsten, Viktoria Hindlycke, Åke Västermark, Ganna Shevchenko, Gaia Olivo, Ken Cheng, Klas Kullander, Ali A. Moazzami, Jonas Bergquist, Pawel K. Olszewski, Helgi B. Schiöth
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1006541

Bdf1 Bromodomains Are Essential for Meiosis and the Expression of Meiotic-Specific Genes
Cited by: 12
Author(s): Encar García-Oliver, Claire Ramus, Jonathan Perot, Marie Arlotto, Morgane Champleboux, Flore Mietton, Christophe Battail, Anne Boland, Jean‐François Deleuze, Myriam Ferro, Yohann Couté, Jérôme Govin
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1004158

Genome-Wide DNA Methylation Analysis Predicts an Epigenetic Switch for GATA Factor Expression in Endometriosis
Cited by: 143
Author(s): Matthew T. Dyson, Damian Roqueiro, Diana Monsivais, Cihangir Mutlu Ercan, Mary Ellen Pavone, David Brooks, Toshiyuki Kakinuma, Masanori Ono, Nadereh Jafari, Yang Dai, Serdar E. Bulun
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pgen.1003953

MYB10 and MYB72 Are Required for Growth under Iron-Limiting Conditions
Cited by: 182
Author(s): Christine M. Palmer, Maria N. Hindt, Holger Schmidt, Stephan Clemens, Mary Lou Guerinot
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pgen.1005793

Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs
Cited by: 106
Author(s): Courtney K Burrows, Nicholas E. Banovich, Bryan J. Pavlovic, Kristen Patterson, Irene Gallego Romero, Jonathan K. Pritchard, Yoav Gilad
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pgen.1003127

Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons
Cited by: 151
Author(s): Steven R. Eichten, Nathanael A. Ellis, Irina Makarevitch, Cheng‐Ting Yeh, Jonathan I. Gent, Lin Guo, Karen M. McGinnis, Xiaoyu Zhang, Patrick S. Schnable, Matthew Vaughn, R. Kelly Dawe, Nathan M. Springer
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pmed.1002352

Signatures of inflammation and impending multiple organ dysfunction in the hyperacute phase of trauma: A prospective cohort study
Cited by: 73
Author(s): Claudia Cabrera, Joanna Manson, Joanna Shepherd, Hew D.T. Torrance, David S. Watson, M. Paula Longhi, Mimoza Hoti, Minal Patel, Michael J. O’Dwyer, Sussan Nourshargh, Daniel J. Pennington, Michael R. Barnes, Karim Brohi
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pntd.0007570

Dramatic changes in gene expression in different forms of Crithidia fasciculata reveal potential mechanisms for insect-specific adhesion in kinetoplastid parasites
Cited by: 13
Author(s): John N. Filosa, Corbett T. Berry, Gordon Ruthel, Stephen M. Beverley, Wesley C. Warren, Chad Tomlinson, Peter J. Myler, Elizabeth A. Dudkin, Megan L. Povelones, Michael Povelones
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pntd.0003724

Global Transcriptional Dynamics of Diapause Induction in Non-Blood-Fed and Blood-Fed Aedes albopictus
Cited by: 84
Author(s): Xin Huang, Monica F. Poelchau, Peter Armbruster
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pntd.0004624

Comprehensive Transcriptome Meta-analysis to Characterize Host Immune Responses in Helminth Infections
Cited by: 25
Author(s): Guohui Zhou, Mary M. Stevenson, Timothy G. Geary, Jianguo Xia
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pntd.0004452

Small RNA Profiling in Dengue Virus 2-Infected Aedes Mosquito Cells Reveals Viral piRNAs and Novel Host miRNAs
Cited by: 111
Author(s): Pascal Miesen, Alasdair Ivens, Amy H. Buck, Ronald P. van Rij
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pntd.0003522

Time since Onset of Disease and Individual Clinical Markers Associate with Transcriptional Changes in Uncomplicated Dengue
Cited by: 31
Author(s): Cornelia A. M. van de Weg, Henk-Jan van den Ham, M Bijl, Fatih Anfasa, Fatiha Zaaraoui-Boutahar, Beti Ernawati Dewi, Leonard Nainggolan, Wilfred F. J. van IJcken, Albert D. M. E. Osterhaus, Benedict Martina, Eric C. M. Van Gorp, Arno C. Andeweg
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pntd.0005677

Amino acid metabolic signaling influences Aedes aegypti midgut microbiome variability
Cited by: 51
Author(s): Sarah M. Short, Emmanuel F. Mongodin, Hannah J. MacLeod, Octávio A. C. Talyuli, George Dimopoulos
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pntd.0008282

Differentiation-dependent susceptibility of human muscle cells to Zika virus infection
Cited by: 11
Author(s): Vincent Legros, Patricia Jeannin, Julien Burlaud‐Gaillard, Thibault Chaze, Quentin Giai Gianetto, Gillian Butler‐Browne, Vincent Mouly, Jim Zoladek, Philippe V. Afonso, Mariela-Natacha Gonzàlez, Mariette Matondo, Ingo Riederer, Philippe Roingeard, Antoine Gessain, Valérie Choumet, Pierre‐Emmanuel Ceccaldi
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0128059

Chronic Hyperglycemia Induces Trans-Differentiation of Human Pancreatic Stellate Cells and Enhances the Malignant Molecular Communication with Human Pancreatic Cancer Cells
Cited by: 20
Author(s): Katalin Kiss, Kornélia Baghy, Sándor Spisák, Szilárd Szanyi, Zsolt Tulassay, Attila Zalatnai, Matthias Löhr, Ralf Jesenofsky, Ilona Kovalszky, Gábor Firneisz
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0109847

IgG4 Immunostaining and Its Implications in Orbital Inflammatory Disease
Cited by: 38
Author(s): Amanda Wong, Stephen R. Planck, Dongseok Choi, Christina A. Harrington, Megan L. Troxell, Donald C. Houghton, Patrick Stauffer, David J. Wilson, Hans E. Grossniklaus, Roger A. Dailey, John D. Ng, Eric A. Steele, Gerald J. Harris, Craig N. Czyz, Jill A. Foster, Valerie A. White, Peter J. Dolman, Michael Kazim, Payal Patel, Deepak P. Edward, Hind Al Katan, Hailah Al Hussain, Dinesh Selva, R. Patrick Yeatts, Bobby S. Korn, Don O. Kikkawa
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0177475

Peculiar Genes Selection: A new features selection method to improve classification performances in imbalanced data sets
Cited by: 6
Author(s): Federica Martina, Marco Beccuti, Gianfranco Balbo, Francesca Cordero
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0048385

Org 214007-0: A Novel Non-Steroidal Selective Glucocorticoid Receptor Modulator with Full Anti-Inflammatory Properties and Improved Therapeutic Index
Cited by: 28
Author(s): M.J.C. van Lierop, Wynand Alkema, Anke Laskewitz, R. Dijkema, Hans M. van der Maaden, Martin J. Smit, Ralf Plate, Paolo Conti, Christan G.J.M. Jans, Cornelis M. Timmers, C. A. A. Van Boeckel, Scott J. Lusher, Ross McGuire, René C. van Schaik, Jacob de Vlieg, Ruben Smeets, Claudia L. Hofstra, Annemieke M. H. Boots, Marcel van Duin, Benno Ingelse, W.G.E.J. Schoonen, Aldo Grefhorst, Theo H. van Dijk, Folkert Kuipers, Wim H.A. Dokter
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0007743

An Integrated Analysis of Molecular Acclimation to High Light in the Marine Diatom Phaeodactylum tricornutum
Cited by: 216
Author(s): Marianne Nymark, Kristin Collier Valle, Tore Brembu, Kasper Hancke, Per Winge, Kjersti Andresen, Geir Johnsen, Atle M. Bones
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pone.0007316

Insights into the Molecular Basis of L-Form Formation and Survival in Escherichia coli
Cited by: 57
Author(s): William A. Glover, Yanqin Yang, Yingying Zhang
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pone.0243992

CYP450 core involvement in multiple resistance strains of Aedes aegypti from French Guiana highlighted by proteomics, molecular and biochemical studies
Cited by: 18
Author(s): Yanouk Epelboin, Lanjiao Wang, Quentin Giai Gianetto, Valérie Choumet, Pascal Gaborit, Jean Issaly, Amandine Guidez, Thibaut Douché, Thibault Chaze, Mariette Matondo, Isabelle Dusfour
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0039570

Assessing Numerical Dependence in Gene Expression Summaries with the Jackknife Expression Difference
Cited by: 3
Author(s): John R. Stevens, Gabriel Nicholas
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0086538

Loss of CD34 Expression in Aging Human Choriocapillaris Endothelial Cells
Cited by: 18
Author(s): Elliott H. Sohn, Miles J. Flamme-Wiese, S. Scott Whitmore, Kai Wang, Budd A. Tucker, Robert F. Mullins
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0096153

Transcriptome Profiling of Human Ulcerative Colitis Mucosa Reveals Altered Expression of Pathways Enriched in Genetic Susceptibility Loci
Cited by: 8
Author(s): Christopher J. Cardinale, Zhi Wei, Jin Li, Junfei Zhu, Mengnan Gu, Robert N. Baldassano, Struan F.A. Grant, Hákon Hákonarson
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0060422

Search for Transcriptional and Metabolic Markers of Grape Pre-Ripening and Ripening and Insights into Specific Aroma Development in Three Portuguese Cultivars
Cited by: 58
Author(s): Ana Patrícia, Alexander Erban, Lisete Sousa, M. S. Pais, Joachim Kopka, Ana Margarida Fortes
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0161513

Preliminary Validation of a High Docosahexaenoic Acid (DHA) and -Linolenic Acid (ALA) Dietary Oil Blend: Tissue Fatty Acid Composition and Liver Proteome Response in Atlantic Salmon (Salmo salar) Smolts
Cited by: 8
Author(s): Waldo G. Nuez-Ortín, Chris Carter, Richard Wilson, Ira Cooke, Peter D. Nichols
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0023604

Profiling Trait Anxiety: Transcriptome Analysis Reveals Cathepsin B (Ctsb) as a Novel Candidate Gene for Emotionality in Mice
Cited by: 46
Author(s): Ludwig Czibere, Laura A. Baur, Anke Wittmann, Katja Gemmeke, Andrea Steiner, Peter Weber, Benno Pütz, Nafees Ahmad, Mirjam Bunck, Cornelia Graf, Regina Widner, Claudia Kühne, Markus Panhuysen, Boris Hambsch, Gabriele Rieder, Thomas Reinheckel, Christoph Peters, Florian Holsboer, Rainer Landgraf, Jan M. Deussing
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0145748

Escherichia coli under Ionic Silver Stress: An Integrative Approach to Explore Transcriptional, Physiological and Biochemical Responses
Cited by: 19
Author(s): Claire Saulou‐Bérion, Ignacio González, Brice Enjalbert, Jean‐Nicolas Audinot, Isabelle Fourquaux, Frédéric Jamme, Muriel Cocaign‐Bousquet, Muriel Mercier‐Bonin, Laurence Girbal
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0083330

Impact of Acute Metal Stress in Saccharomyces cerevisiae
Cited by: 71
Author(s): Dagmar Hosiner, Susanne Gerber, Hella Lichtenberg‐Fraté, Walter Glaser, Christoph Schüller, Edda Klipp
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0239971

Culture-dependent and -independent investigations of bacterial migration into doenjang from its components meju and solar salt
Cited by: 6
Author(s): Jungmin Lee, Seongkook Heo, Yoon-Su Kim, Jong Hoon Lee, Do‐Won Jeong
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0196743

Dietary challenges differentially affect activity and sleep/wake behavior in mus musculus: Isolating independent associations with diet/energy balance and body weight
Cited by: 1
Author(s): Isaac J. Perron, Brendan T. Keenan, Karthikeyani Chellappa, Nicholas F. Lahens, Nicole L. Yohn, Keith R. Shockley, Allan I. Pack, Sigrid C. Veasey
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0049831

Molecular Pathways Involved in Prostate Carcinogenesis: Insights from Public Microarray Datasets
Cited by: 18
Author(s): Sarah C. Baetke, Michiel E. Adriaens, Renaud Seigneuric, Chris T. Evelo, Lars Eijssen
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0008836

MicroRNA-145 Targets YES and STAT1 in Colon Cancer Cells
Cited by: 155
Author(s): Lea H. Gregersen, Anders Jacobsen, Lisa B. Frankel, Jiayu Wen, Anders Krogh, Anders H. Lund
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0009779

Hepatic Gene Expression Profile in Mice Perorally Infected with Echinococcus multilocularis Eggs
Cited by: 30
Author(s): Bruno Gottstein, Matthias Wittwer, Marc Schild, Michael Merli, Stephen L. Leib, Norbert Müller, Joachim Müller, Rolf Jaggi
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0001200

Covert Genetic Selections to Optimize Phenotypes
Cited by: 0
Author(s): Di Wu, Elizabeth Townsley, Alan M. Tartakoff
Software Mentions: 2
Published: almost 19 years ago

10.1371/journal.pone.0166147

SLC7A5 Functions as a Downstream Target Modulated by CRKL in Metastasis Process of Gastric Cancer SGC-7901 Cells
Cited by: 13
Author(s): Junqing Wang, Xiaochun Fei, Wenjun Wu, Xuehua Chen, Liping Su, Zhenggang Zhu, Yunyun Zhou
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0146257

Time-Course Analysis of Brain Regional Expression Network Responses to Chronic Intermittent Ethanol and Withdrawal: Implications for Mechanisms Underlying Excessive Ethanol Consumption
Cited by: 44
Author(s): Maren L. Smith, Marcelo F. López, Kellie J. Archer, Aaron R. Wolen, Howard C. Becker, Michael F. Miles
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0077936

Profiling Circulating MicroRNA Expression in Experimental Sepsis Using Cecal Ligation and Puncture
Cited by: 56
Author(s): Shao-Chun Wu, Johnson Chia‐Shen Yang, Cheng-Shyuan Rau, Yi‐Chun Chen, Tsu-Hsiang Lu, Ming‐Wei Lin, Siou-Ling Tzeng, Yi-Chan Wu, Chi‐Chuan Wu, Ching‐Hua Hsieh
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0090408

The CO-Regulation Database (CORD): A Tool to Identify Coordinately Expressed Genes
Cited by: 9
Author(s): John Fahrenbach, Jorge Andrade, Elizabeth M. McNally
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0236622

A new clinical prognostic nomogram for liver cancer based on immune score
Cited by: 6
Author(s): Qinyan Shen, Guoqing Hu, Jiaming Wu, Liting Lv
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0009114

Functional Overlap between eIF4G Isoforms in Saccharomyces cerevisiae
Cited by: 51
Author(s): Bryan K. Clarkson, Wendy V. Gilbert, Jennifer A. Doudna
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0014101

Interaction with Diurnal and Circadian Regulation Results in Dynamic Metabolic and Transcriptional Changes during Cold Acclimation in Arabidopsis
Cited by: 153
Author(s): Carmen Espinoza, Thomas Degenkolbe, Camila Caldana, Ellen Zuther, Andrea Leisse, Lothar Willmitzer, Dirk K. Hincha, Matthew A. Hannah
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0206312

Comparison of normalization approaches for gene expression studies completed with high-throughput sequencing
Cited by: 53
Author(s): Farnoosh Abbas‐Aghababazadeh, Qian Li, Brooke L. Fridley
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0071425

Analysis of Genome-Wide Changes in the Translatome of Arabidopsis Seedlings Subjected to Heat Stress
Cited by: 93
Author(s): Emilio Yángüez, Ana B. Castro-Sanz, Nuria Fernández-Bautista, Juan Carlos Oliveros, M. Mar Castellano
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0145252

Confounding Factors in the Transcriptome Analysis of an In-Vivo Exposure Experiment
Cited by: 12
Author(s): Oskar Bruning, Wendy Rodenburg, Paul Wackers, Conny van Oostrom, Martijs J. Jonker, R.J. Dekker, Han Rauwerda, Wim A. Ensink, Annemieke de Vries, Timo M. Breit
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0190439

Heterogeneous muscle gene expression patterns in patients with massive rotator cuff tears
Cited by: 7
Author(s): Michael C. Gibbons, Kathleen Fisch, Rajeswari Pichika, Timothy Cheng, Adam J. Engler, Simon Schenk, Joseph R. Lane, Anshu Singh, Samuel R. Ward
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0133894

Molecular Expression Profile Reveals Potential Biomarkers and Therapeutic Targets in Canine Endometrial Lesions
Cited by: 21
Author(s): Fabiana Azevedo Voorwald, Fábio Albuquerque Marchi, Rolando A R Villacis, Carlos Eduardo Fonseca-Alves, Gilson Hélio Toniollo, Renée Laufer Amorim, Sandra A. Drigo, Sílvia Regina Rogatto
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0212127

Leukemia multiclass assessment and classification from Microarray and RNA-seq technologies integration at gene expression level
Cited by: 29
Author(s): Daniel Castillo, Juan Manuel Gálvez, José Benavente Herrera, Fernando Rojas, Olga Valenzuela, Octavio Caba, José Luis Paniza Prados, Ignacio Rojas
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0230884

Global expression and CpG methylation analysis of primary endothelial cells before and after TNFa stimulation reveals gene modules enriched in inflammatory and infectious diseases and associated DMRs
Cited by: 11
Author(s): Brooke Rhead, Xiaorong Shao, Hong Quach, Poonam Ghai, Lisa F. Barcellos, Anne M. Bowcock
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0250239

Identification of ubiquitination-related genes in human glioma as indicators of patient prognosis
Cited by: 7
Author(s): Lei Wang, Yuelin Liu, Chengmin Xuan, Yong Liu, Hengliang Shi, Yong Gao
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0010431

A Comprehensive Panel of Three-Dimensional Models for Studies of Prostate Cancer Growth, Invasion and Drug Responses
Cited by: 298
Author(s): Ville Härmä, Johannes Virtanen, Rami Mäkelä, Antti P. Happonen, John-Patrick Mpindi, Matti Knuuttila, Pekka Kohonen, Jyrki Lötjönen, Olli Kallioniemi, Matthias Nees
Software Mentions: 2
Published: over 16 years ago

10.1371/journal.pone.0039621

A Daphnane Diterpenoid Isolated from Wikstroemia polyantha Induces an Inflammatory Response and Modulates miRNA Activity
Cited by: 9
Author(s): Anthony Khong, Roberto Forestieri, David E. Williams, Brian O. Patrick, Andrea D. Olmstead, Victoria Svinti, Emily K. Schaeffer, François Jean, Michel Roberge, Raymond J. Andersen, Eric Jan
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0017940

Acute Endotoxin-Induced Thymic Atrophy Is Characterized By Intrathymic Inflammatory and Wound Healing Responses
Cited by: 61
Author(s): Matthew J. Billard, Amanda Louise Gruver, Gregory D. Sempowski
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0137995

Enriched Bone Marrow Derived Disseminated Neuroblastoma Cells Can Be a Reliable Source for Gene Expression Studies—A Validation Study
Cited by: 5
Author(s): Fikret Rifatbegovic, Mojtaba Abbasi, Sabine Taschner‐Mandl, Maximilian Kauer, Andreas Weinhäusel, Rupert Handgretinger, Peter F. Ambros
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0066632

Genome-Wide DNA Methylation Analysis Reveals a Potential Mechanism for the Pathogenesis and Development of Uterine Leiomyomas
Cited by: 79
Author(s): Ryo Maekawa, Shun Sato, Yuriko Yamagata, Hiromi Asada, Isao Tamura, Lifa Lee, Maki Okada, Hiroshi Tamura, Eiichi Takaki, Asami Nakai, Norihiro Sugino
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0255293

CARD11 is a prognostic biomarker and correlated with immune infiltrates in uveal melanoma
Cited by: 2
Author(s): Xueying Shi, Shilin Xia, Yan Chu, Nan Yang, Jingyuan Zheng, Qianyi Chen, Fen Zeng, Yuankuan Jiang, Shifeng Fang, Jingrong Lin
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0222188

Genome-wide analysis of DNA methylation profile identifies differentially methylated loci associated with human intervertebral disc degeneration
Cited by: 23
Author(s): Akihiro Ikuno, Koji Akeda, Shin‐ichiro Takebayashi, Motomu Shimaoka, Katsuhiko Okumura, Akihiro Sudo
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0037880

Conserved Expression Signatures between Medaka and Human Pigment Cell Tumors
Cited by: 33
Author(s): Manfred Schartl, Susanne Kneitz, Brigitta Wilde, Toni U. Wagner, Christiaan V. Henkel, Herman P. Spaink, Svenja Meierjohann
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0150154

Urinary Exosomal miRNA Signature in Type II Diabetic Nephropathy Patients
Cited by: 168
Author(s): Denis Delić, Claudia Eisele, RM Schmid, Patrick Baum, Franziska Wiech, Martin Gerl, Heike Zimdahl, Steven S. Pullen, Richard Urquhart
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0001203

Microarray Expression Profiles of 20.000 Genes across 23 Healthy Porcine Tissues
Cited by: 27
Author(s): Henrik Hornshøj, Lene N Conley, Jakob Hedegaard, Peter Sørensen, Frank Panitz, Christian Berthou
Software Mentions: 2
Published: almost 19 years ago

10.1371/journal.pone.0097089

A Range Finding Protocol to Support Design for Transcriptomics Experimentation: Examples of In-Vitro and In-Vivo Murine UV Exposure
Cited by: 7
Author(s): Oskar Bruning, Wendy Rodenburg, Conny T. van Oostrom, Martijs J. Jonker, Mark de Jong, R.J. Dekker, Han Rauwerda, Wim A. Ensink, Annemieke de Vries, Timo M. Breit
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0251461

Multivariate meta-analysis reveals global transcriptomic signatures underlying distinct human naive-like pluripotent states
Cited by: 2
Author(s): Kory R. Johnson, Barbara S. Mallon, Yang C. Fann, Kevin G. Chen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0006779

New Alzheimer Amyloid β Responsive Genes Identified in Human Neuroblastoma Cells by Hierarchical Clustering
Cited by: 14
Author(s): Markus Uhrig, Carina Ittrich, Verena Wiedmann, Yuri P. Knyazev, Annette Weninger, Matthias Riemenschneider, Tobias Hartmann
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0111539

Caspase-1/ASC Inflammasome-Mediated Activation of IL-1β–ROS–NF-κB Pathway for Control of Trypanosoma cruzi Replication and Survival Is Dispensable in NLRP3−/− Macrophages
Cited by: 49
Author(s): Nilay Dey, Mala Sinha, Shivali Gupta, Mariela Natacha González, Rong Fang, Janice J. Endsley, Bruce A. Luxon, Nisha Garg
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0222717

Adverse prognosis of glioblastoma contacting the subventricular zone: Biological correlates
Cited by: 27
Author(s): Sharon Berendsen, Emma J. van Bodegraven, Tatjana Seute, Wim G.M. Spliet, Marjolein Geurts, Jeroen Hendrikse, Laurent Schoysman, Willemijn B Huiszoon, Meri R. J. Varkila, Soufyan Rouss, Erica H. Bell, Jérôme Kroonen, Arnab Chakravarti, Vincent Bours, Tom J. Snijders, Pierre A. Robe
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0193170

Vitamin C alters the amount of specific endoplasmic reticulum associated proteins involved in lipid metabolism in the liver of mice synthesizing a nonfunctional Werner syndrome (Wrn) mutant protein
Cited by: 9
Author(s): Lucie Aumailley, Florence Roux‐Dalvai, Isabelle Kelly, Arnaud Droit, Michel Lebel
Software Mentions: 2
Published: over 8 years ago