bioconductor: limma | Projects | Ecosyste.ms: Papers

10.18632/aging.202882

Transcriptome integration analysis and specific diagnosis model construction for Hodgkin's lymphoma, diffuse large B-cell lymphoma, and mantle cell lymphoma
Cited by: 2
Author(s): Wen‐Xing Li, Shao‐Xing Dai, Sanqi An, Tingting Sun, Justin Liu, Jun Wang, Leyna G. Liu, Yang Xiao, Hua Yang, Lixia Fan, Xiaoli Zhang, Wanqin Liao, Hua You, Luca Tamagnone, Fang Liu, Jing‐Fei Huang, Dahai Liu
Software Mentions: 3
Published: over 5 years ago

10.1007/s00401-020-02247-2

Clear cell meningiomas are defined by a highly distinct DNA methylation profile and mutations in SMARCE1
Cited by: 27
Author(s): Philipp Sievers, Martin Sill, Christina Blume, Arnault Tauziède‐Espariat, Daniel Schrimpf, Damian Stichel, David Reuß, Helin Dogan, Christian Hartmann, Christian Mawrin, Martin Hasselblatt, Walter Stummer, Uta Schick, Jürgen Hench, Stephan Frank, Ralf Ketter, Leonille Schweizer, Jens Schittenhelm, Stéphanie Puget, Sebastian Brandner, Zane Jaunmuktane, Benno Küsters, Zied Abdullaev, Melike Pekmezci, Matija Snuderl, Miriam Ratliff, Christel Herold‐Mende, Andreas Unterberg, Kenneth Aldape, David W. Ellison, Pieter Wesseling, Guido Reifenberger, Wolfgang Wick, Arie Perry, Pascale Varlet, Stefan M. Pfister, David Jones, Andreas von Deimling, Felix Sahm
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-019-44661-x

The ion channels and transporters gene expression profile indicates a shift in excitability and metabolisms during malignant progression of Follicular Lymphoma
Cited by: 18
Author(s): Alberto Magi, Marika Masselli, Cesare Sala, Angela Guerriero, Pasquale Laise, Benedetta Puccini, Luigi Rigacci, C Breschi, Olivia Crociani, Serena Pillozzi, Annarosa Arcangeli
Software Mentions: 3
Published: over 7 years ago

10.3389/fendo.2017.00099

Leptin Induces Mitosis and Activates the Canonical Wnt/β-Catenin Signaling Pathway in Neurogenic Regions of Xenopus Tadpole Brain
Cited by: 14
Author(s): Melissa Cui Bender, Christopher J. Sifuentes, Robert J. Denver
Software Mentions: 3
Published: over 9 years ago

10.3390/md19080429

RKC-B1 Blocks Activation of NF-κB and NLRP3 Signaling Pathways to Suppress Neuroinflammation in LPS-Stimulated Mice
Cited by: 3
Author(s): Man Liu, Yinglin Yang, Shanshan Zhang, Dong-Ni Liu, Lian-Hua Fang, Guanhua Du, Yue-Hua Wang
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2164-11-28

Regional regulation of transcription in the chicken genome
Cited by: 8
Author(s): Haisheng Nie, R.P.M.A. Crooijmans, J.W.M. Bastiaansen, Hendrik‐Jan Megens, Martien A. M. Groenen
Software Mentions: 3
Published: over 16 years ago

10.1155/2020/5156304

Comprehensive Analyses of miRNA-mRNA Network and Potential Drugs in Idiopathic Pulmonary Arterial Hypertension
Cited by: 8
Author(s): Chan Li, Zeyu Zhang, Qian Xu, Ruizheng Shi
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0092596

The Nerve Growth Factor Receptor CD271 Is Crucial to Maintain Tumorigenicity and Stem-Like Properties of Melanoma Cells
Cited by: 79
Author(s): Torben Redmer, Yvonne Welte, Diana Behrens, Iduna Fichtner, Dorothea Przybilla, Wasco Wruck, Marie–Laure Yaspo, Hans Lehrach, Reinhold Schäfer, Christian Regenbrecht
Software Mentions: 3
Published: over 12 years ago

10.3389/fchem.2020.593497

A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis
Cited by: 7
Author(s): Ushashi Banerjee, Santhosh Sankar, Amit Singh, Nagasuma Chandra
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12885-021-08331-4

Hsa_circ_0000301 facilitates the progression of cervical cancer by targeting miR-1228-3p/IRF4 Axis
Cited by: 9
Author(s): Zhanfeng Deng, Fangfang Dai, Quan Zhou, Yanxiang Cheng
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-016-2401-3

Comparative genome-wide transcriptome analysis of Vitis vinifera responses to adapted and non-adapted strains of two-spotted spider mite, Tetranyhus urticae
Cited by: 39
Author(s): José Díaz-Riquelme, Vladimir Zhurov, Cristina Rioja, Ignacio Pérez-Moreno, Rafael Torres‐Pérez, Jérôme Grimplet, Pablo Carbonell‐Bejerano, Sabina Bajda, Thomas Van Leeuwen, José M. Martínez‐Zapater, Miodrag Grbić, Vojislava Grbić
Software Mentions: 3
Published: over 10 years ago

10.1038/s41598-019-44882-0

Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development
Cited by: 15
Author(s): Elo Madissoon, Anastasios Damdimopoulos, Shintaro Katayama, Kaarel Krjutškov, Elisabet Einarsdottir, Katariina Mamia, Bert De Groef, Outi Hovatta, Juha Kere, Pauliina Damdimopoulou
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0164407

Ligand Independent and Subtype-Selective Actions of Thyroid Hormone Receptors in Human Adipose Derived Stem Cells
Cited by: 13
Author(s): Aleksandra Čvoro, Aleksandar Bajić, Aijun Zhang, Marisa Simon, Igor Golić, Douglas H. Sieglaff, Mirjana Maletić-Savatić, Aleksandra Korać, Paul Webb
Software Mentions: 3
Published: almost 10 years ago

10.1186/1755-8794-7-S1-S3

Integrative analysis reveals disease-associated genes and biomarkers for prostate cancer progression
Cited by: 22
Author(s): Yin Li, Wanwipa Vongsangnak, Luonan Chen, Bairong Shen
Software Mentions: 3
Published: over 12 years ago

10.3389/fncel.2014.00148

Deregulated expression of cytoskeleton related genes in the spinal cord and sciatic nerve of presymptomatic SOD1G93A Amyotrophic Lateral Sclerosis mouse model
Cited by: 24
Author(s): Jéssica Ruivo Maximino, Gilson Pereira de Oliveira, Chrystian Junqueira Alves, Gerson Chadi
Software Mentions: 3
Published: over 12 years ago

10.1177/1352458517721356

Hypermethylation of <i>MIR21</i> in CD4+ T cells from patients with relapsing-remitting multiple sclerosis associates with lower miRNA-21 levels and concomitant up-regulation of its target genes
Cited by: 31
Author(s): Sabrina Ruhrmann, Ewoud Ewing, Eliane Piket, Lara Kular, Julio C. C. Lorenzi, Sunjay Jude Fernandes, Hiromasa Morikawa, Shahin Aeinehband, Sergi Sayols-Baixeras, Stella Aslibekyan, Devin Absher, Donna K. Arnett, Jesper Tegnér, David Gomez-Cabrero, Fredrik Piehl, Maja Jagodic
Software Mentions: 3
Published: about 9 years ago

10.3389/fncel.2020.00239

The CNS Myelin Proteome: Deep Profile and Persistence After Post-mortem Delay
Cited by: 46
Author(s): Olaf Jahn, Sophie B Siems, Kathrin Kusch, Dörte Hesse, Ramona B. Jung, Thomas Liepold, Marina Uecker, Ting Sun, Hauke Werner
Software Mentions: 3
Published: about 6 years ago

10.3389/fncel.2016.00230

Altered Expression of Genes Encoding Neurotransmitter Receptors in GnRH Neurons of Proestrous Mice
Cited by: 32
Author(s): Csaba Vastagh, Annie Rodolosse, Norbert Solymosi, Zsolt Liposits
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-019-43512-z

Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-42680-2

Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts
Cited by: 31
Author(s): Yuanhang Liu, Pritha Chanana, Jaime Davila, Xiaonan Hou, Valentina Zanfagnin, Cordelia D. McGehee, Ellen L. Goode, Eric C. Polley, Paul Haluska, S. John Weroha, Chen Wang
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.102161

Identification of 9 key genes and small molecule drugs in clear cell renal cell carcinoma
Cited by: 47
Author(s): Yongwen Luo, Dexin Shen, Liang Chen, Gang Wang, Xuefeng Li, Kaiyu Qian, Yu Xiao, Xinghuan Wang, Lingao Ju
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0228764

Identification of microRNAs involved in NOD-dependent induction of pro-inflammatory genes in pulmonary endothelial cells
Cited by: 4
Author(s): Ann-Kathrin Vlacil, Evelyn Vollmeister, Wilhelm Bertrams, Florian Schoesser, Raghav Oberoi, Jutta Schuett, Harald Schuett, Sonja Huehn, Katrin Bedenbender, Bernd Schmeck, Bernhard Schieffer, Karsten Grote
Software Mentions: 3
Published: over 6 years ago

10.3389/fcimb.2017.00512

Toxoplasma gondii Infection Is Associated with Mitochondrial Dysfunction in-Vitro
Cited by: 33
Author(s): Genevieve Syn, Denise Anderson, Jenefer M. Blackwell, Sarra E. Jamieson
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-019-40857-3

Profiling of gallbladder carcinoma reveals distinct miRNA profiles and activation of STAT1 by the tumor suppressive miRNA-145-5p
Cited by: 23
Author(s): Benjamin Goeppert, Felicia Truckenmueller, Alessandro Ori, Valerie Fritz, Thomas Albrecht, Angelika Fraas, Dominique Scherer, Rosa González Silos, Carsten Sticht, Norbert Gretz, Arianeb Mehrabi, Melanie Bewerunge-Hudler, Stefan Pusch, Justo Lorenzo Bermejo, Péter Dietrich, Peter Schirmacher, Marcus Renner, Stephanie Roessler
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.202922

A novel gene signature for prognosis prediction and chemotherapy response in patients with pancreatic cancer
Cited by: 4
Author(s): Hongcao Lin, Chonghui Hu, Shusen Zheng, Xiang Zhang, Rufu Chen, Quanbo Zhou
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0002987

Identification of Functional Networks of Estrogen- and c-Myc-Responsive Genes and Their Relationship to Response to Tamoxifen Therapy in Breast Cancer
Cited by: 90
Author(s): Elizabeth A. Musgrove, C. Marcelo Sergio, Sherene Loi, Claire K. Inman, Luke R. Anderson, M. Chehani Alles, Mark Pinese, C. Elizabeth Caldon, Judith Schütte, Margaret Gardiner-Garden, Christopher J. Ormandy, Grant A. McArthur, Alison J. Butt, Robert L. Sutherland
Software Mentions: 3
Published: about 18 years ago

10.1038/s41598-019-40963-2

DNA methylation signature of smoking in lung cancer is enriched for exposure signatures in newborn and adult blood
Cited by: 27
Author(s): Kelly M. Bakulski, John Dou, Nan Lin, Stephanie J. London, Justin A. Colacino
Software Mentions: 3
Published: over 7 years ago

10.1186/s40478-021-01249-9

Immune cell deconvolution of bulk DNA methylation data reveals an association with methylation class, key somatic alterations, and cell state in glial/glioneuronal tumors
Cited by: 5
Author(s): Omkar Singh, Drew Pratt, Kenneth Aldape
Software Mentions: 3
Published: about 5 years ago

10.3389/fcimb.2018.00160

Group A Streptococcus M1T1 Intracellular Infection of Primary Tonsil Epithelial Cells Dampens Levels of Secreted IL-8 Through the Action of SpyCEP
Cited by: 20
Author(s): Amelia T. Soderholm, Timothy C. Barnett, Othmar Korn, Tania Rivera-Hernandez, Lisa M. Seymour, Benjamin L. Schulz, Victor Nizet, Christine A. Wells, Matthew J. Sweet, Mark J. Walker
Software Mentions: 3
Published: over 8 years ago

10.1186/s12885-021-08229-1

Identification of NTRK3 as a potential prognostic biomarker associated with tumor mutation burden and immune infiltration in bladder cancer
Cited by: 13
Author(s): Zhao Zhang, Yizhi Yu, Pengfei Zhang, Guofeng Ma, Mingxin Zhang, Ye Liang, Wei Jiao, Haitao Niu
Software Mentions: 3
Published: over 5 years ago

10.18632/oncotarget.26459

NKL homeobox gene NKX2-2 is aberrantly expressed in Hodgkin lymphoma
Cited by: 15
Author(s): Stefan Nagel, Roderick A.F. MacLeod, Claudia Pommerenke, Corinna Meyer, Maren Kaufmann, Hans G. Drexler
Software Mentions: 3
Published: over 7 years ago

10.3389/fcimb.2021.672472

P2x7 Receptor Signaling Blockade Reduces Lung Inflammation and Necrosis During Severe Experimental Tuberculosis
Cited by: 11
Author(s): Igor Santiago-Carvalho, Gislane Almeida-Santos, Caio César Barbosa Bomfim, Paula Carolina de Souza, Juan Carlo Santos e Silva, Bruno Marcel Silva de Melo, Eduardo Pinheiro Amaral, Marcos Vinícios Pinheiro Cione, Elena B. Lasunskaia, Mário Hiroyuki Hirata, José C. Alves‐Filho, Helder I. Nakaya, José María Álvarez, Maria Regina D’Império Lima
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.202876

Identification of prognostic biomarkers associated with the occurrence of portal vein tumor thrombus in hepatocellular carcinoma
Cited by: 10
Author(s): Tong Lin, Lin Zheng, Peipei Mai, E Zhang, Lisheng Peng
Software Mentions: 3
Published: over 5 years ago

10.1186/s12964-016-0142-1

Normalization of TAM post-receptor signaling reveals a cell invasive signature for Axl tyrosine kinase
Cited by: 26
Author(s): Stanley Kimani, Sushil Kumar, Viralkumar Davra, Yun‐Juan Chang, Canan Kasikara, Ke Geng, Wen-I Tsou, Shenyan Wang, Mainul Hoque, Andrej Boháč, Anita Lewis-Antes, Mariana S. De Lorenzo, Sergei V. Kotenko, Raymond B. Birge
Software Mentions: 3
Published: about 10 years ago

10.1155/2021/3170261

lncRNA PAPPA-AS1 Induces the Development of Hypertrophic Scar by Upregulating TLR4 through Interacting with TAF15
Cited by: 5
Author(s): Pengju Fan, Yongjie Wang, Jingjing Li, Man Fang
Software Mentions: 3
Published: about 5 years ago

10.1155/2021/2545459

Identification of Differentially Expressed circRNAs, miRNAs, and Genes in Patients Associated with Cartilaginous Endplate Degeneration
Cited by: 0
Author(s): Haiwei Xu, Yongjin Li, Jianhua Li, Zhenxin Huo, Guowang Li, Lilong Du, Lijun Tian, Bei Xu
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-38441-2

Elastic net-based prediction of IFN-β treatment response of patients with multiple sclerosis using time series microarray gene expression profiles
Cited by: 11
Author(s): Arika Fukushima, Masahiro Sugimoto, Satoru Hiwa, Tomoyuki Hiroyasu
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.25981

RNA based individualized drug selection in breast cancer patients without patient-matched normal tissue
Cited by: 1
Author(s): Michael Förster, Adam Mark, Friederike Egberts, Elisa Rosati, Elke Rodríguez, Martin Stanulla, Dirk Bauerschlag, Christian Schem, Nicolaì Maass, Anu Amallraja, Karla K. Murphy, Bruce Prouse, Raed Sulaiman, Brandon Young, Micaela Mathiak, Georg Hemmrich-Stanisak, David Ellinghaus, Stephan Weidinger, Philip Rosenstiel, Norbert Arnold, Brian Leyland‐Jones, Casey Williams, André Franke, Tobias Meißner
Software Mentions: 3
Published: about 8 years ago

10.1186/s12885-020-07393-0

HLA-DPA1 gene is a potential predictor with prognostic values in multiple myeloma
Cited by: 11
Author(s): Jie Yang, Fei Wang, Baoan Chen
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-018-37411-y

INSIdE NANO: a systems biology framework to contextualize the mechanism-of-action of engineered nanomaterials
Cited by: 25
Author(s): Angela Serra, Ivica Letunić, Vittorio Fortino, Richard D. Handy, Bengt Fadeel, Roberto Tagliaferri, Dario Greco
Software Mentions: 3
Published: over 7 years ago

10.3389/fcell.2021.705291

Autophagy-Related Genes and Long Noncoding RNAs Signatures as Predictive Biomarkers for Osteosarcoma Survival
Cited by: 8
Author(s): Jian Zhang, Rui Ding, Tianlong Wu
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-018-35868-5

In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors
Cited by: 11
Author(s): Suzanne Vanhauwaert, Bieke Decaesteker, Sara De Brouwer, Carina Leonelli, Kaat Durinck, Pieter Mestdagh, Jo Vandesompele, Karen Sermon, Geertrui Denecker, Christophe Van Neste, Franki Speleman, Katleen De Preter
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41418-018-0080-0

A kinome-wide RNAi screen identifies ALK as a target to sensitize neuroblastoma cells for HDAC8-inhibitor treatment
Cited by: 20
Author(s): Jing Shen, Sara Najafi, Sina Stäble, Johannes Fabian, E Koeneke, Fiona R. Kolbinger, Jagoda K. Wrobel, Benjamin Meder, Martin Distel, Tino Heimburg, Wolfgang Sippl, Manfred Jung, Heike Peterziel, D Kranz, Michael Boutros, Frank Westermann, Olaf Witt, Ina Oehme
Software Mentions: 3
Published: over 8 years ago

10.1038/cdd.2017.81

RIP4 inhibits STAT3 signaling to sustain lung adenocarcinoma differentiation
Cited by: 25
Author(s): Jawahar Kopparam, Johanna Chiffelle, Paolo Angelino, Alessandra Piersigilli, Nadine Zangger, Mauro Delorenzi, Etienne Meylan
Software Mentions: 3
Published: over 9 years ago

10.1038/s41418-018-0101-z

The mitochondrial citrate carrier, SLC25A1, drives stemness and therapy resistance in non-small cell lung cancer
Cited by: 75
Author(s): Harvey R. Fernandez, Shreyas M Gadre, Mingjun Tan, Garrett T. Graham, Rami Mosaoa, Martin S Ongkeko, Kyu Ah Kim, Rebecca B. Riggins, Erika Parasido, Iacopo Petrini, Stefania Pacini, Amrita K. Cheema, Rency S. Varghese, Habtom W. Ressom, Kun Zhang, Christopher Albanese, Aykut Üren, Mikell Paige, Giuseppe Giaccone, Maria Laura Avantaggiati
Software Mentions: 3
Published: over 8 years ago

10.1186/s12885-015-1994-2

Low-power photodynamic therapy induces survival signaling in perihilar cholangiocarcinoma cells
Cited by: 28
Author(s): Ruud Weijer, Mans Broekgaarden, Rowan F. van Golen, Esther Bulle, E. E. S. Nieuwenhuis, Aldo Jongejan, Perry D. Moerland, Antoine H. C. van Kampen, Thomas M. van Gulik, Michal Heger
Software Mentions: 3
Published: almost 11 years ago

10.3389/fcell.2021.655950

Prognostic Signature for Lung Adenocarcinoma Patients Based on Cell-Cycle-Related Genes
Cited by: 12
Author(s): Weijia Jiang, Jiameng Xu, Zirui Liao, Guangbin Li, Chengpeng Zhang, Yang Feng
Software Mentions: 3
Published: over 5 years ago

10.1186/bcr1604

Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data
Cited by: 122
Author(s): Anita Grigoriadis, Alan Mackay, Jorge S. Reis‐Filho, Dawn Steele, Christian Iseli, Brian J. Stevenson, C. Victor Jongeneel, Haukur Valgeirsson, Kerry Fenwick, Marjan Iravani, Maria Ignêz Leão, Andrew J.G. Simpson, Robert L. Strausberg, Parmjit Jat, Alan Ashworth, A. Munro Neville, Michael J. O’Hare
Software Mentions: 3
Published: almost 20 years ago

10.1186/1471-2164-12-10

Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array
Cited by: 10
Author(s): Yang Liu, Kunlin Zhang, Wei Dai, Ximiao He, Qian Zhao, Jing Wang, Zhong Sheng Sun
Software Mentions: 3
Published: over 15 years ago

10.1038/s41598-018-34292-z

Comprehensive Analysis of Gene Expression Profiles and DNA Methylome reveals Oas1, Ppie, Polr2g as Pathogenic Target Genes of Gestational Diabetes Mellitus
Cited by: 9
Author(s): Yan Zhang, Tiancheng Zhang, Yunyan Chen
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2180-7-78

Identification of human pathogens isolated from blood using microarray hybridisation and signal pattern recognition
Cited by: 48
Author(s): Herbert Wiesinger-Mayr, Klemens Vierlinger, Rudolf Pichler, Albert Kriegner, Alexander M. Hirschl, Elisabeth Presterl, Levente Bodrossy, Christa Noehammer
Software Mentions: 3
Published: over 19 years ago

10.3389/fcell.2021.671211

Identification of ZNF26 as a Prognostic Biomarker in Colorectal Cancer by an Integrated Bioinformatic Analysis
Cited by: 2
Author(s): Jiaqi Liu, Yimin Li, Yaqi Gan, Qing Xiao, Ruotong Tian, Guang Shu, Gang Yin
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-018-33897-8

Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation
Cited by: 13
Author(s): Mercedes Rivas, María Saura, Andrés Pérez‐Figueroa, Marina Panova, Tomas Johansson, Carl André, Armando Caballero, Emilio Rolán‐Alvarez, Kerstin Johannesson, Humberto Quesada
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-34191-3

Transcriptome analysis of extended-spectrum β-lactamase-producing Escherichia coli and methicillin-resistant Staphylococcus aureus exposed to cefotaxime
Cited by: 12
Author(s): P. R. Brochmann, Andrew Hesketh, Bimal Jana, G. H. Brodersen, Luca Guardabassi
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12885-019-5983-8

Integrated analysis of lncRNA-miRNA-mRNA ceRNA network in squamous cell carcinoma of tongue
Cited by: 208
Author(s): Ruisheng Zhou, Enxin Zhang, Sun Qi-zhong, Zeng Jie Ye, Jianwei Liu, Dajun Zhou, Ying Tang
Software Mentions: 3
Published: about 7 years ago

10.7717/peerj.8611

Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis
Cited by: 7
Author(s): Danli Zhong, Caimei Wu, Jingjing Bai, Duanfu Xu, Xiaofeng Zeng, Qian Wang
Software Mentions: 3
Published: over 6 years ago

10.1038/s41419-018-0342-2

Induction of ER and mitochondrial stress by the alkylphosphocholine erufosine in oral squamous cell carcinoma cells
Cited by: 30
Author(s): Shariq Ansari, Ashwini Kumar Sharma, Himanshu Soni, Doaa M. Ali, Björn Tews, Rainer König, Hansjörg Eibl, Martin R. Berger
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-33807-y

Characterization of the miRNA regulators of the human ovulatory cascade
Cited by: 23
Author(s): Gil M. Yerushalmi, Mali Salmon‐Divon, Libby Ophir, Yuval Yung, Micha Baum, Giovanni Coticchio, Rubens Fadini, Mario Mignini-Renzini, Mariabeatrice Dal Canto, Ronit Machtinger, Ettie Maman, Ariel Hourvitz
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-33478-9

A Comparative Assessment of Human and Chimpanzee iPSC-derived Cardiomyocytes with Primary Heart Tissues
Cited by: 54
Author(s): Bryan J. Pavlovic, Lauren E. Blake, Julien Roux, Claudia Chavarria, Yoav Gilad
Software Mentions: 3
Published: almost 8 years ago

10.7717/peerj.8930

Transcriptome analysis revealed key prognostic genes and microRNAs in hepatocellular carcinoma
Cited by: 24
Author(s): Xi Ma, Lin Zhou, Shusen Zheng
Software Mentions: 3
Published: over 6 years ago

10.3390/brainsci8120227

Integrative Analysis of Global Gene Expression Identifies Opposite Patterns of Reactive Astrogliosis in Aged Human Prefrontal Cortex
Cited by: 9
Author(s): César Payán‐Gómez, Diego Avendaño Rodríguez, Diana Amador-Muñoz, Sandra Ramírez-Clavijo
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-018-33272-7

Increased levels of circulating MMP3 correlate with severe rejection in face transplantation
Cited by: 18
Author(s): Branislav Kollar, Andrey V. Shubin, Thiago J. Borges, Sotirios Tasigiorgos, Thet Su Win, Christine G. Lian, Simon T. Dillon, Xuesong Gu, Iris Wyrobnik, Gëorge F. Murphy, Bohdan Pomahac, Towia A. Libermann, Leonardo V. Riella
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12885-021-08765-w

A TP53 mutation model for the prediction of prognosis and therapeutic responses in head and neck squamous cell carcinoma
Cited by: 9
Author(s): Congyu Shi, Shan Liu, Xudong Tian, Xiaoyi Wang, Pan Gao
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2407-10-532

Robust assignment of cancer subtypes from expression data using a uni-variate gene expression average as classifier
Cited by: 7
Author(s): Martin Lauss, Attila Frigyesi, Tobias Rydén, Mattias Höglund
Software Mentions: 3
Published: almost 16 years ago

10.7717/peerj.7873

Identification of crucial genes in abdominal aortic aneurysm by WGCNA
Cited by: 61
Author(s): Siliang Chen, Dan Yang, Chuxiang Lei, Yuan Li, Xiaoning Sun, Mengyin Chen, Xiaoxian Wu, Yuehong Zheng
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41419-021-03955-7

LncRNA RCAT1 promotes tumor progression and metastasis via miR-214-5p/E2F2 axis in renal cell carcinoma
Cited by: 22
Author(s): Renbo Guo, Benkui Zou, Yiran Liang, Jiasheng Bian, Jian Xu, Qian Zhou, Chao Zhang, Tao Chen, Mei Yang, Huansheng Wang, Fajun Pei, Zhonghua Xu
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2407-14-246

Gene expression profiling reveals activation of the FA/BRCA pathway in advanced squamous cervical cancer with intrinsic resistance and therapy failure
Cited by: 41
Author(s): Ovidiu Bălăcescu, Loredana Bălăcescu, Oana Tudoran, Nicolae Todor, Meda Rus, Rareș Buiga, Sergiu Şuşman, Bogdan Fetică, Laura Pop, Laura Iuliana Maja, Simona Vișan, Claudia Ordeanu, Ioana Berindan‐Neagoe, Viorica Nagy
Software Mentions: 3
Published: over 12 years ago

10.1186/s12885-021-08547-4

Correlation between vascular endothelial growth factor pathway and immune microenvironment in head and neck squamous cell carcinoma
Cited by: 4
Author(s): Chao Zhu, Liqun Gu, Zelong Liu, Li Jiang, Meiling Yao, Changyun Fang
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-021-07655-6

Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines
Cited by: 9
Author(s): Virginia Mwape, Fredrick M. Mobegi, Roshan Regmi, Toby E. Newman, Lars G. Kamphuis, Mark Derbyshire
Software Mentions: 3
Published: over 5 years ago

10.1155/2020/2064582

ID1 As a Prognostic Biomarker and Promising Drug Target Plays a Pivotal Role in Deterioration of Clear Cell Renal Cell Carcinoma
Cited by: 1
Author(s): Xiangmin Qiu, Yue Gu, Yilu Ni, Qianyin Li
Software Mentions: 3
Published: almost 6 years ago

10.18632/aging.101028

Ischemic stroke patients are biologically older than their chronological age
Cited by: 46
Author(s): Carolina Soriano‐Tárraga, Eva Giralt-Steinhauer, Marina Mola-Caminal, Rosa María Vivanco-Hidalgo, Ángel Ois, Ana Rodríguez-Campello, Elisa Cuadrado-Godia, Sergi Sayols-Baixeras, Roberto Elosúa, Jaume Roquer, Jordi Jiménez‐Conde
Software Mentions: 3
Published: about 10 years ago

10.18632/aging.102926

Development of an immune-related prognostic index associated with hepatocellular carcinoma
Cited by: 24
Author(s): Bo Hu, Xiaobo Yang, Xinting Sang
Software Mentions: 3
Published: over 6 years ago

10.18632/aging.103645

Bioinformatics analysis of the clinical value and potential mechanisms of AHNAK2 in papillary thyroid carcinoma
Cited by: 12
Author(s): Zhenyu Xie, Yu Lun, Xin Li, Yuzhen He, Song Wu, Shiyue Wang, Jing Sun, Yuchen He, Jian Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12885-016-2936-3

Global DNA methylation profiling uncovers distinct methylation patterns of protocadherin alpha4 in metastatic and non-metastatic rhabdomyosarcoma
Cited by: 11
Author(s): Lucia Tombolan, Elena Poli, Paolo Martini, Angelica Zin, Caterina Millino, Beniamina Pacchioni, Barbara Celegato, Gianni Bisogno, Chiara Romualdi, Angelo Rosolen, Gerolamo Lanfranchi
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41419-021-04107-7

PPFIBP1 induces glioma cell migration and invasion through FAK/Src/JNK signaling pathway
Cited by: 16
Author(s): Caihua Dong, Xinying Li, Yang Jiao, Detian Yuan, Yuanshuai Zhou, Yina Zhang, Guohua Shi, Ruobing Zhang, Jianping Liu, Peng Fu, Minxuan Sun
Software Mentions: 3
Published: about 5 years ago

10.1186/s12885-018-5061-7

Metabolic control of PPAR activity by aldehyde dehydrogenase regulates invasive cell behavior and predicts survival in hepatocellular and renal clear cell carcinoma
Cited by: 18
Author(s): Diāna Andrējeva, Jan-Michael Kugler, Thanh Hung Nguyen, Anders Malmendal, Magnus Holm, Birgitte Groenkaer Toft, Anand C Loya, Stephen M. Cohen
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12885-020-06719-2

Construction of an integrated human osteosarcoma database, HOsDb, based on literature mining, microarray analysis, and database retrieval
Cited by: 2
Author(s): Yun-Yu Sun, Lishan Wang, Changkuan Li, Rui Gu, Weidong Zang, Wei Song, Peng Xia
Software Mentions: 3
Published: over 6 years ago

10.3389/fcell.2020.602174

A Prognostic Model for Colon Cancer Patients Based on Eight Signature Autophagy Genes
Cited by: 26
Author(s): Jiasheng Xu, Siqi Dai, Ying Yuan, Qian Xiao, Kefeng Ding
Software Mentions: 3
Published: almost 6 years ago

10.3389/fcell.2021.668738

Screening for Core Genes Related to Pathogenesis of Alzheimer’s Disease
Cited by: 3
Author(s): Long-Xiu Yang, Yuan Qin, Chongdong Jian
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-12-610

Expression QTL mapping in regulatory and helper T cells from the BXD family of strains reveals novel cell-specific genes, gene-gene interactions and candidate genes for auto-immune disease
Cited by: 10
Author(s): Rudi Alberts, Hairong Chen, Claudia Pommerenke, August B. Smit, Sabine Spijker, Robert W. Williams, Robert Geffers, Dunja Bruder, Klaus Schughart
Software Mentions: 3
Published: almost 15 years ago

10.7717/peerj.6555

Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA
Cited by: 33
Author(s): Wangxiao Xia, Qin Yu, Gong‐Hua Li, Yaowen Liu, Fu-Hui Xiao, Libin Yang, Zia Ur Rahman, Haotian Wang, Qing‐Peng Kong
Software Mentions: 3
Published: over 7 years ago

10.3390/ijms22020832

Common Transcriptional Program of Liver Fibrosis in Mouse Genetic Models and Humans
Cited by: 3
Author(s): Kaja Blagotinšek Cokan, Žiga Urlep, Miha Moškon, Miha Mraz, Xiang Yi Kong, Winnie Eskild, Damjana Rozman, Peter Juvan, Tadeja Režen
Software Mentions: 3
Published: over 5 years ago

10.3390/medicina57090861

Gene Expression Analysis in Patients with Cocaine-Induced Midline Destructive Lesions
Cited by: 3
Author(s): Matteo Trimarchi, Giacomo Bertazzoni, Alessandro Vinciguerra, Celia Pardini, Fabio Simeoni, Davide Cittaro, Mario Bussi, Dejan Lazarevic
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2021.580834

Construction of circRNA-miRNA-mRNA Network for Exploring Underlying Mechanisms of Lubrication Disorder
Cited by: 2
Author(s): Shengnan Cong, Jinlong Li, Jingjing Zhang, Jingyi Feng, Aixia Zhang, Lianjun Pan, Jianhua Ma
Software Mentions: 3
Published: over 5 years ago

10.3389/fcell.2021.718638

Identification of ARHGEF38, NETO2, GOLM1, and SAPCD2 Associated With Prostate Cancer Progression by Bioinformatic Analysis and Experimental Validation
Cited by: 8
Author(s): Zhuolun Sun, Yunfei Mao, Xu Zhang, Shuo Lu, Hua Wang, Chi Zhang, Chutian Xiao, Yinghao Cao, Yunhao Qing, Yu Wang, Ké Li
Software Mentions: 3
Published: about 5 years ago

10.1038/s41419-021-03932-0

An integrative transcriptome study reveals Ddit4/Redd1 as a key regulator of cancer cachexia in rodent models
Cited by: 14
Author(s): Mengyuan Niu, Li Li, Zhonglan Su, Lulu Wei, Wenyuan Pu, Chen Zhao, Yibing Ding, Junaid Wazir, Wangsen Cao, Shiyu Song, Qian Gao, Hongwei Wang
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2020.584232

HS-5 and HS-27A Stromal Cell Lines to Study Bone Marrow Mesenchymal Stromal Cell-Mediated Support to Cancer Development
Cited by: 24
Author(s): Annalisa Adamo, Pietro Delfino, Alessandro Gatti, Alice Bonato, Paul Takam Kamga, Ilaria Tanasi, Stefano Ugel, Angela Mercuri, Simone Caligola, Mauro Krampera
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41419-020-03181-7

Calcium and TRPV4 promote metastasis by regulating cytoskeleton through the RhoA/ROCK1 pathway in endometrial cancer
Cited by: 53
Author(s): Xingchen Li, Yuan Cheng, Zhiqi Wang, Jingyi Zhou, Yuanyuan Jia, Xijing He, Lijun Zhao, Yangyang Dong, Fan Yuan, Xiao Yang, Boqiang Shen, Xiangsong Wu, Jiaqi Wang, Chunyang Xiong, Lihui Wei
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41419-018-0865-6

A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma
Cited by: 35
Author(s): Berglind O. Einarsdottir, Jan Ch Karlsson, Elin Söderberg, Mattias F. Lindberg, Elisa Funck‐Brentano, Henrik Jespersen, Siggeir F. Brynjólfsson, Roger Olofsson Bagge, Louise Carstam, Martin Scobie, Tobias Koolmeister, Olov Wallner, Ulrika Stierner, Ulrika Warpman Berglund, Lars Ny, Lisa M. Nilsson, Erik Larsson, Thomas Helleday, Jonas A. Nilsson
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-018-5000-7

Murine host response to Neisseria gonorrhoeae upper genital tract infection reveals a common transcriptional signature, plus distinct inflammatory responses that vary between reproductive cycle phases
Cited by: 11
Author(s): Ian Francis, Epshita A. Islam, Adam C. Gower, Yazdani B. Shaik‐Dasthagirisaheb, Scott D. Gray-Owen, Lee M. Wetzler
Software Mentions: 3
Published: about 8 years ago

10.3389/fcell.2021.739509

Integrated Analysis of Stemness-Related LncRNAs Helps Predict the Immunotherapy Responsiveness of Gastric Cancer Patients
Cited by: 1
Author(s): Quan Jiang, Lingli Chen, Hao Chen, Zhaoqing Tang, Fenglin Liu, Yihong Sun
Software Mentions: 3
Published: about 5 years ago

10.3389/fcell.2020.561907

DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA
Cited by: 19
Author(s): Laura Smyth, Christopher Patterson, Elizabeth Swan, Alexander P. Maxwell, Amy Jayne McKnight
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2164-15-S1-S13

Application of microRNA and mRNA expression profiling on prognostic biomarker discovery for hepatocellular carcinoma
Cited by: 35
Author(s): Lin Wei, Baofeng Lian, Yuannv Zhang, Wei Li, Jianren Gu, Xiang He, Lu Xie
Software Mentions: 3
Published: over 12 years ago

10.18632/aging.102943

Genetic networks in Parkinson’s and Alzheimer’s disease
Cited by: 23
Author(s): Jack Kelly, Rana Moyeed, Camille Carroll, Shouqing Luo, Xinzhong Li
Software Mentions: 3
Published: over 6 years ago

10.3389/fcell.2021.694769

Comparison of Genome-Wide DNA Methylation Profiles of Human Fetal Tissues Conceived by in vitro Fertilization and Natural Conception
Cited by: 4
Author(s): Ye Liu, Xinzhu Li, Songchang Chen, Li Wang, Ya‐Jing Tan, Xiaocui Li, Lin Tang, Junyu Zhang, Dandan Wu, Yanting Wu, Xinmei Liu, Yimin Zhu, Jian‐Zhong Sheng, Jiexue Pan, Li Jin, He‐Feng Huang
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-230X-10-60

The Role of T cell PPAR γ in mice with experimental inflammatory bowel disease
Cited by: 68
Author(s): Amir J. Guri, Saroj Kant Mohapatra, William Horne, Raquel Hontecillas, Josep Bassaganya‐Riera
Software Mentions: 3
Published: over 16 years ago

10.3389/fcell.2021.703629

N6-Methylandenosine-Related lncRNA Signature Is a Novel Biomarkers of Prognosis and Immune Response in Colon Adenocarcinoma Patients
Cited by: 14
Author(s): Peiling Zhang, Guolong Liu, Lin Lü
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-017-3672-z

Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos
Cited by: 12
Author(s): Han Rauwerda, J.F.B. Pagano, Wim C. de Leeuw, Wim A. Ensink, Ulrike Nehrdich, Mark de Jong, Martijs J. Jonker, Herman P. Spaink, Timo M. Breit
Software Mentions: 3
Published: over 9 years ago

10.7717/peerj.8907

Weighted gene correlation network analysis reveals novel biomarkers associated with mesenchymal stromal cell differentiation in early phase
Cited by: 9
Author(s): Bin Xiao, Guozhu Wang, Weiwei Li
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-017-3816-1

Integrating transcriptomics and metabolomics for the analysis of the aroma profiles of Saccharomyces cerevisiae strains from diverse origins
Cited by: 30
Author(s): Inês Mendes, Isabelle Sanchez, Ricardo Franco-Duarte, Carole Camarasa, Dorit Elisabeth Schuller, Sylvie Dequin, Maria João Sousa
Software Mentions: 3
Published: over 9 years ago

Projects: bioconductor: limma

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Papers Mentioning limma 7,776