bioconductor: limma | Projects | Ecosyste.ms: Papers

10.7150/jca.49557

Construction of novel mRNA-miRNA-lncRNA regulatory networks associated with prognosis of ovarian cancer
Cited by: 18
Author(s): Lingling Gao, Xiao Li, Xin Nie, Qin Guo, Qing Liu, Yue Qi, Juanjuan Liu, Bei Lin
Software Mentions: 4
Published: over 6 years ago

10.7150/jca.49392

Identifying Key Genes for Nasopharyngeal Carcinoma by Prioritized Consensus Differentially Expressed Genes Caused by Aberrant Methylation
Cited by: 9
Author(s): Yunqin Chen, Chun Zhou, Hua-Bin Li, Hong Li, Yixue Li
Software Mentions: 4
Published: over 5 years ago

10.7150/jca.50462

Classification of Clear Cell Renal Cell Carcinoma based on Tumor Suppressor Genomic Profiling
Cited by: 2
Author(s): Weimin Zhong, Fengling Zhang, Chaoqun Huang, Yao Lin, Jian Huang
Software Mentions: 4
Published: over 5 years ago

10.3390/nu12123602

Epigenetic Patterns in Five-Year-Old Children Exposed to a Low Glycemic Index Dietary Intervention during Pregnancy: Results from the ROLO Kids Study
Cited by: 10
Author(s): Aisling A. Geraghty, A. Sexton-Oates, Eileen C. O’Brien, Richard Saffery, Fionnuala M. McAuliffe
Software Mentions: 4
Published: almost 6 years ago

10.7717/peerj.8763

Identification of key genes and pathways affected in epicardial adipose tissue from patients with coronary artery disease by integrated bioinformatics analysis
Cited by: 6
Author(s): Liao Tan, Qian Xu, Qianchen Wang, Ruizheng Shi, Guogang Zhang
Software Mentions: 4
Published: over 6 years ago

10.1186/s13058-020-01295-6

Secreted breast tumor interstitial fluid microRNAs and their target genes are associated with triple-negative breast cancer, tumor grade, and immune infiltration
Cited by: 24
Author(s): Thilde Terkelsen, Francesco Russo, Pavel Gromov, Vilde Drageset Haakensen, Søren Brunak, Irina Gromova, Anders Krogh, Elena Papaleo
Software Mentions: 4
Published: about 6 years ago

10.1186/s13058-019-1159-3

On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer
Cited by: 32
Author(s): Richard J. Bownes, Arran Turnbull, Carlos Martínez-Pérez, David Cameron, Andrew H. Sims, Olga Oikonomidou
Software Mentions: 4
Published: over 7 years ago

10.7150/jca.51173

Identification of a Prognostic Signature Model with Tumor Microenvironment for predicting Disease-free Survival after Radical Prostatectomy
Cited by: 6
Author(s): Hao Zhao, Xuening Zhang, Zhan Shi, Bingxin Guo, Wenli Zhang, Kun He, Xueqi Hu, Songhe Shi
Software Mentions: 4
Published: over 5 years ago

10.1155/2021/4338838

A Radioresponse-Related lncRNA Biomarker Signature for Risk Classification and Prognosis Prediction in Non-Small-Cell Lung Cancer
Cited by: 14
Author(s): Jiahang Song, Shuming Zhang, Yuanyuan Sun, Junjie Gu, Ziqi Ye, Xinchen Sun, Qiyun Tang
Software Mentions: 4
Published: almost 5 years ago

10.7150/jca.52105

Identification of the hub genes and prognostic indicators of gastric cancer and correlation of indicators with tumor-infiltrating immune cell levels
Cited by: 4
Author(s): Yun Ji, Lu Gao, Can Zhang, Xu Sun, Liping Dai, Zhenyu Ji, Jianying Zhang, Zhida Zhang, Weimin Cao, Yang Zhao, Liguo Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/s13058-020-01318-2

MDM2 inhibition in combination with endocrine therapy and CDK4/6 inhibition for the treatment of ER-positive breast cancer
Cited by: 35
Author(s): Neil Portman, Heloisa Helena Milioli, Sarah Alexandrou, Rhiannon Coulson, Aliza Yong, Kristine J. Fernandez, Karin K.M. Chia, Ensar Halilovic, Davendra Segara, Andrew Parker, Sue Haupt, Ygal Haupt, Wayne D. Tilley, Alexander Swarbrick, C. Elizabeth Caldon, Elgene Lim
Software Mentions: 4
Published: about 6 years ago

10.7150/jca.57225

Integrating 13 Microarrays to Construct a 6 RNA-binding proteins Prognostic Signature for Gastric Cancer patients
Cited by: 0
Author(s): Liqun Zhou, Qi Zhou, You Wu, Lin Xin
Software Mentions: 4
Published: over 5 years ago

10.1002/jcb.29128

NCF2, MYO1F, S1PR4, and FCN1 as potential noninvasive diagnostic biomarkers in patients with obstructive coronary artery: A weighted gene co‐expression network analysis
Cited by: 24
Author(s): Xiangang Mo, Wei Liu, Yunan Yang, Saber Imani, Shan Lu, Guorong Dan, Xuqiang Nie, Jun Yan, Rong Zhan, Xiaohui Li, Youcai Deng, Bingbo Chen, Yuchen Cai
Software Mentions: 4
Published: about 7 years ago

10.1111/jcmm.14585

Differential coexpression networks in bronchiolitis and emphysema phenotypes reveal heterogeneous mechanisms of chronic obstructive pulmonary disease
Cited by: 11
Author(s): Jiangyue Qin, Ting Yang, Ni Zeng, Chun Wan, Lijuan Gao, Xiaoou Li, Lei Chen, Yongchun Shen, Fuqiang Wen
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-019-5669-2

Elevated temperatures cause loss of seed set in common bean (Phaseolus vulgaris L.) potentially through the disruption of source-sink relationships
Cited by: 39
Author(s): Afshin Soltani, Sarathi M. Weraduwage, Thomas D. Sharkey, David B. Lowry
Software Mentions: 4
Published: over 7 years ago

10.1016/j.ebiom.2018.09.024

Glucocorticoid deficiency causes transcriptional and post-transcriptional reprogramming of glutamine metabolism
Cited by: 10
Author(s): Meltem Weger, Benjamin D. Weger, Benjamin Görling, Gernot Poschet, Melek Yıldız, Rüdiger Hell, Burkhard Luy, Teoman Akçay, Tülay Güran, Thomas Dickmeis, Ferenc Müller, Nils Krone
Software Mentions: 4
Published: almost 8 years ago

10.7717/peerj.7313

Bioinformatics analysis of microarray data to identify the candidate biomarkers of lung adenocarcinoma
Cited by: 37
Author(s): Tingting Guo, Hongwen Ma, Yuting Zhou
Software Mentions: 4
Published: about 7 years ago

10.3389/fgene.2020.00912

Identification and Validation of an Immunological Expression-Based Prognostic Signature in Breast Cancer
Cited by: 7
Author(s): Jianying Pei, Yan Li, Tianxiong Su, Qiaomei Zhang, Xiaohai He, Dan Tao, Yanyun Wang, Manqiu Yuan, Yanping Li
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2164-15-341

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics
Cited by: 34
Author(s): Ghanasyam Rallapalli, Eric Kemen, Alexandre Robert-Seilaniantz, Cécile Segonzac, Graham J. Etherington, Kee Hoon Sohn, Dan MacLean, Jonathan D. G. Jones
Software Mentions: 4
Published: over 12 years ago

10.18632/oncotarget.13806

Bronchial airway gene expression signatures in mouse lung squamous cell carcinoma and their modulation by cancer chemopreventive agents
Cited by: 20
Author(s): Donghai Xiong, Jing Pan, Qi Zhang, Éva Szabó, Mark Steven Miller, Ronald A. Lubet, Ming You, Yian Wang
Software Mentions: 4
Published: almost 10 years ago

10.1111/jcmm.15650

Combined analysis of RNA‐sequence and microarray data reveals effective metabolism‐based prognostic signature for neuroblastoma
Cited by: 4
Author(s): Xinyao Meng, Chenzhao Feng, Erhu Fang, Jiexiong Feng, Xiang Zhao
Software Mentions: 4
Published: about 6 years ago

10.7717/peerj.3394

SIX4 promotes metastasis via activation of the PI3K-AKT pathway in colorectal cancer
Cited by: 26
Author(s): Guodong Li, Fang Hu, Xuelai Luo, Jian Hu, Yongzeng Feng
Software Mentions: 4
Published: over 9 years ago

10.18632/oncotarget.15068

Genome-scale analysis identifies GJB2 and ERO1LB as prognosis markers in patients with pancreatic cancer
Cited by: 39
Author(s): Tao Zhu, Yuanfeng Gao, Yixin Chen, Zhibin Wang, Ji‐Ye Yin, Xiao‐Yuan Mao, Xi Li, Wei Zhang, Hong‐Hao Zhou, Zhao‐Qian Liu
Software Mentions: 4
Published: over 9 years ago

10.3390/plants9121812

Comparative Transcriptome Analysis of Iron and Zinc Deficiency in Maize (Zea mays L.)
Cited by: 23
Author(s): Mallana Gowdra Mallikarjuna, Nepolean Thirunavukkarasu, R.C. Sharma, Kaliyugam Shiriga, Firoz Hossain, Jayant S. Bhat, Amitha Cr Mithra, Soma S. Marla, K.M. Manjaiah, A. Ramachandra Rao, H. S. Gupta
Software Mentions: 3
Published: over 5 years ago

10.1186/s12885-021-08634-6

Overexpression of UBE2C in esophageal squamous cell carcinoma tissues and molecular analysis
Cited by: 6
Author(s): Rong Li, Xing-Feng Pang, Zhi‐Guang Huang, Lihua Yang, Zhigang Peng, Jie Ma, Rong‐Quan He
Software Mentions: 3
Published: about 5 years ago

10.1186/s12885-021-08203-x

A genomic-clinicopathologic Nomogram for the preoperative prediction of lymph node metastasis in gastric cancer
Cited by: 5
Author(s): Xin Zhong, Feichao Xuan, Yun Qian, Junhai Pan, Suihan Wang, Wenchao Chen, Tianyu Lin, Hepan Zhu, Xianfa Wang, Guanyu Wang
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2407-11-450

Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa
Cited by: 30
Author(s): Stefan Enroth, Alvaro Rada-Iglesisas, Robin Andersson, Ola Wallerman, Alkwin Wanders, Lars Påhlman, Jan Komorowski, Claes Wadelius
Software Mentions: 3
Published: almost 15 years ago

10.1186/s12885-021-08550-9

Quantification of m6A RNA methylation modulators pattern was a potential biomarker for prognosis and associated with tumor immune microenvironment of pancreatic adenocarcinoma
Cited by: 30
Author(s): Lianzi Wang, Shubing Zhang, Huimin Li, Yang Xu, Qiang Wu, Jilong Shen, Tao Li, Yuanhong Xu
Software Mentions: 3
Published: about 5 years ago

10.1186/s12885-020-07529-2

Increased E2F2 predicts poor prognosis in patients with HCC based on TCGA data
Cited by: 12
Author(s): Zhili Zeng, Zebiao Cao, Ying Tang
Software Mentions: 3
Published: almost 6 years ago

10.1186/1471-2407-13-585

The oncogenic properties of EWS/WT1 of desmoplastic small round cell tumors are unmasked by loss of p53 in murine embryonic fibroblasts
Cited by: 10
Author(s): Pratiti Bandopadhayay, Anissa Jabbour, Christopher D. Riffkin, Marika Salmanidis, Lavinia Gordon, Dean Popovski, Lin Rigby, David M. Ashley, D. Neil Watkins, David M. Thomas, Elizabeth Algar, Paul G. Ekert
Software Mentions: 3
Published: almost 13 years ago

10.1186/1471-2407-14-64

Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma
Cited by: 21
Author(s): Marion Fehlker, Matthew R. Huska, Thomas Jöns, Miguel A. Andrade‐Navarro, Wolfgang Kemmner
Software Mentions: 3
Published: over 12 years ago

10.1186/s12885-021-08318-1

Highly heterogeneous-related genes of triple-negative breast cancer: potential diagnostic and prognostic biomarkers
Cited by: 12
Author(s): Yiduo Liu, Linxin Teng, Shiyi Fu, Guiyang Wang, Zhengjun Li, Chao Ding, Haodi Wang, Lei Bi
Software Mentions: 3
Published: over 5 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/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

10.1186/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

10.1186/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

10.1186/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

10.1186/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

10.1186/1471-2407-14-246

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/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

10.1186/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

10.1186/1471-230X-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

10.1186/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

10.1186/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

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

10.1186/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

10.1186/1471-2164-11-28

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

10.1186/s12864-015-2169-x

Genome-wide mapping of Hif-1α binding sites in zebrafish
Cited by: 29
Author(s): David Greenald, Justin Jeyakani, Bernd Pelster, Ian Sealy, Sinnakaruppan Mathavan, Fredericus J. van Eeden
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-019-5556-x

Linear models enable powerful differential activity analysis in massively parallel reporter assays
Cited by: 272
Author(s): Leslie Myint, Dimitrios Avramopoulos, Loyal A. Goff, Kasper D. Hansen
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-11-134

Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles
Cited by: 32
Author(s): Robert Kitchen, Victoria Sabine, Andrew H. Sims, E.J. Macaskill, Lorna Renshaw, Jeremy Thomas, Jano van Hemert, JM Dixon, John M.S. Bartlett
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2164-11-27

Genomics Portals: integrative web-platform for mining genomics data
Cited by: 13
Author(s): Kaustubh Shinde, Mukta Phatak, Johannes M. Freudenberg, Jing Chen, Qian Li, Joshi K Vineet, Zhen Hu, Krishnendu Ghosh, Jarosław Meller, Mario Medvedovic
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2164-14-770

The periodontal pathogen Porphyromonas gingivalis changes the gene expression in vascular smooth muscle cells involving the TGFbeta/Notch signalling pathway and increased cell proliferation
Cited by: 28
Author(s): Boxi Zhang, Ali Ateia Elmabsout, Hazem Khalaf, Vladimir Basic, Kartheyaene Jayaprakash, Robert L. Kruse, Torbjörn Bengtsson, Allan Sirsjö
Software Mentions: 3
Published: over 13 years ago

10.1186/s12864-018-4525-0

MethCNA: a database for integrating genomic and epigenomic data in human cancer
Cited by: 11
Author(s): Gaofeng Deng, Jian Yang, Qing Zhang, Zhi‐Xiong Jim Xiao, Haoyang Cai
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-021-07426-3

Transcriptome analysis of the transdifferentiation of canine BMSCs into insulin producing cells
Cited by: 2
Author(s): Jinglu Wang, Pengxiu Dai, Tong Zou, Yangou Lv, Wen Zhao, Xinke Zhang, Yihua Zhang
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-15-494

Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast
Cited by: 2
Author(s): Lucas D. Ward, Junbai Wang, Harmen J. Bussemaker
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2164-10-588

The pitfalls of platform comparison: DNA copy number array technologies assessed
Cited by: 94
Author(s): Christina Curtis, Andy G. Lynch, Mark J. Dunning, Inmaculada Spiteri, John C. Marioni, James Hadfield, Suet-Feung Chin, James D. Brenton, Simon Tavaré, Carlos Caldas
Software Mentions: 3
Published: over 17 years ago

10.1186/s12864-021-07653-8

Genome-wide identification of cyclin-dependent kinase (CDK) genes affecting adipocyte differentiation in cattle
Cited by: 12
Author(s): Cuili Pan, Zhaoxiong Lei, Shuzhe Wang, Xingping Wang, Dawei Wei, Xiaoyan Cai, Zhuoma Luoreng, Lei Wang, Yun Ma
Software Mentions: 3
Published: about 5 years ago

10.1186/s12864-015-1644-8

Non-thermal plasma treatment altered gene expression profiling in non-small-cell lung cancer A549 cells
Cited by: 49
Author(s): Jue Hou, Jie Ma, K.N. Yu, Wei Li, Cheng Cheng, Lingzhi Bao, Wei Han
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-020-6721-y

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments
Cited by: 50
Author(s): Alemu Takele Assefa, Jo Vandesompele, Olivier Thas
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-019-5460-4

RNA-sequencing analysis of shell gland shows differences in gene expression profile at two time-points of eggshell formation in laying chickens
Cited by: 22
Author(s): Samiullah Khan, Shu‐Biao Wu, Juliet R. Roberts
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-13-147

Genome-wide analysis of Pax8 binding provides new insights into thyroid functions
Cited by: 40
Author(s): Sergio Ruiz‐Llorente, Enrique Carrillo Santa de Pau, Ana Sastre-Perona, Cristina Montero‐Conde, Gonzalo Goméz-López, James A. Fagin, Alfonso Valencia, David G. Pisano, Pilar Santisteban
Software Mentions: 3
Published: over 14 years ago

10.1186/s12864-019-5634-0

Transcriptomic reprogramming of barley seminal roots by combined water deficit and salt stress
Cited by: 34
Author(s): Alina Osthoff, Petra Donà dalle Rose, Jutta A. Baldauf, Hans‐Peter Piepho, Frank Hochholdinger
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-016-3060-0

In vivo Ebola virus infection leads to a strong innate response in circulating immune cells
Cited by: 49
Author(s): Ignacio Caballero, Anna N. Honko, Stephen K. Gire, S Winnicki, Marta Melé, Chiara Gerhardinger, Aaron E. Lin, Pardis C. Sabeti, Lisa E. Hensley, John H. Connor
Software Mentions: 3
Published: about 10 years ago

10.1186/s12864-017-3616-7

Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence
Cited by: 13
Author(s): Biju Joseph Ampattu, Laura Hagmann, Chunguang Liang, Marcus Dittrich, Andreas Schlüter, Jochen Blom, Elizaveta Krol, Alexander Goesmann, Anke Becker, Thomas Dandekar, Tobias Müller, Christoph Schoen
Software Mentions: 3
Published: over 9 years ago

10.1186/s12864-015-2081-4

Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors
Cited by: 50
Author(s): Jason Piper, Salam A. Assi, Pierre Cauchy, Christophe Ladroue, Peter N. Cockerill, Constanze Bonifer, Sascha Ott
Software Mentions: 3
Published: almost 11 years ago

10.1186/s12864-018-5303-8

Higher plane of nutrition pre-weaning enhances Holstein calf mammary gland development through alterations in the parenchyma and fat pad transcriptome
Cited by: 13
Author(s): Mario Vailati-Riboni, Ryan Bucktrout, Siyuan Zhan, Ashley Geiger, Joshua C McCann, R.M. Akers, Juan J. Loor
Software Mentions: 3
Published: almost 8 years ago

10.1186/1471-2164-9-131

The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution
Cited by: 127
Author(s): Kirstin Replogle, Arthur P. Arnold, Gregory F. Ball, Mark Band, Staffan Bensch, Eliot A. Brenowitz, Shu Dong, Jenny Drnevich, Margaret Ferris, Julia M. George, George Gong, Dennis Hasselquist, Álvaro Gonzalez Hernández, Ryan Kim, Harris A. Lewin, Lei Liu, Peter V. Lovell, Claudio V. Mello, Sara Naurin, Sandra L. Rodriguez-Zas, Jyothi Thimmapuram, Juli Wade, David F. Clayton
Software Mentions: 3
Published: over 18 years ago

10.1186/1471-2164-11-165

Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery
Cited by: 53
Author(s): Thomas Neußer, Tino Polen, René Geißen, Rolf Wagner
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2164-14-514

Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data
Cited by: 15
Author(s): Leandro Hermida, Carine Poussin, Michael Stadler, Sylvain Gubian, Alain Sewer, Dimos Gaidatzis, Hans-Rudolf Hotz, Florian Martin, Vincenzo Belcastro, Stéphane Cano, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 3
Published: over 13 years ago

10.1186/1471-2164-14-688

Guide: a desktop application for analysing gene expression data
Cited by: 5
Author(s): Jarny Choi
Software Mentions: 3
Published: over 13 years ago

10.1186/s12864-015-1445-0

Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells
Cited by: 28
Author(s): Daniel J. Trombly, Troy W. Whitfield, Srivatsan Padmanabhan, Jonathan A. R. Gordon, Jane B. Lian, André J. van Wijnen, Sayyed K. Zaidi, Janet L. Stein
Software Mentions: 3
Published: over 11 years ago

10.1186/s12864-015-1223-z

Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
Cited by: 14
Author(s): Benjamin B. Green, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-8-464

Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex
Cited by: 50
Author(s): Brian D. Eads, John K. Colbourne, Elizabeth A. Bohuski, Justen Andrews
Software Mentions: 3
Published: over 19 years ago

10.1186/1471-2164-10-419

Reciprocal regulation of microRNA and mRNA profiles in neuronal development and synapse formation
Cited by: 32
Author(s): Sergei A. Manakov, Seth G. N. Grant, Anton J. Enright
Software Mentions: 3
Published: about 17 years ago

10.1186/s12864-017-3488-x

Conserved gene expression in sperm reservoirs between birds and mammals in response to mating
Cited by: 23
Author(s): Mohammad Atikuzzaman, Manuel Álvarez‐Rodríguez, Alejandro Vicente-Carrillo, Martin Johnsson, Dominic Wright, Heriberto Rodríguez-Martinez
Software Mentions: 3
Published: over 9 years ago

10.1186/s13040-016-0122-4

Elevated transcriptional levels of aldolase A (ALDOA) associates with cell cycle-related genes in patients with NSCLC and several solid tumors
Cited by: 25
Author(s): Fan Zhang, Jiediao Lin, Xiaoyu Zuo, Yingping Zhuang, Chao‐Qun Hong, Guojun Zhang, Xiaojiang Cui, Yukun Cui
Software Mentions: 3
Published: over 9 years ago

10.1016/j.bbrep.2015.08.012

Xanthophylls lutein and zeaxanthin modify gene expression and induce synthesis of hyaluronan in keratinocyte model of human skin
Cited by: 9
Author(s): Rasia Li, Stephen D. Turner, David L. Brautigan
Software Mentions: 3
Published: almost 11 years ago

10.1155/2019/6469420

Integrated Analysis of Oncogenic Networks in Colorectal Cancer Identifies GUCA2A as a Molecular Marker
Cited by: 24
Author(s): Hui Zhang, Yuanyuan Du, Zhuo Wang, Rui Lou, Jianzhong Wu, Jifeng Feng
Software Mentions: 3
Published: about 7 years ago

10.1007/s10522-016-9638-8

The functional consequences of age-related changes in microRNA expression in skeletal muscle
Cited by: 49
Author(s): Ana Soriano‐Arroquia, Louise House, Luke Tregilgas, Elizabeth G. Canty‐Laird, Katarzyna Goljanek‐Whysall
Software Mentions: 3
Published: over 10 years ago

10.1093/bioinformatics/btv425

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
Cited by: 72
Author(s): Marek Gierliński, Christian Callebaut, Pietà Schofield, Nicholas J. Schurch, Alexander Sherstnev, Vijender Singh, Nicola Wrobel, Karim Gharbi, Gordon G. Simpson, Tom Owen-Hughes, Mark Blaxter, Geoffrey J. Barton
Software Mentions: 3
Published: about 11 years ago

10.1093/bioinformatics/bts680

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
Cited by: 1,196
Author(s): Andrew E. Teschendorff, Francesco Marabita, Matthias Lechner, Thomas E. Bartlett, Jesper Tegnér, David Gomez-Cabrero, Stephan Beck
Software Mentions: 3
Published: almost 14 years ago

10.1093/bioinformatics/btx513

ChAMP: updated methylation analysis pipeline for Illumina BeadChips
Cited by: 496
Author(s): Yuan Tian, Tiffany Morris, Amy P Webster, Zhen Yang, Stephan Beck, Andrew Feber, Andrew E. Teschendorff
Software Mentions: 3
Published: about 9 years ago

10.1093/bioinformatics/bts656

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
Cited by: 62
Author(s): Clare Pacini, Francesco Iorio, Emanuel Gonçalvès, Murat Iskar, Thomas Klabunde, Peer Bork, Julio Sáez-Rodríguez
Software Mentions: 3
Published: almost 14 years ago

10.1093/bioinformatics/btx355

Hierarchical probabilistic models for multiple gene/variant associations based on next-generation sequencing data
Cited by: 5
Author(s): Dimitrios V Vavoulis, Jenny C. Taylor, Anna Schuh
Software Mentions: 3
Published: over 9 years ago

10.1186/s13062-018-0223-8

Predicting clinical outcomes in neuroblastoma with genomic data integration
Cited by: 9
Author(s): Ilyes Baali, Durmus Alp Emre Acar, Tunde Aderinwale, Saber Hafezqorani, Hilal Kazan
Software Mentions: 3
Published: almost 8 years ago

10.1242/bio.054189

A stem cell based in vitro model of NAFLD enables the analysis of patient specific individual metabolic adaptations in response to a high fat diet and AdipoRon interference
Cited by: 6
Author(s): Nina Graffmann, Audrey Ncube, Soraia Martins, Aurelian Robert Fiszl, Philipp Reuther, Martina Bohndorf, Wasco Wruck, Mathias Beller, Constantin Czekelius, James Adjaye
Software Mentions: 3
Published: over 6 years ago

10.1186/s40659-016-0085-4

Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile
Cited by: 16
Author(s): Min Wang, Jingjun Yan, Xingxing He, Qiang Zhong, Zhan Chen, Shusheng Li
Software Mentions: 3
Published: over 10 years ago

10.1186/s40659-018-0192-5

Dysregulation of NCAPG, KNL1, miR-148a-3p, miR-193b-3p, and miR-1179 may contribute to the progression of gastric cancer
Cited by: 52
Author(s): Bin Song, Juan Du, Defeng Song, Jian Ren, Yan Feng
Software Mentions: 3
Published: almost 8 years ago

10.3390/biology10050432

Identifying an lncRNA-Related ceRNA Network to Reveal Novel Targets for a Cutaneous Squamous Cell Carcinoma
Cited by: 7
Author(s): Yaqin Xu, Yingying Dong, Yansha Deng, Qian-Rong Qi, Mi Wu, Hongmei Liang, Qiuyun She, Qing Guo
Software Mentions: 3
Published: over 5 years ago

10.1155/2020/8571932

AHNAK2 Is Associated with Poor Prognosis and Cell Migration in Lung Adenocarcinoma
Cited by: 9
Author(s): Shusen Zhang, Yuanyuan Lu, Ling Qi, Hongyan Wang, Zhihua Wang, Zhigang Cai
Software Mentions: 3
Published: about 6 years ago

10.1155/2020/4037639

A Five-Gene Signature for Recurrence Prediction of Hepatocellular Carcinoma Patients
Cited by: 6
Author(s): Zeyu Wang, Ningning Zhang, Jiayu Lv, Cuihua Ma, Jun Gu, Yawei Du, Yulan Qiu, Zhiguang Zhang, Man Li, Yong Jiang, Jianqiu Zhao, Hui-Qin Du, Zhiwei Zhang, Yan Zhang
Software Mentions: 3
Published: almost 6 years ago

10.1155/2021/5584681

Biodata Mining of Differentially Expressed Genes between Acute Myocardial Infarction and Unstable Angina Based on Integrated Bioinformatics
Cited by: 4
Author(s): Siyu Guo, Zhihong Huang, Xinkui Liu, Jingyuan Zhang, Peizhi Ye, Chao Wu, Shan Lu, Shanshan Jia, Xiaomeng Zhang, Xiuping Chen, Miaomiao Wang, Jiarui Wu
Software Mentions: 3
Published: about 5 years ago

10.1155/2021/3947350

Identification of MEDAG as a Hub Candidate Gene in the Onset and Progression of Type 2 Diabetes Mellitus by Comprehensive Bioinformatics Analysis
Cited by: 3
Author(s): Jing Yang, Ping Yü
Software Mentions: 3
Published: over 5 years ago

10.1155/2017/2421459

Prediction and Validation of Hub Genes Associated with Colorectal Cancer by Integrating PPI Network and Gene Expression Data
Cited by: 19
Author(s): Yong Xiong, Wenxian You, Rong Wang, Linglong Peng, Zhongxue Fu
Software Mentions: 3
Published: over 9 years ago

10.1155/2021/6653802

Multiomics Analysis of Transcriptome, Epigenome, and Genome Uncovers Putative Mechanisms for Dilated Cardiomyopathy
Cited by: 5
Author(s): Li Liu, Jianjun Huang, Yan Liu, Xingshou Pan, Zhile Li, Liufang Zhou, Tengfang Lai, Chengcai Chen, Baomin Wei, Jianjiao Mo, Qinjiang Wei, Yan Wang, Xian-Nan Huang, Zhen Zhang, Zhuohua Zhang, Meidan Huang, Fengzhen He, Zhaohe Huang
Software Mentions: 3
Published: over 5 years ago

10.1155/2021/8357585

Comprehensive Analysis of CD163 as a Prognostic Biomarker and Associated with Immune Infiltration in Glioblastoma Multiforme
Cited by: 3
Author(s): Hao Li, Di Wang, Bolong Yi, Heng Cai, Zhuo Xi, Xin Lou, Zhen Li
Software Mentions: 3
Published: about 5 years ago

10.1042/BSR20201482

Survival prediction in patients with colon adenocarcinoma via multiomics data integration using a deep learning algorithm
Cited by: 21
Author(s): Jiudi Lv, Junjie Wang, Shang XiuJuan, Fangfang Liu, Shanshan Guo
Software Mentions: 3
Published: almost 6 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776