bioconductor: limma | Projects | Ecosyste.ms: Papers

10.1186/s12885-020-06743-2

INHBA is a prognostic predictor for patients with colon adenocarcinoma
Cited by: 40
Author(s): Xueying Li, Weiming Yu, Chao Liang, Yuan Xu, Miaozun Zhang, Xiaoyun Ding, Xianlei Cai
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2407-14-353

Investigation of HOXA9 promoter methylation as a biomarker to distinguish oral cancer patients at low risk of neck metastasis
Cited by: 16
Author(s): Kenichiro Uchida, Ratna Veeramachaneni, Bing Huey, Aditi Bhattacharya, Brian L. Schmidt, Donna G. Albertson
Software Mentions: 1
Published: over 12 years ago

10.1186/1471-2407-10-599

Prioritizing genes associated with prostate cancer development
Cited by: 33
Author(s): Ivan P. Gorlov, Kanishka Sircar, Hongya Zhao, Sankar N. Maity, Nora M. Navone, Olga Y. Gorlova, Patricia Troncoso, Curtis A. Pettaway, Jin Young Byun, Christopher J. Logothetis
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12885-018-4546-8

Gene expression profiling of 1200 pancreatic ductal adenocarcinoma reveals novel subtypes
Cited by: 55
Author(s): Liang Zhao, Hongya Zhao, Hong Yan
Software Mentions: 1
Published: over 8 years ago

10.1186/s12885-020-06869-3

SCDb: an integrated database of stomach cancer
Cited by: 7
Author(s): Erli Gu, Wei Song, Ajing Liu, Wang Hong
Software Mentions: 1
Published: over 6 years ago

10.1186/s12885-021-08525-w

Bioinformatics analysis of C3 and CXCR4 demonstrates their potential as prognostic biomarkers in clear cell renal cell carcinoma (ccRCC)
Cited by: 5
Author(s): Jing Quan, Yuchen Bai, Yunbei Yang, Er Lei Han, Hong Bai, Qi Zhang, Dahong Zhang
Software Mentions: 1
Published: about 5 years ago

10.1186/s12885-020-07725-0

Identification of a novel six autophagy-related genes signature for the prognostic and a miRNA-related autophagy predictor for anti-PD-1 therapy responses in prostate cancer
Cited by: 9
Author(s): Lei Wu, Quan Wen, Guojun Yue, Qiong Luo, Dongxu Peng, Ying Pan, Guihai Zhang
Software Mentions: 1
Published: over 5 years ago

10.1186/s12885-018-4633-x

Interleukin 8 is a biomarker of telomerase inhibition in cancer cells
Cited by: 3
Author(s): Peter D. Solomon, Yujuan Dong, Shaillay Kumar Dogra, Romi Gupta
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2407-10-627

Tumour auto-antibody screening: performance of protein microarrays using SEREX derived antigens
Cited by: 19
Author(s): René Stempfer, Parvez Syed, Klemens Vierlinger, Rudolf Pichler, Eckart Meese, Petra Leidinger, Nicole Ludwig, Albert Kriegner, Christa Nöhammer, Andreas Weinhäusel
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12885-020-07590-x

Expression and prognostic analyses of the insulin-like growth factor 2 mRNA binding protein family in human pancreatic cancer
Cited by: 9
Author(s): Xiaoping Chen, Shu-Yi Hu, Chen Zhu, Xihu Qin
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12885-021-08293-7

A circular RNAs dataset landscape reveals potential signatures for the detection and prognosis of early-stage lung adenocarcinoma
Cited by: 5
Author(s): Zhiying Chen, Jiahui Wei, Min Li, Yufei Zhao
Software Mentions: 1
Published: about 5 years ago

10.1186/s12885-020-07598-3

Identification and validation of a six-gene signature associated with glycolysis to predict the prognosis of patients with cervical cancer
Cited by: 14
Author(s): Luya Cai, Chuan Hu, Shanshan Yu, Lixiao Liu, Xiaobo Yu, Jiahua Chen, Xuan Li, Fan Lin, Cheng Zhang, Wenfeng Li, Xiaojian Yan
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12885-021-08166-z

Bioinformatics analysis of mRNA and miRNA microarray to identify the key miRNA-mRNA pairs in cisplatin-resistant ovarian cancer
Cited by: 3
Author(s): Xue Bai, Shupeng Li, Xiance Jin, Lifeng Liu
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2407-14-54

A panel of genes methylated with high frequency in colorectal cancer
Cited by: 132
Author(s): Susan M. Mitchell, Jason P. Ross, Horace R. Drew, Thu Ho, Glenn Brown, Neil F. W. Saunders, Konsta Duesing, Michael Buckley, Robert Dunne, Iain Beetson, Keith N. Rand, Aidan McEvoy, Melissa L. Thomas, Rohan T. Baker, David Wattchow, Graeme P. Young, Trevor Lockett, Susanne K. Pedersen, Lawrence C. LaPointe, Peter L. Molloy
Software Mentions: 1
Published: over 12 years ago

10.1186/s12885-021-08637-3

Dysregulated paired related homeobox 1 impacts on hepatocellular carcinoma phenotypes
Cited by: 0
Author(s): Weronika Piorońska, Zeribe C. Nwosu, Mei Han, Michael Büttner, Matthias Ebert, Steven Dooley, Christoph Meyer
Software Mentions: 1
Published: about 5 years ago

10.1186/s12885-021-08591-0

Integration of RNA-Seq and proteomics data identifies glioblastoma multiforme surfaceome signature
Cited by: 13
Author(s): Saiful Effendi Syafruddin, Wan Fahmi Wan Mohamad Nazarie, Nurshahirah Ashikin Moidu, Bee Hong Soon, M. Aiman Mohtar
Software Mentions: 1
Published: about 5 years ago

10.1186/s12885-016-2539-z

Efficient generation of patient-matched malignant and normal primary cell cultures from clear cell renal cell carcinoma patients: clinically relevant models for research and personalized medicine
Cited by: 21
Author(s): Nazleen Lobo, Craig Gedye, Anthony J. Apostoli, Kevin R. Brown, Joshua Paterson, Natalie Stickle, Michael Robinette, Neil Fleshner, Robert J. Hamilton, Girish S. Kulkarni, Alexandre R. Zlotta, Andrew Evans, Antonio Finelli, Jason Moffat, Michael A.S. Jewett, Laurie Ailles
Software Mentions: 1
Published: about 10 years ago

10.1186/s12885-020-07100-z

Candidate methylation sites associated with endocrine therapy resistance in ER+/HER2- breast cancer
Cited by: 6
Author(s): Maryam Soleimani Dodaran, Simone Borgoni, Emre Sofyalı, Pernette J. Verschure, Stefan Wiemann, Perry D. Moerland, Antoine H. C. van Kampen
Software Mentions: 1
Published: about 6 years ago

10.1186/s12885-017-3100-4

The prognostic utility of the transcription factor SRF in docetaxel-resistant prostate cancer: in-vitro discovery and in-vivo validation
Cited by: 14
Author(s): Dara Lundon, Aidan Boland, Maria Prencipe, Grace Hurley, Amanda O’Neill, Elaine W. Kay, Sinéad Aherne, Padraig Doolan, Stephen F. Madden, Martin Clynes, Colm Morrissey, John M. Fitzpatrick, R. William G. Watson
Software Mentions: 1
Published: over 9 years ago

10.1186/s12885-021-07959-6

Integrative genomic expression analysis reveals stable differences between lung cancer and systemic sclerosis
Cited by: 0
Author(s): Heng Li, Liping Ding, Xiaoping Hong, Yulan Chen, Rui Liao, Tingting Wang, Shuhui Meng, Zhuhua Jiang, Dongzhou Liu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12885-019-5838-3

Novel significant stage-specific differentially expressed genes in hepatocellular carcinoma
Cited by: 52
Author(s): Arjun Sarathi, Ashok Palaniappan
Software Mentions: 1
Published: about 7 years ago

10.1186/s12885-016-2355-5

Progesterone receptor blockade in human breast cancer cells decreases cell cycle progression through G2/M by repressing G2/M genes
Cited by: 12
Author(s): Susan E. Clare, Akash Gupta, Mi Ran Choi, Manish Ranjan, Oukseub Lee, Jun Wang, David Ivancic, Julie Kim, Seema A. Khan
Software Mentions: 1
Published: over 10 years ago

10.1186/s12885-018-4251-7

Comparative analysis of histologically classified oligodendrogliomas reveals characteristic molecular differences between subgroups
Cited by: 15
Author(s): Chris Lauber, Barbara Klink, Michael Seifert
Software Mentions: 1
Published: over 8 years ago

10.1186/s12885-020-07184-7

Low dose environmental radon exposure and breast tumor gene expression
Cited by: 5
Author(s): Cheng Peng, Natalie DuPré, Trang VoPham, Yujing J. Heng, Gabrielle M. Baker, Christopher A. Rubadue, Kimberly Glass, Abhijeet R. Sonawane, Oana A. Zeleznik, Peter Kraft, Susan E. Hankinson, A. Heather Eliassen, Jaime E. Hart, Francine Laden, Rulla M. Tamimi
Software Mentions: 1
Published: about 6 years ago

10.1186/s12885-018-4852-1

Development of acquired resistance to lapatinib may sensitise HER2-positive breast cancer cells to apoptosis induction by obatoclax and TRAIL
Cited by: 17
Author(s): Alex J. Eustace, Neil T. Conlon, Martina S.J. McDermott, Brigid C. Browne, Patrick C. O’Leary, Frankie A. Holmes, Virginia Espina, Lance A. Liotta, Joyce O’Shaughnessy, Clair Gallagher, Lorraine O’Driscoll, Sweta Rani, Stephen F. Madden, Neil A. O’Brien, Charles Ginther, Dennis J. Slamon, Naomi Walsh, William M. Gallagher, Radosław Zagożdżon, R. William G. Watson, Norma O’Donovan, John Crown
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12885-019-5927-3

Estimation of immune cell content in tumor using single-cell RNA-seq reference data
Cited by: 28
Author(s): Xiaoqing Yu, Yian Ann Chen, José R. Conejo-Garcia, Christine H. Chung, Xuefeng Wang
Software Mentions: 1
Published: about 7 years ago

10.1186/s12872-020-01701-z

Investigation of the underlying genes and mechanism of familial hypercholesterolemia through bioinformatics analysis
Cited by: 7
Author(s): Dinghui Wang, Bin Liu, Tianhua Xiong, Wenlong Yu, Sheng Qiang
Software Mentions: 1
Published: about 6 years ago

10.1186/s12872-021-02011-8

SCD leads to the development and progression of acute myocardial infarction through the AMPK signaling pathway
Cited by: 3
Author(s): Lijie Wang, Feng Yu
Software Mentions: 1
Published: over 5 years ago

10.1186/s12906-017-1911-0

Comprehensive evaluation of gene expression signatures in response to electroacupuncture stimulation at Zusanli (ST36) acupoint by transcriptomic analysis
Cited by: 2
Author(s): Jing-Shan Wu, Hsin-Yi Lo, Chia-Cheng Li, Fengyuan Chen, Chien-Yun Hsiang, Tin-Yun Ho
Software Mentions: 1
Published: about 9 years ago

10.1186/s12906-016-1349-9

Identification of more objective biomarkers for Blood-Stasis syndrome diagnosis
Cited by: 21
Author(s): Jingqiu Liao, Yongmei Liu, Jie Wang
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12906-017-1586-6

Exploration of anti-cancer effects and mechanisms of Zuo-Jin-Wan and its alkaloid components in vitro and in orthotopic HepG2 xenograft immunocompetent mice
Cited by: 32
Author(s): Shun Ting Chou, Chien Yun Hsiang, Hsin Yi Lo, Hui Huang, Ming Tsung Lai, Ching Liang Hsieh, Su‐Yin Chiang, Tin Yun Ho
Software Mentions: 1
Published: over 9 years ago

10.1186/s12906-019-2577-6

Qianggan extract improved nonalcoholic steatohepatitis by modulating lncRNA/circRNA immune ceRNA networks
Cited by: 18
Author(s): Meizhen Zhu, Meng Li, Wenjun Zhou, Yang Yang, Fenghua Li, Li Zhang, Guang Ji
Software Mentions: 1
Published: about 7 years ago

10.1186/1471-213X-12-4

Fine scale analysis of gene expression in Drosophila melanogaster gonads reveals Programmed cell death 4 promotes the differentiation of female germline stem cells
Cited by: 16
Author(s): Amy Cash, Justen Andrews
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-213X-7-48

Novel subdomains of the mouse olfactory bulb defined by molecular heterogeneity in the nascent external plexiform and glomerular layers
Cited by: 11
Author(s): Eric O. Williams, Yuanyuan Xiao, Heather M. Sickles, Paul Shafer, Golan Yona, Jean Yee Hwa Yang, David M. Lin
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-213X-11-20

FGF signalling through RAS/MAPK and PI3K pathways regulates cell movement and gene expression in the chicken primitive streak without affecting E-cadherin expression
Cited by: 66
Author(s): Katharine M. Hardy, Tatiana A. Yatskievych, JH Konieczka, Alexander S. Bobbs, Parker B. Antin
Software Mentions: 1
Published: over 15 years ago

10.1186/s12902-021-00687-9

Relationship between insulin sensitivity and gene expression in human skeletal muscle
Cited by: 6
Author(s): Hemang Parikh, Targ Elgzyri, Amra Ciric Alibegovic, Natalie Hiscock, Ola Ekström, Karl-Fredrik Eriksson, Allan Vaag, Leif Groop, Kristoffer Ström, Ola Hansson
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2148-10-151

Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon
Cited by: 21
Author(s): Claudia Voelckel, Mehdi Mirzaei, Michael Reichelt, Zhiwei Luo, Dana Pascovici, P. B. Heenan, Silvia Schmidt, Bart J. Janssen, Paul A. Haynes, Peter J. Lockhart
Software Mentions: 1
Published: over 16 years ago

10.1186/s12862-014-0239-3

Female responses to experimental removal of sexual selection components in Drosophila melanogaster
Cited by: 18
Author(s): Paolo Innocenti, Ilona Flis, Edward H. Morrow
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12862-015-0327-z

Evolution of lysine acetylation in the RNA polymerase II C-terminal domain
Cited by: 20
Author(s): Corinne Simonti, Katherine S. Pollard, Sebastian Schröder, Daniel He, Benoit G. Bruneau, Melanie Ott, John A. Capra
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-14-265

Simultaneous miRNA and mRNA transcriptome profiling of human myoblasts reveals a novel set of myogenic differentiation-associated miRNAs and their target genes
Cited by: 71
Author(s): Petr Dmitriev, Ana Barat, Anna Polesskaya, Mary J. O’Connell, Robert Thomas, Philippe Dessen, Thomas A. Walsh, Vladimir Lazar, Ahmed Turki, Gilles Carnac, Dalila Laoudj-Chenivesse, Marc Lipinski, Yegor S. Vassetzky
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-9-540

Microarray analysis identifies candidate genes for key roles in coral development
Cited by: 124
Author(s): Lauretta C. Grasso, John Maindonald, Stephen Rudd, David C. Hayward, Robert Saint, David J. Miller, Eldon E. Ball
Software Mentions: 1
Published: almost 18 years ago

10.1186/s12864-016-2424-9

Nonlinear transcriptomic response to dietary fat intake in the small intestine of C57BL/6J mice
Cited by: 7
Author(s): Tenzin Nyima, Michael Müller, Guido Hooiveld, Melissa J. Morine, Marco Scotti
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-12-490

Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus
Cited by: 59
Author(s): Florbela A. Vieira, Sílvia F. Gregório, Serena Ferraresso, Michael A. S. Thorne, Rita A. Costa, Massimo Milan, Luca Bargelloni, Melody S. Clark, Adelino V.M. Canário, Deborah M. Power
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-14-224

Identification of microRNA-mRNA functional interactions in UVB-induced senescence of human diploid fibroblasts
Cited by: 50
Author(s): Ruth Greussing, Matthias Hackl, Pornpimol Charoentong, Alexander Pauck, Rossella Monteforte, Maria Cavinato, Edith Hofer, Marcel Scheideler, Michael Neuhaus, Lucia Mičutková, Christoph Mueck, Zlatko Trajanoski, Johannes Grillari, Pidder Jansen‐Dürr
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-10-460

'Bois noir' phytoplasma induces significant reprogramming of the leaf transcriptome in the field grown grapevine
Cited by: 136
Author(s): Matjaž Hren, Petra Nikolić, Ana Rotter, Andrej Blejec, Nancy Terrier, Maja Ravnikar, Marina Dermastia, Kristina Gruden
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2164-14-911

A unique in vivo experimental approach reveals metabolic adaptation of the probiotic Propionibacterium freudenreichii to the colon environment
Cited by: 32
Author(s): Taous Saraoui, Sandrine Parayre, Grégory Guernec, Valentin Loux, Jérôme Montfort, Aurélie Le Cam, Gaëlle Boudry, Gwenaël Jan, Hélène Falentin
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12864-018-4826-3

Genome-wide DNA methylation patterns of bovine blastocysts derived from in vivo embryos subjected to in vitro culture before, during or after embryonic genome activation
Cited by: 48
Author(s): Dessie Salilew‐Wondim, Mohammed Saeed‐Zidane, M. Hoelker, Samuel Gebremedhn, Mikhaël Poirier, Hari Om Pandey, Ernst Tholen, Christiane Neuhoff, Eva Held, U. Besenfelder, V. Havlíček, F. Rings, Éric Fournier, Dominic Gagné, Marc‐André Sirard, Claude Robert, Ahmed Gad, K. Schellander, Dawit Tesfaye
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-9-432

Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat (Triticum aestivum L.) by using Wheat Genome Array
Cited by: 280
Author(s): Dandan Qin, Haiyan Wu, Huiru Peng, Yingyin Yao, Zhongfu Ni, Zhenxing Liu, Chunlei Zhou, Qixin Sun
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-15-1085

Deciphering regulatory variation of THI genes in alcoholic fermentation indicate an impact of Thi3p on PDC1 expression
Cited by: 16
Author(s): Christian Brion, Chloé Ambroset, Pierre Delobel, Isabelle Sanchez, Bruno Blondin
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-15-709

Uncovering molecular events associated with the chemosuppressive effects of flaxseed: a microarray analysis of the laying hen model of ovarian cancer
Cited by: 13
Author(s): Karen Hales, Sheree C. Speckman, Nawneet K. Kurrey, Dale B. Hales
Software Mentions: 1
Published: over 12 years ago

10.1186/s12864-015-1772-1

Integrated analyses of zebrafish miRNA and mRNA expression profiles identify miR-29b and miR-223 as potential regulators of optic nerve regeneration
Cited by: 30
Author(s): Paula I. Fuller-Carter, Kim W. Carter, Denise Anderson, Alan R. Harvey, Keith M. Giles, Jennifer Rodger
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2164-10-30

Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies
Cited by: 57
Author(s): Henrik Hornshøj, Emøke Bendixen, Lene N Conley, P. Andersen, Jakob Hedegaard, Frank Panitz, Christian Berthou
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2164-9-486

p53 induces distinct epigenetic states at its direct target promoters
Cited by: 52
Author(s): Lukáš Vrba, Damian J. Junk, Petr Novák, Bernard W. Futscher
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-9-421

Gene expression profiling in hepatic tissue of newly weaned pigs fed pharmacological zinc and phytase supplemented diets
Cited by: 25
Author(s): Michelle M. Martínez-Montemayor, G. M. Hill, Nancy E. Raney, V. D. Rilington, Robert J. Tempelman, Jane E. Link, Christopher Wilkinson, A. M. Ramos, Catherine W. Ernst
Software Mentions: 1
Published: about 18 years ago

10.1186/s12864-020-6768-9

PretiMeth: precise prediction models for DNA methylation based on single methylation mark
Cited by: 4
Author(s): Jie Tang, Jianxiao Zou, Xiaoran Zhang, Mei Fan, Qi Tian, Shuyao Fu, Shihong Gao, Shicai Fan
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-018-5413-3

Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species
Cited by: 20
Author(s): Rahul Rane, Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò, Philippa C. Griffin, Guojie Zhang, Siu Fai Lee, Ary A. Hoffmann, John G. Oakeshott
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-13-274

Defining new criteria for selection of cell-based intestinal models using publicly available databases
Cited by: 46
Author(s): Jon Christensen, Sara El-Gebali, Manuela Natoli, Thierry Sengstag, Mauro Delorenzi, Susanne Bentz, Hanifa Bouzourène, Martı́n Rumbo, Armando Felsani, Sanna Siissalo, Jouni Hirvonen, Maya R Vila, Piercarlo Saletti, Michel Aguet, Pascale Anderle
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2164-7-252

Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma
Cited by: 451
Author(s): Ilhem Diboun, Lorenz Wernisch, Christine A. Orengo, M Koltzenburg
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2164-15-1114

Genes associated with thermosensitive genic male sterility in rice identified by comparative expression profiling
Cited by: 21
Author(s): Yufang Pan, Qiaofeng Li, Zhizheng Wang, Yang Wang, Rui Ma, Lili Zhu, Guangcun He, Rongzhi Chen
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-13-447

Genetic module and miRNome trait analyses reflect the distinct biological features of endothelial progenitor cells from different anatomic locations
Cited by: 22
Author(s): Cheng-Chung Cheng, Hung-Hao Lo, Tse‐Shun Huang, Yi-Chieh Cheng, Shi-Ting Chang, Shing‐Jyh Chang, Hsei–Wei Wang
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2164-12-123

Comparative tissue transcriptomics reveal prompt inter-organ communication in response to local bacterial kidney infection
Cited by: 15
Author(s): Jorrit Boekel, Örjan Källskog, Monica Rydén-Aulin, Mikael Rhen, Agneta Richter‐Dahlfors
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-10-236

Transcriptomics reveals extensive inducible biotransformation in the soil-dwelling invertebrate Folsomia candida exposed to phenanthrene
Cited by: 65
Author(s): Benjamin Nota, Mirte Bosse, Bauke Ylstra, Nico M. van Straalen, Dick Roelofs
Software Mentions: 1
Published: over 17 years ago

10.1186/s12864-015-1393-8

Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level
Cited by: 70
Author(s): Roland Prielhofer, Stephanie P. Cartwright, Alexandra B. Graf, Minoska Valli, Roslyn M. Bill, Diethard Mattanovich, Brigitte Gasser
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-15-829

Profiling of the embryonic Atlantic halibut (Hippoglossus hippoglossus L.) transcriptome reveals maternal transcripts as potential markers of embryo quality
Cited by: 29
Author(s): Maren Mommens, Jorge M.O. Fernandes, Knut Erik Tollefsen, Ian A. Johnston, Igor Babiak
Software Mentions: 1
Published: almost 12 years ago

10.1186/1471-2164-12-81

Population transcriptomics of Drosophila melanogaster females
Cited by: 45
Author(s): Lena Müller, Stephan Hütter, Rayna Stamboliyska, Sarah S. Saminadin-Peter, Wolfgang Stephan, John Parsch
Software Mentions: 1
Published: over 15 years ago

10.1186/1471-2164-14-869

TE-array—a high throughput tool to study transposon transcription
Cited by: 12
Author(s): Veena P. Gnanakkan, Andrew E. Jaffe, Lixin Dai, Jie Fu, Sarah J. Wheelan, Hyam I. Levitsky, Jef D. Boeke, Kathleen H. Burns
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-13-173

Genome-wide expression profiling shows transcriptional reprogramming in Fusarium graminearum by Fusarium graminearum virus 1-DK21 infection
Cited by: 33
Author(s): Won Kyong Cho, Jisuk Yu, Kyung-Mi Lee, Moonil Son, Kyung-Hee Min, Yin-Won Lee, Kook‐Hyung Kim
Software Mentions: 1
Published: over 14 years ago

10.1186/s12864-018-5220-x

RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database
Cited by: 19
Author(s): Pierre R. Bushel, Florian Caiment, Han Wu, Raegan O’Lone, Frank Day, John N. Calley, Aaron T. Smith, Jianying Li
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2164-11-6

An evolutionary consequence of dosage compensation on Drosophila melanogaster female X-chromatin structure?
Cited by: 35
Author(s): Yu Zhang, Brian Oliver
Software Mentions: 1
Published: over 16 years ago

10.1186/s12864-016-3458-8

CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation
Cited by: 27
Author(s): Julien Prunier, S. Caron, John Mackay
Software Mentions: 1
Published: over 9 years ago

10.1186/s12864-021-07994-4

Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection
Cited by: 3
Author(s): Christopher P. Kozakiewicz, Alexandra K. Fraik, Austin H. Patton, Manuel Ruiz‐Aravena, David G. Hamilton, Rodrigo Hamede, Hamish McCallum, Paul A. Hohenlohe, Mark J. Margres, Matthew T. Jones, Andrew Storfer
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12864-016-2580-y

Prediction of hybrid performance in maize with a ridge regression model employed to DNA markers and mRNA transcription profiles
Cited by: 26
Author(s): Carola Zenke-Philippi, Alexander Thiemann, Felix Seifert, Tobias A. Schrag, Albrecht E. Melchinger, Stefan Scholten, Matthias Frisch
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-13-76

Sexual and asexual oogenesis require the expression of unique and shared sets of genes in the insect Acyrthosiphon pisum
Cited by: 33
Author(s): Aurore Gallot, Shuji Shigenobu, Tomomi Hashiyama, Stéphanie Jaubert-Possamai, Denis Tagu
Software Mentions: 1
Published: over 14 years ago

10.1186/s12864-018-4518-z

Identification of placental nutrient transporters associated with intrauterine growth restriction and pre-eclampsia
Cited by: 57
Author(s): Xiao Huang, Pascale Anderle, Lu Hostettler, Marc Baumann, Daniel Surbek, Edgar Ontsouka, Christiane Albrecht
Software Mentions: 1
Published: over 8 years ago

10.1186/1471-2164-9-474

Differential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolation
Cited by: 88
Author(s): Adam Asare, Svetlana A Kolchinsky, Gongxun Zhong, Thomas J. Wang, Khadir Raddassi, Katarzyna Bourcier, Vicki Seyfert-Margolis
Software Mentions: 1
Published: almost 18 years ago

10.1186/1471-2164-11-235

Plasmodium falciparum spermidine synthase inhibition results in unique perturbation-specific effects observed on transcript, protein and metabolite levels
Cited by: 29
Author(s): John Vw Becker, Linda Mtwisha, Bridget Genevieve Crampton, Stoyan Stoychev, Anna C. van Brummelen, Shaun Reeksting, Abraham I. Louw, Lyn‐Marié Birkholtz, D Mancama
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-13-243

The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L.
Cited by: 109
Author(s): Philip R. Young, Justin Graham Lashbrooke, Erik Alexandersson, Dan Jacobson, C. Moser, Riccardo Velasco, Melané A. Vivier
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-11-414

ChIP on Chip: surprising results are often artifacts
Cited by: 65
Author(s): Torsten Waldminghaus, Kirsten Skarstad
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-14-527

Dissecting the psoriasis transcriptome: inflammatory- and cytokine-driven gene expression in lesions from 163 patients
Cited by: 107
Author(s): William R. Swindell, Andrew Johnston, John J. Voorhees, James T. Elder, Jóhann E. Guðjónsson
Software Mentions: 1
Published: over 13 years ago

10.1186/s12864-016-2988-4

CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems
Cited by: 21
Author(s): Anne Abot, Grégory Arnal, Lucas Auer, Adèle Lazuka, Delphine Labourdette, Sophie Lamarre, Lidwine Trouilh, Élisabeth Laville, Vincent Lombard, Gabrielle Potocki-Véronèse, Bernard Henrissat, Michael O’Donohue, Guillermina Hernandez-Raquet, Claire Dumon, Véronique Anton Leberre
Software Mentions: 1
Published: about 10 years ago

10.1186/s12864-020-06992-2

Candidate stress biomarkers for queen failure diagnostics
Cited by: 13
Author(s): Alison McAfee, Joseph Milone, Abigail Chapman, Leonard J. Foster, Jeffery S. Pettis, David R. Tarpy
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-016-2623-4

Cyclic AMP signaling restricts activation and promotes maturation and antioxidant defenses in astrocytes
Cited by: 37
Author(s): Sonia Paco, Manuela Hummel, Virginia Plá, Lauro Sumoy, Fernando Aguado
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-12-501

Temporal transcriptome changes induced by MDV in marek's disease-resistant and -susceptible inbred chickens
Cited by: 35
Author(s): Ying Yu, Juan Luo, Apratim Mitra, Shuang Chang, Fei Tian, Huanmin Zhang, Ping Yuan, Huaijun Zhou, Jiuzhou Song
Software Mentions: 1
Published: almost 15 years ago

10.1186/1471-2164-9-173

Transcriptome architecture across tissues in the pig
Cited by: 46
Author(s): André Luiz Julien Ferraz, Alejandro González-Ojeda, Manel López‐Béjar, Lana Teixeira Fernandes, Anna Castelló, Josep María Folch, Miguel Pérez‐Enciso
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-13-305

De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system
Cited by: 34
Author(s): Mark P. Peterson, Danielle J. Whittaker, Shruthi Ambreth, Suhas Sureshchandra, Aaron Buechlein, Ram Podicheti, Jeong-Hyeon Choi, Zhao Lai, Keithanne Mockatis, John K. Colbourne, Haixu Tang, Ellen D. Ketterson
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-14-631

Efficient utilization of aerobic metabolism helps Tibetan locusts conquer hypoxia
Cited by: 27
Author(s): Dejian Zhao, Zhenyu Zhang, Arianne Cease, Jon F. Harrison, Le Kang
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-14-861

The role of Dichaete in transcriptional regulation during Drosophila embryonic development
Cited by: 32
Author(s): J. Aleksić, Enrico Ferrero, Bettina Fischer, Shih Pei Shen, Steven Russell
Software Mentions: 1
Published: almost 13 years ago

10.1186/1471-2164-9-388

Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate
Cited by: 61
Author(s): Onguma Natalang, Emmanuel Bischoff, Guillaume Deplaine, Caroline Proux, Marie‐Agnès Dillies, Odile Sismeiro, Ghislaine Guigon, Serge Bonnefoy, Jintana Patarapotikul, Odile Mercereau–Puijalon, Jean‐Yves Coppée, Peter H. David
Software Mentions: 1
Published: about 18 years ago

10.1186/1471-2164-9-78

Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl (Ambystoma)
Cited by: 47
Author(s): Robert B. Page, S. Randal Voss, Amy Samuels, Jeramiah J. Smith, Srikrishna Putta, Christopher K. Beachy
Software Mentions: 1
Published: over 18 years ago

10.1186/1471-2164-14-121

Comparative transcriptomics reveals different strategies of Trichodermamycoparasitism
Cited by: 222
Author(s): Lea Atanasova, Stéphane Le Crom, Sabine Gruber, Fanny Coulpier, Verena Seidl‐Seiboth, Christian P. Kubicek, Irina S. Druzhinina
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-6-124

Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts
Cited by: 77
Author(s): Willem Albert Rensink, Yuandan Lee, Jia Liu, Stacey Iobst, Shuai Ouyang, C. Robin Buell
Software Mentions: 1
Published: about 21 years ago

10.1186/s12864-017-3878-0

Whole-transcriptome analysis delineates the human placenta gene network and its associations with fetal growth
Cited by: 46
Author(s): Maya A. Deyssenroth, Shouneng Peng, Ke Hao, Luca Lambertini, Carmen J. Marsit, Jia Chen
Software Mentions: 1
Published: about 9 years ago

10.1186/s12864-019-5557-9

Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles
Cited by: 19
Author(s): Rayner González-Prendes, Raquel Quintanilla, Emilio Mármol-Sánchez, Ramona N. Pena, María Ballester, Tainã Figueiredo Cardoso, Arianna Manunza, J. Casellas, Ángela Cánovas, Isabel Dı́az, J. L. Noguera, Anna Castelló, A. Mercadé, Marcel Amills
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2164-11-256

Validation of a mouse xenograft model system for gene expression analysis of human acute lymphoblastic leukaemia
Cited by: 18
Author(s): A. Lacey Samuels, Violet K. Peeva, Rachael A. Papa, Martin J Firth, Richard W. Francis, Alex H. Beesley, Richard B. Lock, Ursula R. Kees
Software Mentions: 1
Published: over 16 years ago

10.1186/1471-2164-14-37

Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2by RNA-Seq
Cited by: 77
Author(s): Chad E. Niederhuth, O. Rahul Patharkar, John C. Walker
Software Mentions: 1
Published: over 13 years ago

10.1186/1471-2164-8-350

Cadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator
Cited by: 85
Author(s): Laetitia Houot, Martin Floutier, Benoît Marteyn, Magali Michaut, Antoine Picciocchi, Pierre Legrain, Jean-Christophe Aude, Corinne Cassier‐Chauvat, Franck Chauvat
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2164-13-239

Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis
Cited by: 28
Author(s): Eva Apweiler, Katrin Sameith, Thanasis Margaritis, Nathalie Brabers, Loes van de Pasch, Linda V. Bakker, Dik van Leenen, Frank C. P. Holstege, Patrick Kemmeren
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2164-11-82

Transcriptional changes in response to X chromosome dosage in the mouse: implications for X inactivation and the molecular basis of Turner Syndrome
Cited by: 55
Author(s): Alexandra M. Lopes, Paul S. Burgoyne, Andrew Ojarikre, Julien Bauer, Carole A. Sargent, António Amorim, Nabeel A. Affara
Software Mentions: 1
Published: over 16 years ago

10.1186/s12864-015-1372-0

Genome-wide expression analysis suggests a crucial role of dysregulation of matrix metalloproteinases pathway in undifferentiated thyroid carcinoma
Cited by: 31
Author(s): Jesús Espinal-Enríquez, Said Muñoz-Montero, Iván Imaz-Rosshandler, Aldo J Huerta-Verde, Carmen Mejía, Enrique Hernández‐Lemus
Software Mentions: 1
Published: over 11 years ago

10.1186/1471-2164-11-312

Plasmodium infection alters Anopheles gambiae detoxification gene expression
Cited by: 43
Author(s): Rute C. Félix, Pie Müller, Vera Ribeiro, Hilary Ranson, Henrique Silveira
Software Mentions: 1
Published: over 16 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776