bioconductor: affy | Projects | Ecosyste.ms: Papers

10.3390/genes10030206

Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair
Cited by: 1
Author(s): Guillaume Brysbaert, Jérôme de Ruyck, Marc Aumercier, Marc F. Lensink
Software Mentions: 2
Published: over 5 years ago

10.1242/bio.032508

Whole-transcriptome splicing profiling of E7.5 mouse primary germ layers reveals frequent alternative promoter usage during mouse early embryogenesis
Cited by: 6
Author(s): Xukun Lu, Zhen-Ao Zhao, Xiaoqing Wang, Xiaoxin Zhang, Yunfeng Zhai, Wenbo Deng, Zhaohong Yi, Lei Li
Software Mentions: 2
Published: over 6 years ago

10.3390/genes11080914

Using Micro- and Macro-Level Network Metrics Unveils Top Communicative Gene Modules in Psoriasis
Cited by: 2
Author(s): Reyhaneh Naderi, Homa Mollaei, Arne Elofsson, Saman Hosseini Ashtiani
Software Mentions: 2
Published: over 4 years ago

10.6026/97320630015799

Towards the early detection of ductal carcinoma (a common type of breast cancer) using biomarkers linked to the PPAR(γ) signaling pathway
Cited by: 21
Author(s): Ghazala Sultan, Swaleha Zubair, Iftikhar Aslam Tayubi, Hans-Uwe Dahms‬, Inamul Hasan Madar
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.gdata.2015.06.022

Gene expression profiling of DBA/2J mice cochleae treated with l-methionine and valproic acid
Cited by: 1
Author(s): Fuyuki Miya, Hideki Mutai, Masato Fujisawa, Keith A. Boroevich, Tatsuo Matsunaga, Tatsuhiko Tsunoda
Software Mentions: 2
Published: about 9 years ago

10.1093/bioinformatics/bts629

AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data
Cited by: 13
Author(s): Mario Fasold, Hans Binder
Software Mentions: 2
Published: about 12 years ago

10.1186/gb-2007-8-4-r49

Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression
Cited by: 215
Author(s): Shisong Ma, Hans J. Bohnert
Software Mentions: 2
Published: almost 18 years ago

10.1111/j.1474-9726.2009.00467.x

Gene expression profiles associated with aging and mortality in humans
Cited by: 55
Author(s): Richard A. Kerber, Elizabeth O’Brien, Richard M. Cawthon
Software Mentions: 2
Published: over 15 years ago

10.1186/gb-2007-8-8-r161

The global role of ppGpp synthesis in morphological differentiation and antibiotic production in Streptomyces coelicolor A3(2)
Cited by: 126
Author(s): Andrew Hesketh, Wenqiong Joan Chen, Jamie Ryding, Sherman Chang, Mervyn J. Bibb
Software Mentions: 2
Published: almost 18 years ago

10.1186/s13040-014-0032-2

Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells
Cited by: 2
Author(s): Kirsti Laurila, Reija Autio, Lingjia Kong, Elisa Närvä, Samer M.I. Hussein, Timo Otonkoski, Riitta Lahesmaa, Harri Lähdesmäki
Software Mentions: 2
Published: almost 10 years ago

10.1186/gb-2012-13-10-r94

Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis
Cited by: 21
Author(s): Lidija Berke, Gabino F. Sánchez-Pérez, Berend Snel
Software Mentions: 2
Published: almost 13 years ago

10.1136/bmjpo-2017-000092

Peripheral blood RNA gene expression in children with pneumococcal meningitis: a prospective case–control study
Cited by: 18
Author(s): Benard W. Kulohoma, Fiona Marriage, Olga Vasieva, Limangeni Mankhambo, Kha Minh Nguyen, Malcolm E. Molyneux, Elizabeth Molyneux, Philip J. Day, Enitan D. Carrol
Software Mentions: 2
Published: over 7 years ago

10.1186/1752-0509-5-105

Construction of a computable cell proliferation network focused on non-diseased lung cells
Cited by: 63
Author(s): Jurjen W. Westra, Walter K. Schlage, Brian P. Frushour, Stephan Gebel, Natalie L. Catlett, Wanjiang Han, Sean Eddy, Arnd Hengstermann, Andrea Matthews, Carole Mathis, Rosemarie B. Lichtner, Carine Poussin, Marja Talikka, Emilija Veljkovic, Aaron A. Van Hooser, Benjamin Chun‐Yu Wong, Michael J. Maria, Manuel C. Peitsch, Renée Deehan, Julia Hoeng
Software Mentions: 2
Published: over 13 years ago

10.1186/s13059-014-0561-5

NF-κB-direct activation of microRNAs with repressive effects on monocyte-specific genes is critical for osteoclast differentiation
Cited by: 63
Author(s): Lorenzo de la Rica, Antonio García-Gómez, Natalia Ramirez Comet, Javier Rodríguez-Ubreva, Laura Ciudad, Roser Vento‐Tormo, Damiana Álvarez-Errico, Mireia García, Carmen Gómez-Vaquero, Esteban Ballestar
Software Mentions: 2
Published: almost 10 years ago

10.1186/1752-0509-5-168

A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue
Cited by: 75
Author(s): Walter K. Schlage, Jurjen W. Westra, Stephan Gebel, Natalie L. Catlett, Carole Mathis, Brian P. Frushour, Arnd Hengstermann, Aaron A. Van Hooser, Carine Poussin, Ben Wong, Michael Lietz, Jennifer Park, David A. Drubin, Emilija Veljkovic, Manuel C. Peitsch, Julia Hoeng, Renée Deehan
Software Mentions: 2
Published: about 13 years ago

10.1186/1752-0509-7-51

Transcriptome meta-analysis reveals a central role for sex steroids in the degeneration of hippocampal neurons in Alzheimer’s disease
Cited by: 30
Author(s): Jessica M. Winkler, Howard S. Fox
Software Mentions: 2
Published: almost 12 years ago

10.1186/1752-0509-3-31

Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo
Cited by: 194
Author(s): J. Joshua Smith, Renée Deehan Kenney, David Gagné, Brian P. Frushour, William Ladd, Heidi L. Galonek, Kristine Israelian, Jun Tae Song, Giedre Razvadauskaite, Amy V. Lynch, David P. Carney, Robin J. Johnson, Siva Lavu, André Iffland, Peter J. Elliott, Philip Lambert, Keith O. Elliston, Michael R. Jirousek, Jill C. Milne, Olivier Boss
Software Mentions: 2
Published: over 15 years ago

10.18632/oncotarget.10242

Globally increased ultraconserved noncoding RNA expression in pancreatic adenocarcinoma
Cited by: 35
Author(s): Jinmai Jiang, Ana Clara P. Azevedo-Pouly, Roxana S. Redis, Eun Joo Lee, Yuriy Gusev, David Allard, Dhruvitkumar S. Sutaria, Mohamed Badawi, Ola A. Elgamal, Megan R. Lerner, Daniel J. Brackett, George A. Calin, Thomas D. Schmittgen
Software Mentions: 2
Published: over 8 years ago

10.1186/gm327

Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types
Cited by: 45
Author(s): Gunes Gundem, Núria López‐Bigas
Software Mentions: 2
Published: almost 13 years ago

10.18632/oncotarget.11233

Heterogeneity in mechanisms of emergent resistance in pediatric T-cell acute lymphoblastic leukemia
Cited by: 16
Author(s): Babasaheb D. Yadav, A. Lacey Samuels, Julia E. Wells, Rosemary Sutton, Nicola C. Venn, Katerina Bendak, Denise Anderson, Glenn M. Marshall, Catherine Cole, Alex H. Beesley, Ursula R. Kees, Richard B. Lock
Software Mentions: 2
Published: over 8 years ago

10.1186/1753-6561-5-S4-S11

Gene expression pattern in swine neutrophils after lipopolysaccharide exposure: a time course comparison
Cited by: 4
Author(s): Gema Sanz, Ángeles Jiménez-Marín, Rocío Bautista, Noé Fernández, M. Gonzalo Claros, Juan J. Garrido
Software Mentions: 2
Published: over 13 years ago

10.1186/s13073-016-0305-0

Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma
Cited by: 12
Author(s): Colin Flinders, Larry Lam, Liudmilla Rubbi, Roberto Ferrari, Sorel Fitz‐Gibbon, Pao‐Yang Chen, Michael J. Thompson, Heather R. Christofk, David B. Agus, Daniel Ruderman, Parag Mallick, Matteo Pellegrini
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2229-14-174

The 2HA line of Medicago truncatulahas characteristics of an epigenetic mutant that is weakly ethylene insensitive
Cited by: 11
Author(s): Sergey Kurdyukov, Ulrike Mathesius, Kim E. Nolan, Michael B. Sheahan, Nicholas Goffard, Bernard J. Carroll, Ray J. Rose
Software Mentions: 2
Published: over 10 years ago

10.1186/s12967-020-02252-9

Transcriptional insights into the CD8+ T cell response in mono-HIV and HCV infection
Cited by: 3
Author(s): Siyao Li, Zining Zhang, Yongjun Jiang, Yajing Fu, Hong Shang
Software Mentions: 2
Published: over 4 years ago

10.1186/s41065-020-00119-z

Identification of differentially expressed miRNAs in differentiating benign from malignant pleural effusion
Cited by: 7
Author(s): Qiyu Bao, Yaping Xu, Ming Ding, Ping Chen
Software Mentions: 2
Published: over 4 years ago

10.1007/s00418-020-01866-w

Genes regulating hormone stimulus and response to protein signaling revealed differential expression pattern during porcine oocyte in vitro maturation, confirmed by lipid concentration
Cited by: 4
Author(s): Błażej Chermuła, Michal Ješeta, Patrycja Sujka‐Kordowska, Aneta Konwerska, Maurycy Jankowski, Wiesława Kranc, Ievgeniia Kocherova, Piotr Celichowski, Paweł Antosik, Dorota Bukowska, Irena Milaković, Marie Machatková, Leszek Pawełczyk, Dariusz Iżycki, Maciej Zabel, Paul Mozdziak, Bartosz Kempisty, Hanna Piotrowska‐Kempisty
Software Mentions: 2
Published: over 4 years ago

10.1002/iid3.375

Data mining combined with experiments to validate CEP55 as a prognostic biomarker in colorectal cancer
Cited by: 8
Author(s): Lin Kang, Xiaojian Zhu, Chen Luo, Fanqin Bu, Jinfeng Zhu, Zhengming Zhu
Software Mentions: 2
Published: about 4 years ago

10.18632/oncotarget.12992

Ammonium tetrathiomolybdate treatment targets the copper transporter ATP7A and enhances sensitivity of breast cancer to cisplatin
Cited by: 38
Author(s): Cristine Chisholm, Haitao Wang, Ada Hang Heng Wong, Guelaguetza Vázquez-Ortíz, Weiping Chen, Xiaoling Xu, Chu Xia Deng
Software Mentions: 2
Published: about 8 years ago

10.1186/1755-8794-1-17

Pro-neural transcription factors as cancer markers
Cited by: 33
Author(s): Maria Vias, Charles E. Massie, Philip East, Helen E. Scott, Anne Y. Warren, Zhe Zhou, Alexander Yu. Nikitin, David E. Neal, Ian G. Mills
Software Mentions: 2
Published: over 16 years ago

10.7150/jca.40621

The Prediction of Survival in Hepatocellular Carcinoma Based on A Four Long Non-coding RNAs Expression Signature
Cited by: 5
Author(s): Zongxing Yang, Yuhan Yang, Gang Zhou, Yan Luo, Wenjun Yang, Yuan Zhou, Jin Yang
Software Mentions: 2
Published: almost 5 years ago

10.7150/jca.47629

Development and validation of a metastasis-related Gene Signature for predicting the Overall Survival in patients with Pancreatic Ductal Adenocarcinoma
Cited by: 24
Author(s): Mei Wu, Xiaobin Li, Rui Li, Yuan Hu, Wei Liu, Ziwen Liu
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12916-020-01735-2

Considerations for target oxygen saturation in COVID-19 patients: are we under-shooting?
Cited by: 82
Author(s): Niraj Shenoy, Rebecca A. Luchtel, Perminder Gulani
Software Mentions: 2
Published: over 4 years ago

10.1186/1471-2334-13-393

Vitamin B6 reduces hippocampal apoptosis in experimental pneumococcal meningitis
Cited by: 22
Author(s): Denise C. Zysset-Burri, Caroline L. Bellac, Stephen L. Leib, Matthias Wittwer
Software Mentions: 2
Published: about 11 years ago

10.1186/1471-2164-11-640

Gene expression profile of the skin in the 'hairpoor' (HrHp) mice by microarray analysis
Cited by: 12
Author(s): Bong-Kyu Kim, In‐Cheol Baek, Hwa Young Lee, Jeong-Ki Kim, Hyo Jeong Song, Sungjoo Kim Yoon
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-13-225

Probing the Xenopus laevis inner ear transcriptome for biological function
Cited by: 10
Author(s): TuShun R. Powers, Selene Virk, Casilda Trujillo-Provencio, Elba E. Serrano
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2164-13-313

Mapping the polysaccharide degradation potential of Aspergillus niger
Cited by: 35
Author(s): Mikael Rørdam Andersen, Malene Giese, Ronald P. de Vries, Jens Nielsen
Software Mentions: 2
Published: over 12 years ago

10.1111/jcmm.15898

Down‐regulation of EOMES drives T‐cell exhaustion via abolishing EOMES‐mediated repression of inhibitory receptors of T cells in liver cancer
Cited by: 7
Author(s): Hongwei He, Yong Yi, Xiaoyan Cai, Jiaxing Wang, Xiaochun Ni, Yi‐Peng Fu, Shuang–Jian Qiu
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12864-016-3446-z

Compendium of TCDD-mediated transcriptomic response datasets in mammalian model systems
Cited by: 17
Author(s): Stephenie D. Prokopec, Kathleen E. Houlahan, Ren Sun, John D. Watson, Cindy Q. Yao, Jamie Lee, Christine P’ng, Renée Pang, Alexander H. Wu, Lauren C. Chong, Ashley B. Smith, Nicholas J. Harding, Ivy D. Moffat, Jere Lindén, Sanna Lensu, Allan B. Okey, Raimo Pohjanvirta, Paul C. Boutros
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2164-8-105

Putative null distributions corresponding to tests of differential expression in the Golden Spike dataset are intensity dependent
Cited by: 15
Author(s): Daniel P. Gaile, Jeffrey C. Miecznikowski
Software Mentions: 2
Published: almost 18 years ago

10.1186/1471-2164-10-S1-S19

A distribution-free convolution model for background correction of oligonucleotide microarray data
Cited by: 15
Author(s): Zhongxue Chen, Monnie McGee, Qingzhong Liu, Megan Kong, Youping Deng, Richard H. Scheuermann
Software Mentions: 2
Published: over 15 years ago

10.1186/1471-2164-11-205

Detection of novel 3' untranslated region extensions with 3' expression microarrays
Cited by: 14
Author(s): Lieven Thorrez, Léon-Charles Tranchevent, Hui-Wen Chang, Yves Moreau, Frans Schuit
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-10-613

Increased epithelial stem cell traits in advanced endometrial endometrioid carcinoma
Cited by: 14
Author(s): Shing‐Jyh Chang, Tao‐Yeuan Wang, Chan‐Yen Tsai, Tzu-Fang Hu, Margaret Dah‐Tsyr Chang, Hsei‐Wei Wang
Software Mentions: 2
Published: almost 15 years ago

10.1172/JCI134132

Orally bioavailable CDK9/2 inhibitor shows mechanism-based therapeutic potential in MYCN-driven neuroblastoma
Cited by: 38
Author(s): Evon Poon, Tong Liang, Yann Jamin, Susanne Walz, Colin Kwok, Anne Hakkert, Karen Barker, Zuzanna Urban, Khin Thway, Rhamy Zeid, Albert Hallsworth, Gary Box, Marli E. Ebus, Marco P. Licciardello, Yordan Sbirkov, Glori Lazaro, Elizabeth Calton, Barbara Martins Da Costa, Melanie Valenti, Alexis de Haven Brandon, Hannah Webber, Nicolas Tardif, Gilberto S. Almeida, Rossitza Christova, Gunther Boysen, Mark W. Richards, Giuseppe Barone, Anthony M. Ford, Richard Bayliss, Paul A. Clarke, Johann S. de Bono, Nathanael S. Gray, Julian Blagg, Simon P. Robinson, Suzanne A. Eccles, Daniella Zheleva, James E. Bradner, Jan J. Molenaar, Igor Vivanco, Martin Eilers, Paul Workman, Charles Y. Lin, Louis Chesler
Software Mentions: 2
Published: about 4 years ago

10.1093/jxb/eru173

Salt stress and senescence: identification of cross-talk regulatory components
Cited by: 107
Author(s): Annapurna Devi Allu, Aleksandra Maria Soja, Anhui Wu, Jędrzej Szymański, Salma Balazadeh
Software Mentions: 2
Published: over 10 years ago

10.1186/1471-2164-7-33

Tests for differential gene expression using weights in oligonucleotide microarray experiments
Cited by: 9
Author(s): Pingzhao Hu, Joseph Beyene, Celia M.T. Greenwood
Software Mentions: 2
Published: over 18 years ago

10.1186/1471-2164-10-49

Infection and genotype remodel the entire soybean transcriptome
Cited by: 45
Author(s): Long Zhou, Santiago X. Mideros, Lei Bao, Regina Hanlon, Francisco Arredondo, Sucheta Tripathy, Konstantinos Krampis, Adam Jerauld, Clive Evans, S. K. St. Martin, M. A. Saghai Maroof, Ina Hoeschele, Anne E. Dorrance, Brett M. Tyler
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2164-14-922

TIPMaP: a web server to establish transcript isoform profiles from reliable microarray probes
Cited by: 1
Author(s): Neelima Chitturi, Govindkumar Balagannavar, Darshan S. Chandrashekar, Sadashivam Abinaya, Vasan S Srini, Kshitish K. Acharya
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12958-017-0261-6

Expression of genes associated with BMP signaling pathway in porcine oocytes before and after IVM – a microarray approach
Cited by: 12
Author(s): Joanna Budna, Marta Rybska, Sylwia Ciesiółka, Artur Bryja, Sylwia Borys, Wiesława Kranc, Katarzyna Wojtanowicz-Markiewicz, Michal Ješeta, Ewa Sumelka, Dorota Bukowska, Paweł Antosik, Klaus‐Peter Brüssow, M Bruska, Michał Nowicki, Maciej Zabel, Bartosz Kempisty
Software Mentions: 2
Published: over 7 years ago

10.18632/oncotarget.12038

COL3A1 and SNAP91: novel glioblastoma markers with diagnostic and prognostic value
Cited by: 52
Author(s): Yuanfeng Gao, Xiao‐Yuan Mao, Tao Zhu, Chen-Xue Mao, Zhixiong Liu, Zhibin Wang, Ling Li, Xi Li, Ji‐Ye Yin, Wei Zhang, Hong‐Hao Zhou, Zhao‐Qian Liu
Software Mentions: 2
Published: about 8 years ago

10.1186/1939-8433-5-17

The Rice Oligonucleotide Array Database: an atlas of rice gene expression
Cited by: 156
Author(s): Peijian Cao, Ki‐Hong Jung, Daeseok Choi, Daehee Hwang, Jun Zhu, Pamela C. Ronald
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2105-9-520

Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data
Cited by: 51
Author(s): Carl Pelz, Molly Kulesz‐Martin, Grover C. Bagby, Rosalie C. Sears
Software Mentions: 2
Published: almost 16 years ago

10.1186/1471-2164-13-369

Jasmonate and ethylene dependent defence gene expression and suppression of fungal virulence factors: two essential mechanisms of Fusarium head blight resistance in wheat?
Cited by: 103
Author(s): Sven Gottwald, Birgit Samans, Stefanie Lück, Wolfgang Friedt
Software Mentions: 2
Published: over 12 years ago

10.1038/s41597-021-00808-y

Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials
Cited by: 17
Author(s): Laura Aliisa Saarimäki, Antonio Federico, Iseult Lynch, Anastasios G. Papadiamantis, Andreas Tsoumanis, Georgia Melagraki, Antreas Afantitis, Angela Serra, Dario Greco
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2164-16-S2-S2

Discovering monotonic stemness marker genes from time-series stem cell microarray data
Cited by: 24
Author(s): Hsei‐Wei Wang, Hsin‐Yun Sun, Ting‐Yu Chang, Hung-Hao Lo, Wei‐Chung Cheng, George C. Tseng, Chin‐Teng Lin, Shing‐Jyh Chang, Nikhil R. Pal, I‐Fang Chung
Software Mentions: 2
Published: almost 10 years ago

10.1038/srep43941

Androgen receptor is a potential novel prognostic marker and oncogenic target in osteosarcoma with dependence on CDK11
Cited by: 12
Author(s): Yunfei Liao, Slim Sassi, Stefan Halvorsen, Yong Feng, Jacson K. Shen, Yan Gao, Gregory M. Coté, Edwin Choy, David C. Harmon, Henry J. Mankin, Francis J. Hornicek, Zhenfeng Duan
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-5259-8

PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli
Cited by: 15
Author(s): Clémentine Dressaire, Vânia Pobre, Sandrine Laguerre, Laurence Girbal, Cecília M. Arraiano, Muriel Cocaign‐Bousquet
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-017-05538-z

Heterogeneity of tumor-infiltrating lymphocytes ascribed to local immune status rather than neoantigens by multi-omics analysis of glioblastoma multiforme
Cited by: 25
Author(s): Lin Feng, Hai-Peng Qian, Xuexin Yu, Kan Liu, Ting Xiao, Chengli Zhang, Manchao Kuang, Shujun Cheng, Xueji Li, Jinghai Wan, Kaitai Zhang
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-9-341

Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design
Cited by: 53
Author(s): Alessandro Fazio, Michael C. Jewett, Pascale Daran‐Lapujade, Roberta Mustacchi, Renata Usaite, Jack T. Pronk, Christopher T. Workman, Jens Nielsen
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2164-11-132

Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations
Cited by: 47
Author(s): Hsei Wei Wang, Yu-Hsueh Wu, Jui Yu Hsieh, Muh Lii Liang, Meng En Chao, Da Jung Liu, Ming Hsu, Tai-Tong Wong
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-9-197

Transcriptome analysis identifies pathways associated with enhanced maternal performance in QSi5 mice
Cited by: 18
Author(s): Palaniappan Ramanathan, Ian Martin, Margaret Gardiner-Garden, Peter Thomson, Rabun Taylor, Christopher J. Ormandy, C. Moran, Peter Williamson
Software Mentions: 2
Published: over 16 years ago

10.1038/s41598-018-21581-w

A Potential Prognostic Long Noncoding RNA Signature to Predict Recurrence among ER-positive Breast Cancer Patients Treated with Tamoxifen
Cited by: 30
Author(s): Kang Wang, Jie Li, Yong Xiong, Zhen Zeng, Xiang Zhang, Hongyuan Li
Software Mentions: 2
Published: almost 7 years ago

10.18632/oncotarget.15681

The histone demethylase<i>KDM3A</i>regulates the transcriptional program of the androgen receptor in prostate cancer cells
Cited by: 74
Author(s): Stephen Wilson, Lingling Fan, Natasha Sahgal, Jianfei Qi, Fabian V. Filipp
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2164-12-226

Genome-wide dynamics of a bacterial response to antibiotics that target the cell envelope
Cited by: 56
Author(s): Andrew Hesketh, C.P. Hill, Jehan Mokhtar, Gabriela Balíková Novotná, Ngat T. Tran, Mervyn J. Bibb, Hee‐Jeon Hong
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-7-254

Proximal genomic localization of STAT1 binding and regulated transcriptional activity
Cited by: 18
Author(s): Samuel Wormald, Douglas J. Hilton, Gordon K. Smyth, Terence P. Speed
Software Mentions: 2
Published: about 18 years ago

10.1186/1471-2164-7-215

Inferring direct regulatory targets from expression and genome location analyses: a comparison of transcription factor deletion and overexpression
Cited by: 20
Author(s): Lin Tang, Xiao Liu, Neil D. Clarke
Software Mentions: 2
Published: over 18 years ago

10.1038/s41598-018-29763-2

Establishing normal metabolism and differentiation in hepatocellular carcinoma cells by culturing in adult human serum
Cited by: 19
Author(s): Renske D.M. Steenbergen, Martin Oti, Rob ter Horst, Wilson Tat, Christopher J. Neufeldt, Alexandr Belovodskiy, Tiing Tiing Chua, Woo Jung Cho, Michael Joyce, Bas E. Dutilh, D. Lorne Tyrrell
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-017-3761-z

Associating transcriptional modules with colon cancer survival through weighted gene co-expression network analysis
Cited by: 48
Author(s): Rong Liu, Wei Zhang, Zhao‐Qian Liu, Hong‐Hao Zhou
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-018-33985-9

Gene expression dataset for whole cochlea of Macaca fascicularis
Cited by: 5
Author(s): Hideki Mutai, Fuyuki Miya, Hiroaki Shibata, Yasuhiro Yasutomi, Tatsuhiko Tsunoda, Tatsuo Matsunaga
Software Mentions: 2
Published: about 6 years ago

10.1186/s12967-015-0492-2

Systems biology analysis reveals NFAT5 as a novel biomarker and master regulator of inflammatory breast cancer
Cited by: 36
Author(s): Andrea Remo, Ines Simeone, Massimo Pancione, Pietro Parcesepe, Pascal Finetti, Luigi Cerulo, Halima Bensmail, Daniel Birnbaum, Steven J. Van Laere, Vittorio Colantuoni, Franco Bonetti, François Bertucci, Erminia Manfrin, Michele Ceccarelli
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-019-43700-x

Heparin Differentially Impacts Gene Expression of Stromal Cells from Various Tissues
Cited by: 16
Author(s): Sandra Laner-Plamberger, Michaela Oeller, Rodolphe Poupardin, Linda Krisch, Sarah Hochmann, Ravi Kr Kalathur, Karin Pachler, Christina Kreutzer, Gerrit Erdmann, Eva Rohde, Dirk Strunk, Katharina Schallmoser
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-46359-6

Mitochondrial Akt Signaling Modulated Reprogramming of Somatic Cells
Cited by: 11
Author(s): Yuhan Chen, Ching-Chieh Su, Wu Deng, Leslie F. Lock, Peter Donovan, Matthew A. Kayala, Pierre Baldi, Hsiao-Chen Lee, Ping H. Wang
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-48150-z

Assessing phenotype order in molecular data
Cited by: 6
Author(s): Ludwig Lausser, Lisa Schäfer, Lyn-Rouven Schirra, Robin Szekely, Florian Schmid, Hans A. Kestler
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-10-197

Gene set internal coherence in the context of functional profiling
Cited by: 32
Author(s): David Montaner, Pablo Mínguez, Fátima Al‐Shahrour, Joaquı́n Dopazo
Software Mentions: 2
Published: over 15 years ago

10.1038/s41598-019-51054-7

Crosstalk between protein N-glycosylation and lipid metabolism in Saccharomyces cerevisiae
Cited by: 13
Author(s): Antonisamy William James, Chidambaram Ravi, Malathi Srinivasan, Vasanthi Nachiappan
Software Mentions: 2
Published: about 5 years ago

10.1186/1471-2164-7-145

Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis
Cited by: 44
Author(s): Ella Palmer, Andrew D. Miller, Tom C. Freeman
Software Mentions: 2
Published: over 18 years ago

10.1186/s12864-015-1659-1

Six host-range restricted poxviruses from three genera induce distinct gene expression profiles in an in vivo mouse model
Cited by: 12
Author(s): Kristy Offerman, Armin Deffur, Olivia Carulei, Robert J. Wilkinson, Nicola Douglass, Anna‐Lise Williamson
Software Mentions: 2
Published: over 9 years ago

10.18632/oncotarget.19504

Coexpression analysis identifies nuclear reprogramming barriers of somatic cell nuclear transfer embryos
Cited by: 21
Author(s): Yongchun Zuo, Guanghua Su, Cheng Liu, Kun Liu, Yang Feng, Zhuying Wei, Chunling Bai, Guifang Cao, Guangpeng Li
Software Mentions: 2
Published: over 7 years ago

10.18632/oncotarget.10982

A seven-gene signature predicts overall survival of patients with colorectal cancer
Cited by: 47
Author(s): Huarong Chen, Xiaoqiang Sun, Weiting Ge, Yun Qian, Rui Bai, Shu Zheng
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-016-2750-y

Comprehensive analyses of the annexin gene family in wheat
Cited by: 44
Author(s): Lei Xu, Yimiao Tang, Shiqing Gao, Shichao Su, Hong Lin, Weiwei Wang, Zhaofeng Fang, Xueyin Li, Jinxiu Ma, Wei Quan, Hui Sun, Xia Li, Yongbo Wang, Xiangzheng Liao, Jiangang Gao, Fengting Zhang, Lei Li, Changping Zhao
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-020-77601-1

Loss of FOXF1 expression promotes human lung-resident mesenchymal stromal cell migration via ATX/LPA/LPA1 signaling axis
Cited by: 10
Author(s): Pengxiu Cao, Neff Walker, Russell R. Braeuer, Serina Mazzoni-Putman, Yoshiro Aoki, Keizo Misumi, David Wheeler, Ragini Vittal, Vibha N. Lama
Software Mentions: 2
Published: almost 4 years ago

10.1186/1471-2164-14-182

Distinct angiogenesis roles and surface markers of early and late endothelial progenitor cells revealed by functional group analyses
Cited by: 94
Author(s): Cheng Chung Cheng, Shing Jyh Chang, Yu Neng Chueh, Tsung Hui Huang, Po Hsun Huang, Soo‐Chen Cheng, Tsung Neng Tsai, Jaw Wen Chen, Hsei Wei Wang
Software Mentions: 2
Published: almost 12 years ago

10.1186/1471-2148-11-47

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana
Cited by: 140
Author(s): Mark T.A. Donoghue, Channa Keshavaiah, Sandesh H Swamidatta, Charles Spillane
Software Mentions: 2
Published: almost 14 years ago

10.1186/s13287-018-0864-7

The presence of human mesenchymal stem cells of renal origin in amniotic fluid increases with gestational time
Cited by: 18
Author(s): Shaifur Rahman, Lucas‐Sebastian Spitzhorn, Wasco Wruck, Carsten Hagenbeck, Percy Balan, Nina Graffmann, Martina Bohndorf, Audrey Ncube, Pascale V. Guillot, Tanja Fehm, James Adjaye
Software Mentions: 2
Published: over 6 years ago

10.1186/s13287-018-1050-7

Key genes and integrated modules in hematopoietic differentiation of human embryonic stem cells: a comprehensive bioinformatic analysis
Cited by: 11
Author(s): Pengfei Li, Mengyao Wu, Qiwang Lin, Shu Wang, Tong Chen, Hua Jiang
Software Mentions: 2
Published: about 6 years ago

10.1186/s13287-019-1475-7

Acute myeloid leukemia cells secrete microRNA-4532-containing exosomes to mediate normal hematopoiesis in hematopoietic stem cells by activating the LDOC1-dependent STAT3 signaling pathway
Cited by: 25
Author(s): Chen Zhao, Feng Du, Yang Zhao, Shanshan Wang, Ling Qi
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12885-020-06829-x

Microarray data analysis on gene and miRNA expression to identify biomarkers in non-small cell lung cancer
Cited by: 30
Author(s): Xiang Jin, Yinghui Guan, Zhen Zhang, Hongyue Wang
Software Mentions: 2
Published: over 4 years ago

10.18632/oncotarget.22347

Systemic bioinformatics analysis of recurrent aphthous stomatitis gene expression profiles
Cited by: 20
Author(s): Jian Wu, Zhengping Chen, Anquan Shang, Weiwei Wang, Chen Zong-ning, Yunjuan Tao, Yue Zhou, Wanxiang Wang
Software Mentions: 2
Published: about 7 years ago

10.1038/tp.2015.158

Transcriptomic and genetic studies identify NFAT5 as a candidate gene for cocaine dependence
Cited by: 16
Author(s): Noèlia Fernàndez‐Castillo, Judit Cabana‐Domínguez, Jordi Soriano, Cristina Sánchez-Mora, Carlos Roncero, Lara Grau-López, Elena Ros-Cucurull, Constanza Daigre, Marjolein M. J. Van Donkelaar, Barbara Franke, Miguel Casas, Marta Ribasés, Bru Cormand
Software Mentions: 2
Published: about 9 years ago

10.1186/1471-2407-12-527

Pancreatic cancer circulating tumour cells express a cell motility gene signature that predicts survival after surgery
Cited by: 57
Author(s): Gregory Sergeant, Rudy van Eijsden, Tania Roskams, Van Duppen, Baki Topal
Software Mentions: 2
Published: about 12 years ago

10.18632/aging.203493

Calorie intake rather than food quantity consumed is the key factor for the anti-aging effect of calorie restriction
Cited by: 3
Author(s): Yaru Liang, Yuqi Gao, Rui Hua, Maoyang Lu, Huiling Chen, Zhuoran Wang, Liyuan Li, Kaiqiang Hu, Yuemiao Yin, Kang Xu, Gao Hong-qi, Qingfei Liu, Ying Qiu, Zhao Wang
Software Mentions: 2
Published: about 3 years ago

10.18632/oncotarget.24843

A TRPV2 interactome-based signature for prognosis in glioblastoma patients
Cited by: 15
Author(s): Pau Doñate-Macián, Antonio Gómez, Irene R. Dégano, Alex Perálvarez‐Marín
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0008836

MicroRNA-145 Targets YES and STAT1 in Colon Cancer Cells
Cited by: 155
Author(s): Lea H. Gregersen, Anders Jacobsen, Lisa B. Frankel, Jiayu Wen, Anders Krogh, Anders H. Lund
Software Mentions: 2
Published: almost 15 years ago

10.1186/s12885-019-5952-2

L1TD1 - a prognostic marker for colon cancer
Cited by: 9
Author(s): Deepankar Chakroborty, Maheswarareddy Emani, Рику Клен, Camilla Böckelman, Jaana Hagström, Caj Haglund, Ari Ristimäki, Riitta Lahesmaa, Laura L. Elo
Software Mentions: 2
Published: over 5 years ago

10.1186/1479-7364-7-24

Transcriptomics to study the effect of a Mediterranean-inspired diet on inflammation in Crohn's disease patients
Cited by: 151
Author(s): Gareth Marlow, Stephanie Ellett, Isobel Ferguson, Shuotun Zhu, Nishi Karunasinghe, Amalini Jesuthasan, Dug Yeo Han, Alan G. Fraser, Lynnette R. Ferguson
Software Mentions: 2
Published: almost 11 years ago

10.1186/1471-2407-6-200

Selection of suitable reference genes for accurate normalization of gene expression profile studies in non-small cell lung cancer
Cited by: 89
Author(s): Silvia Saviozzi, Francesca Cordero, Marco Lo Iacono, Silvia Novello, Scagliotti V. Giorgio, Raffaele Calogero
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pone.0224922

Verification of hub genes in the expression profile of aortic dissection
Cited by: 7
Author(s): Weitie Wang, Qing Liu, Yong Wang, Hulin Piao, Bo Li, Zhicheng Zhu, Dan Li, Tiance Wang, Rihao Xu, Kexiang Liu
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0060275

CLL Cells Respond to B-Cell Receptor Stimulation with a MicroRNA/mRNA Signature Associated with MYC Activation and Cell Cycle Progression
Cited by: 32
Author(s): Valerie Pede, Ans Rombout, Jolien Vermeíre, Evelien Naessens, Pieter Mestdagh, Nore Robberecht, Hanne Vanderstraeten, Nadine Van Roy, Jo Vandesompele, Franki Speleman, Jan Philippé, Bruno Verhasselt
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0049248

Mid-Gestational Gene Expression Profile in Placenta and Link to Pregnancy Complications
Cited by: 65
Author(s): Liis Uusküla, Jaana Männik, Kristiina Rull, Ave Minajeva, Sulev Kõks, Pille Vaas, Pille Teesalu, Jüri Reimand, Maris Laan
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0136426

Development of a Novel Method for Analyzing Pseudomonas aeruginosa Twitching Motility and Its Application to Define the AmrZ Regulon
Cited by: 8
Author(s): Binjie Xu, Daniel J. Wozniak
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0035618

Exploring the Transcriptome of Ciliated Cells Using In Silico Dissection of Human Tissues
Cited by: 72
Author(s): Alexander E. Ivliev, Peter A C ‘t Hoen, Willeke M. C. van Roon‐Mom, Dorien J.M. Peters, Marina G. Sergeeva
Software Mentions: 2
Published: over 12 years ago

Projects: bioconductor: affy

Papers Mentioning affy 989