bioconductor: affy | Projects | Ecosyste.ms: Papers

10.18632/aging.102161

Identification of 9 key genes and small molecule drugs in clear cell renal cell carcinoma
Cited by: 47
Author(s): Yongwen Luo, Dexin Shen, Liang Chen, Gang Wang, Xuefeng Li, Kaiyu Qian, Yu Xiao, Xinghuan Wang, Lingao Ju
Software Mentions: 3
Published: over 5 years ago

10.18632/aging.202380

Diagnostic and prognostic values of AKR1C3 and AKR1D1 in hepatocellular carcinoma
Cited by: 8
Author(s): Pengfei Zhu, Ru Feng, Lei Xu, Ling Yuan, Zhicheng Du, Wenlong Zhai, Kunlun Chen
Software Mentions: 3
Published: almost 4 years ago

10.18632/aging.102612

ASPM promotes glioblastoma growth by regulating G1 restriction point progression and Wnt-β-catenin signaling
Cited by: 29
Author(s): Xin Chen, Lijie Huang, Yang Yang, Suhua Chen, Jianjun Sun, Chang-cheng Ma, Jingcheng Xie, Yongmei Song, Jun Yang
Software Mentions: 3
Published: almost 5 years ago

10.1186/ar2855

Insights in to the pathogenesis of axial spondyloarthropathy based on gene expression profiles
Cited by: 45
Author(s): Srilakshmi M Sharma, Dongseok Choi, Stephen R. Planck, Christina A. Harrington, Carrie R. Austin, J. A. Lewis, Tessa N. Diebel, Tammy M. Martin, Justine R. Smith, James T. Rosenbaum
Software Mentions: 3
Published: almost 16 years ago

10.1186/s12859-017-1564-5

Two-way learning with one-way supervision for gene expression data
Cited by: 3
Author(s): Monica Wong, David M. Mutch, Paul D. McNicholas
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-14-39

puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis
Cited by: 7
Author(s): Xuejun Liu, Zhenzhu Gao, Lili Zhang, Magnus Rattray
Software Mentions: 3
Published: almost 12 years ago

10.1186/1471-2105-11-553

Algorithm-driven Artifacts in median polish summarization of Microarray data
Cited by: 50
Author(s): Federico M. Giorgi, Anthony Bolger, Marc Lohse, Björn Usadel
Software Mentions: 3
Published: about 14 years ago

10.1186/1471-2105-15-238

Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models
Cited by: 92
Author(s): Florian Martin, Alain Sewer, Marja Talikka, Yu‐Tao Xiang, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2105-11-257

Detecting microRNA activity from gene expression data
Cited by: 33
Author(s): Stephen F. Madden, Susan Carpenter, Ian B. Jeffery, Harry Björkbacka, Katherine A. Fitzgerald, Luke A. J. O’Neill, Desmond G. Higgins
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2105-10-50

EMMA 2 – A MAGE-compliant system for the collaborative analysis and integration of microarray data
Cited by: 66
Author(s): Michael Dondrup, Stefan P. Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane Katja Kleindt, H. Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J. Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann
Software Mentions: 3
Published: almost 16 years ago

10.1186/1471-2105-11-127

Effects of scanning sensitivity and multiple scan algorithms on microarray data quality
Cited by: 5
Author(s): Andrew Williams, Errol M. Thomson
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2105-6-199

Cited by: 84
Author(s): Per Broberg
Software Mentions: 3
Published: almost 20 years ago

10.1186/1471-2105-12-381

Discovering biological connections between experimental conditions based on common patterns of differential gene expression
Cited by: 21
Author(s): Adam C. Gower, Avrum Spira, Marc E. Lenburg
Software Mentions: 3
Published: about 13 years ago

10.1186/1471-2105-8-195

Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips
Cited by: 20
Author(s): Andrew Harrison, Caroline Johnston, Christine A. Orengo
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2105-8-108

Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays
Cited by: 52
Author(s): Jun Lü, Joseph C. Lee, Marc Salit, Margaret C. Cam
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2105-10-191

Unsupervised assessment of microarray data quality using a Gaussian mixture model
Cited by: 4
Author(s): Brian E. Howard, Beate Sick, Steffen Heber
Software Mentions: 3
Published: over 15 years ago

10.1186/1471-2105-12-369

Thawing Frozen Robust Multi-array Analysis (fRMA)
Cited by: 38
Author(s): Matthew N. McCall, Rafael A. Irizarry
Software Mentions: 3
Published: about 13 years ago

10.1186/1741-7007-8-96

Serious limitations of the QTL/Microarray approach for QTL gene discovery
Cited by: 29
Author(s): Ricardo A. Verdugo, Charles R. Farber, Craig H Warden, Juan F. Medrano
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2407-10-573

Comparative survival analysis of breast cancer microarray studies identifies important prognostic genetic pathways
Cited by: 24
Author(s): Jeffrey C. Miecznikowski, Dan Wang, Song Liu, Lara Sucheston, David Gold
Software Mentions: 3
Published: about 14 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 14 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 7 years ago

10.1186/1471-2164-10-202

Distinct patterns of gene and protein expression elicited by organophosphorus pesticides in Caenorhabditis elegans
Cited by: 43
Author(s): John A. Lewis, M. Szilágyi, Elizabeth Gehman, William E. Dennis, David A. Jackson
Software Mentions: 3
Published: almost 16 years ago

10.1186/1471-2164-13-355

Dose-dependent effects of small-molecule antagonists on the genomic landscape of androgen receptor binding
Cited by: 7
Author(s): Zhou Zhu, Minmin Shi, Wenyue Hu, Heather Estrella, Jon Engebretsen, Tim Nichols, David M. Briere, Natilie Hosea, Gerrit Los, Paul A. Rejto, Andrea Fanjul
Software Mentions: 3
Published: almost 13 years ago

10.1186/1471-2164-15-1176

Distinct gene signatures in aortic tissue from ApoE-/-mice exposed to pathogens or Western diet
Cited by: 8
Author(s): Carolyn D. Kramer, Ellen O. Weinberg, Adam C. Gower, Xianbao He, Samrawit Mekasha, Connie Slocum, Lea M. Beaulieu, Lee M. Wetzler, Yuriy O. Alekseyev, Frank C. Gibson, Jane E. Freedman, Robin R. Ingalls, Caroline A. Genco
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12864-017-3667-9

Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes
Cited by: 23
Author(s): Leticia Díaz-Beltrán, Francisco J. Esteban, Maya Varma, Alp Ortuzk, Maude M. David, Dennis P. Wall
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-11-315

A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays
Cited by: 3
Author(s): Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masanori Kawakita, Takayuki Sakaguchi, Nori Kurata
Software Mentions: 3
Published: over 14 years ago

10.1186/1755-8794-3-32

A sequence-based approach to identify reference genes for gene expression analysis
Cited by: 39
Author(s): Raj Chari, Kim M. Lonergan, Larissa A. Pikor, Bradley P. Coe, Chang-Qi Zhu, Tommy H.T. Chan, Calum MacAulay, Ming‐Sound Tsao, Stephen Lam, Raymond T. Ng, Wan L. Lam
Software Mentions: 3
Published: over 14 years ago

10.1186/1755-8794-5-35

Direct integration of intensity-level data from Affymetrix and Illumina microarrays improves statistical power for robust reanalysis
Cited by: 42
Author(s): Arran Turnbull, Robert Kitchen, Alexey Larionov, Lorna Renshaw, JM Dixon, Andrew H. Sims
Software Mentions: 3
Published: over 12 years ago

10.1186/s12920-020-00750-9

Weighted correlation network bioinformatics uncovers a key molecular biosignature driving the left-sided heart failure
Cited by: 8
Author(s): Jiamin Zhou, Wei Zhang, Chunying Wei, Zhiliang Zhang, Dasong Yi, Xiaoping Peng, Jianheng Peng, Rong Yin, Zeqi Zheng, Hongmei Qi, Yunfeng Wei, Tong-Chun Wen
Software Mentions: 3
Published: over 4 years ago

10.1186/1471-2180-7-78

Identification of human pathogens isolated from blood using microarray hybridisation and signal pattern recognition
Cited by: 48
Author(s): Herbert Wiesinger-Mayr, Klemens Vierlinger, Rudolf Pichler, Albert Kriegner, Alexander M. Hirschl, Elisabeth Presterl, Levente Bodrossy, Christa Noehammer
Software Mentions: 3
Published: almost 18 years ago

10.1186/1471-2180-10-159

Revealing fosfomycin primary effect on Staphylococcus aureus transcriptome: modulation of cell envelope biosynthesis and phosphoenolpyruvate induced starvation
Cited by: 32
Author(s): Marko Petek, Špela Baebler, Drago Kuzman, Ana Rotter, Zdravko Podlesek, Kristina Gruden, Maja Ravnikar, U. Urleb
Software Mentions: 3
Published: almost 15 years ago

10.1186/s12868-015-0186-y

mRNA and microRNA analysis reveals modulation of biochemical pathways related to addiction in the ventral tegmental area of methamphetamine self-administering rats
Cited by: 38
Author(s): Peter Bösch, Miles C. Benton, Donia Macartney-Coxson, Bronwyn M. Kivell
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2229-9-67

Transcriptomic analysis of tomato carpel development reveals alterations in ethylene and gibberellin synthesis during pat3/pat4 parthenocarpic fruit set
Cited by: 39
Author(s): Laura Pascual, José Blanca, Joaquı́n Cañizares, Fernado Nuez
Software Mentions: 3
Published: over 15 years ago

10.1186/s12870-015-0568-4

Comprehensive meta-analysis, co-expression, and miRNA nested network analysis identifies gene candidates in citrus against Huanglongbing disease
Cited by: 43
Author(s): Nidhi Rawat, Sandhya.P. Kiran, Dongliang Du, Fred G. Gmitter, Zhanao Deng
Software Mentions: 3
Published: over 9 years ago

10.1186/s13104-015-1141-9

Dysregulated mechanisms underlying Duchenne muscular dystrophy from co-expression network preservation analysis
Cited by: 15
Author(s): Kavitha Mukund, Shankar Subramaniam
Software Mentions: 3
Published: over 9 years ago

10.1186/1756-0500-3-255

Expression analysis of flavonoid biosynthesis genes during Arabidopsis thaliana silique and seed development with a primary focus on the proanthocyanidin biosynthetic pathway
Cited by: 48
Author(s): Christiane Katja Kleindt, Ralf Stracke, Marcus Frank, Bernd Weißhaar
Software Mentions: 3
Published: about 14 years ago

10.1186/s12918-017-0520-3

Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology
Cited by: 13
Author(s): Joanna H. Sier, Alfred E. Thumser, Nick Plant
Software Mentions: 3
Published: almost 7 years ago

10.1186/1752-0509-7-52

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum
Cited by: 21
Author(s): Katherine Lawler, K. E. Hammond‐Kosack, Alvis Brāzma, Richard M. R. Coulson
Software Mentions: 3
Published: almost 12 years ago

10.1186/1752-0509-4-67

An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer
Cited by: 56
Author(s): Raj Chari, Bradley P. Coe, Emily A. Vucic, William W. Lockwood, Wan L. Lam
Software Mentions: 3
Published: over 14 years ago

10.3762/bjnano.6.252

Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials
Cited by: 49
Author(s): Andrew Williams, Sabina Halappanavar
Software Mentions: 3
Published: almost 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: almost 8 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 9 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: about 6 years ago

10.1155/2013/512086

Systems Approaches Evaluating the Perturbation of Xenobiotic Metabolism in Response to Cigarette Smoke Exposure in Nasal and Bronchial Tissues
Cited by: 46
Author(s): Anita Iskandar, Florian Martin, Marja Talikka, Walter K. Schlage, Radina Kostadinova, Carole Mathis, Julia Hoeng, Manuel C. Peitsch
Software Mentions: 3
Published: almost 12 years ago

10.1042/BSR20191247

HPO-Shuffle: an associated gene prioritization strategy and its application in drug repurposing for the treatment of canine epilepsy
Cited by: 5
Author(s): Shuguang Wang, Xiangyu Meng, Yuxing Wang, Ye-Mao Liu, Jingbo Xia
Software Mentions: 3
Published: about 5 years ago

10.1038/s41408-019-0249-x

Maternal embryonic leucine zipper kinase is a novel target for diffuse large B cell lymphoma and mantle cell lymphoma
Cited by: 7
Author(s): Anke Maes, Ken Maes, Philip Vlummens, Hendrik De Raeve, Julie Devin, Vanessa Szablewski, Kim De Veirman, Eline Menu, Jérôme Moreaux, Karin Vanderkerken, Elke De Bruyne
Software Mentions: 3
Published: about 5 years ago

10.1038/s41416-020-01252-2

Discovery of a biomarker candidate for surgical stratification in high-grade serous ovarian cancer
Cited by: 10
Author(s): Haonan Lu, Paula Cunnea, Katherine Nixon, Natasha Rinne, Eric O. Aboagye, Christina Fotopoulou
Software Mentions: 3
Published: almost 4 years ago

10.1111/j.1365-2141.2006.06342.x

Gene expression profiling reveals consistent differences between clinical samples of human leukaemias and their model cell lines
Cited by: 15
Author(s): Nicolas Leupin, Aléxandre Kuhn, Barbara Hügli, Tobias Grob, Rolf Jaggi, Andreas Tobler, Mauro Delorenzi, Martin F. Fey
Software Mentions: 3
Published: about 18 years ago

10.1002/brb3.1879

Identifying functionally relevant candidate genes for inflexible ethanol intake in mice and humans using a guilt‐by‐association approach
Cited by: 8
Author(s): Luana Martins de Carvalho, Pablo Augusto de Souza Fonseca, Isadora Marques Paiva, Samara Damasceno, Agatha Sondertoft Braga Pedersen, Daniel Almeida da Silva e Silva, Corinde E. Wiers, Nora D. Volkow, Ana Lúcia Brunialti Godard
Software Mentions: 3
Published: about 4 years ago

10.1093/braincomms/fcab053

Activating transcription factor 4-dependent lactate dehydrogenase activation as a protective response to amyloid beta toxicity
Cited by: 8
Author(s): Teresa Niccoli, Fiona Kerr, Inge Snoeren, Daniel K. Fabian, Benjamin Aleyakpo, Dobril Ivanov, Oyinkan Sofola-Adesakin, Adam Cryar, Jennifer Adcott, Janet Thornton, Linda Partridge
Software Mentions: 3
Published: over 3 years ago

10.1186/s12935-020-01237-4

An individualized immune prognostic signature in lung adenocarcinoma
Cited by: 5
Author(s): Lishan Sun, Gening Jiang, Diego González-Rivas, Peng Zhang
Software Mentions: 3
Published: over 4 years ago

10.1186/s12935-020-01604-1

Identification of NEO1 as a prognostic biomarker and its effects on the progression of colorectal cancer
Cited by: 1
Author(s): Meng Zhang, Zhou Zhou, Xuekai Pan, Yunjiao Zhou, Haiou Li, Peishan Qiu, Mengna Zhang, Ruyi Peng, Haizhou Wang, Lan Liu, Jing Liu, Qiu Zhao
Software Mentions: 3
Published: about 4 years ago

10.1186/s12935-019-0859-1

Eleven genes associated with progression and prognosis of endometrial cancer (EC) identified by comprehensive bioinformatics analysis
Cited by: 54
Author(s): Jinhui Liu, Shulin Zhou, Siyue Li, Yi Jiang, Yicong Wan, Xiaoling Ma, Wenjun Cheng
Software Mentions: 3
Published: over 5 years ago

10.1039/c3mb25485b

Transcriptional feedback in the insulin signalling pathway modulates ageing in both Caenorhabditis elegans and Drosophila melanogaster
Cited by: 5
Author(s): Dobril Ivanov, Irene Papatheodorou, Matthias Ziehm, Janet M. Thornton
Software Mentions: 3
Published: almost 12 years ago

10.1186/1476-4598-11-41

Gene expression changes as markers of early lapatinib response in a panel of breast cancer cell lines
Cited by: 23
Author(s): Fiona O’Neill, Stephen F. Madden, Sinéad Aherne, Martin Clynes, John Crown, Padraig Doolan, Robert O’Connor
Software Mentions: 3
Published: over 12 years ago

10.1210/me.2013-1254

RIP140 Represses the “Brown-in-White” Adipocyte Program Including a Futile Cycle of Triacyclglycerol Breakdown and Synthesis
Cited by: 41
Author(s): Evangelos Kiskinis, Lemonia Chatzeli, Ed Curry, Myrsini Kaforou, Andrea Frontini, Saverio Cinti, Giovanni Montana, Malcolm G. Parker, Mark Christian
Software Mentions: 3
Published: over 10 years ago

10.1186/s40462-016-0069-6

Gene expression in the brain of a migratory songbird during breeding and migration
Cited by: 19
Author(s): John Boss, Miriam Liedvogel, Max Lundberg, Peter Olsson, Nils Reischke, Sara Naurin, Susanne Åkesson, Dennis Hasselquist, Anthony P. H. Wright, Mats Grahn, Staffan Bensch
Software Mentions: 3
Published: almost 9 years ago

10.1007/s12253-015-9926-7

Exploring the Molecular Mechanism and Biomakers of Liver Cancer Based on Gene Expression Microarray
Cited by: 8
Author(s): Pengfei Liu, Wenhua Jiang, He Ren, Huilai Zhang, Jihui Hao
Software Mentions: 3
Published: over 9 years ago

10.7717/peerj.11319

Identification of P2RY13 as an immune-related prognostic biomarker in lung adenocarcinoma: A public database-based retrospective study
Cited by: 6
Author(s): Jiang Lin, Chunlei Wu, Dehua Mao, Quanteng Hu
Software Mentions: 3
Published: over 3 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: almost 4 years ago

10.1371/journal.pcbi.1002838

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions
Cited by: 107
Author(s): Wenlian Qiao, Gerald Quon, Elizabeth Csaszar, Mei Yu, Quaid Morris, Peter W. Zandstra
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pcbi.1003837

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks
Cited by: 59
Author(s): Hojung Nam, Miguel A. Campodonico, Aarash Bordbar, Daniel R. Hyduke, Sangwoo Kim, Daniel C. Zielinski, Bernhard Ø. Palsson
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pgen.0030217

Localization of Candidate Regions Maintaining a Common Polymorphic Inversion (2La) in Anopheles gambiae
Cited by: 76
Author(s): Bradley J. White, Matthew W. Hahn, Marco Pombi, Bryan J. Cassone, Neil F. Lobo, Frédéric Simard, Nora J. Besansky
Software Mentions: 3
Published: almost 17 years ago

10.1371/journal.pgen.1005101

The Fun30 Chromatin Remodeler Fft3 Controls Nuclear Organization and Chromatin Structure of Insulators and Subtelomeres in Fission Yeast
Cited by: 52
Author(s): Babett Steglich, Annelie Strålfors, Olga Khorosjutina, Jenna Persson, Agata Smialowska, J.P. Javerzat, Karl Ekwall
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pgen.0010026

A Global Survey of Gene Regulation during Cold Acclimation in Arabidopsis thaliana
Cited by: 384
Author(s): Matthew A. Hannah, Arnd G. Heyer, Dirk K. Hincha
Software Mentions: 3
Published: over 19 years ago

10.1371/journal.pone.0015706

Gene Expression of Axon Growth Promoting Factors in the Deer Antler
Cited by: 26
Author(s): Wolfgang Pita-Thomas, Carmen M. Fernandez‐Martos, Mónica Yunta, Rodrigo M. Maza, Rosa Navarro-Ruíz, Marcos Javier Lopez-Rodríguez, David Reigada, Manuel Nieto‐Sampedro, Manuel Nieto‐Díaz
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pone.0225080

Identifying candidate diagnostic markers for early stage of non-small cell lung cancer
Cited by: 1
Author(s): Zhen Wu, Xu Zhang, Zhijun He, Liyun Hou
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0121730

Gene Expression Profiles Associated with Pediatric Relapsed AML
Cited by: 23
Author(s): Costa Bachas, Gerrit Jan Schuurhuis, C. Michel Zwaan, Marry M. van den Heuvel‐Eibrink, Monique L. den Boer, Eveline S.J.M. de Bont, Zinia J. Kwidama, Dirk Reinhardt, Ursula Creutzig, Valérie de Haas, Gertjan J. L. Kaspers, Jacqueline Cloos
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0013091

Modeling Oncogenic Signaling in Colon Tumors by Multidirectional Analyses of Microarray Data Directed for Maximization of Analytical Reliability
Cited by: 293
Author(s): Magdalena Skrzypczak, Krzysztof Goryca, Tymon Rubel, Agnieszka Paziewska, Michał Mikula, Dorota Jarosz, Jacek Pachlewski, Jacek Olędzki, Jerzy Ostrowsk
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0050985

Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke
Cited by: 50
Author(s): Ana-Maria Buga, Claus‐Jürgen Scholz, Krishan Kumar, James G. Herndon, Dragoş Ovidiu Alexandru, Gabriel Radu Cojocaru, Thomas Dandekar, Aurel Popa‐Wagner
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0037287

Chemical PARP Inhibition Enhances Growth of Arabidopsis and Reduces Anthocyanin Accumulation and the Activation of Stress Protective Mechanisms
Cited by: 45
Author(s): Philipp Schulz, Jenny Neukermans, Katrien Van Der Kelen, Per Mühlenbock, Frank Van Breusegem, Graham Noctor, Markus Teige, Michael Metzlaff, Matthew A. Hannah
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0019322

Generation of a Predictive Melphalan Resistance Index by Drug Screen of B-Cell Cancer Cell Lines
Cited by: 19
Author(s): Martin Boegsted, Johanne Marie Holst, Kirsten Fogd, Steffen Falgreen, Susanne Sørensen, Alexander Schmitz, Anne Bukh, Hans Erik Johnsen, Mette Nyegaard, Karen Dybkær
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0054398

miRNA Gene Promoters Are Frequent Targets of Aberrant DNA Methylation in Human Breast Cancer
Cited by: 114
Author(s): Lukáš Vrba, J. Muñoz-Rodríguez, Martha R. Stampfer, Bernard W. Futscher
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0148771

Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis
Cited by: 41
Author(s): Venkata Suresh Bonthala, Katie Mayes, Joanna Moreton, Martin Blythe, Victoria Wright, Sean May, Festo Massawe, Sean Mayes, Jamie Twycross
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0039205

Effect of Chemical Mutagens and Carcinogens on Gene Expression Profiles in Human TK6 Cells
Cited by: 15
Author(s): Lode Godderis, Reuben Thomas, Alan Hubbard, Ali Mustafa Tabish, Peter Hoet, Luoping Zhang, Martyn T. Smith, Hendrik Veulemans, Cliona M. McHale
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0001151

Gene Expression Analysis of In Vivo Fluorescent Cells
Cited by: 35
Author(s): Konstantin Khodosevich, Dragoš Inta, Peter H. Seeburg, Hannah Monyer
Software Mentions: 3
Published: about 17 years ago

10.1371/journal.pone.0086329

Investigation of Radiosensitivity Gene Signatures in Cancer Cell Lines
Cited by: 43
Author(s): John Hall, Rohan Iype, Joana Senra, Janet Taylor, Lucile Armenoult, Kenneth Oguejiofor, Yaoyong Li, Ian J. Stratford, Peter L. Stern, Mark J. O’Connor, Crispin Miller, Catharine M L West
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0045894

Identification of Common Prognostic Gene Expression Signatures with Biological Meanings from Microarray Gene Expression Datasets
Cited by: 18
Author(s): Jun Yao, Qi Zhao, Ying Yuan, Li Zhang, Xiaoming Liu, W. K. Alfred Yung, John N. Weinstein
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0171164

NKL homeobox gene activities in hematopoietic stem cells, T-cell development and T-cell leukemia
Cited by: 33
Author(s): Stefan Nagel, Claudia Pommerenke, Michaela Scherr, Corinna Meyer, Maren Kaufmann, Karin Battmer, Roderick A.F. MacLeod, Hans Drexler
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0052493

Anti-Inflammatory Lactobacillus rhamnosus CNCM I-3690 Strain Protects against Oxidative Stress and Increases Lifespan in Caenorhabditis elegans
Cited by: 134
Author(s): Gianfranco Grompone, Patricia Martorell, Silvia Llopis, Núria González, Salvador Genovés, Ana Paula Mulet, Tamara Fernández-Calero, Inés Tiscornia, Mariela Bollati-Fogolín, Isabelle Chambaud, Benoît Foligné, Agustín Montserrat, Daniel Ramón
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0204438

Loss of the Spinocerebellar Ataxia type 3 disease protein ATXN3 alters transcription of multiple signal transduction pathways
Cited by: 22
Author(s): Li Zeng, David Zhang, Hayley S. McLoughlin, Annie J. Zalon, L. Aravind, Henry L. Paulson
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0254697

Cell-cell adhesion regulates Merlin/NF2 interaction with the PAF complex
Cited by: 1
Author(s): Anne E. Roehrig, Kristina Klupsch, Juan Oses-Prieto, Selim Chaib, Stephen Henderson, Warren Emmett, Lucy C. Young, Silvia Šurinová, Andreas Blees, Anett Pfeiffer, Maha Tijani, Fabian Brunk, Nicole Hartig, Marta Muñoz-Alegre, Alexander Hergovich, Barbara Jennings, Alma L. Burlingame, Pablo Rodríguez‐Viciana
Software Mentions: 3
Published: about 3 years ago

10.1371/journal.pone.0147151

Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs
Cited by: 32
Author(s): Han Rauwerda, Paul Wackers, J.F.B. Pagano, Mark de Jong, Wim A. Ensink, R.J. Dekker, Ulrike Nehrdich, Herman P. Spaink, Martijs J. Jonker, Timo M. Breit
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0054664

Whole Genome Gene Expression Analysis Reveals Casiopeína-Induced Apoptosis Pathways
Cited by: 31
Author(s): Alejandra Idan Valencia-Cruz, Laura Uribe-Figueroa, Rodrigo Galindo‐Murillo, Karol Baca-López, Anllely Grizett Gutiérrez, Adriana Vázquez-Aguirre, Lena Ruíz-Azuara, Enrique Hernández‐Lemus, Carmen Mejía
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0149475

Diagnosis of Coronary Heart Diseases Using Gene Expression Profiling; Stable Coronary Artery Disease, Cardiac Ischemia with and without Myocardial Necrosis
Cited by: 10
Author(s): Nabila Kazmi, Tom R. Gaunt
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0035322

Nuclear Reprogramming: Kinetics of Cell Cycle and Metabolic Progression as Determinants of Success
Cited by: 23
Author(s): Sebastian T. Balbach, Telma C. Esteves, Franchesca D. Houghton, Marcin Siatkowski, Martin J. Pfeiffer, Chizuko Tsurumi, Benoı̂t Kanzler, Georg Fuellen, Michele Boiani
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0131103

The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis
Cited by: 13
Author(s): Kim L. Johnson, Sascha Ramm, Christian Kappel, Sally Ward, Ottoline Leyser, Tomoaki Sakamoto, Takeshi Kurata, Michael W. Bevan, Michael Lenhard
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0226212

NKL homeobox gene activities in normal and malignant myeloid cells
Cited by: 12
Author(s): Stefan Nagel, Michaela Scherr, Roderick A.F. MacLeod, Claudia Pommerenke, Max Koeppel, Corinna Meyer, Maren Kaufmann, Iris Dallmann, Hans Drexler
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0003220

Fibrotic Myofibroblasts Manifest Genome-Wide Derangements of Translational Control
Cited by: 93
Author(s): Ola Larsson, Deanna Diebold, Danhua Fan, Mark S. Peterson, Richard Seonghun Nho, Peter B. Bitterman, Craig A. Henke
Software Mentions: 3
Published: about 16 years ago

10.1371/journal.pone.0092596

The Nerve Growth Factor Receptor CD271 Is Crucial to Maintain Tumorigenicity and Stem-Like Properties of Melanoma Cells
Cited by: 79
Author(s): Torben Redmer, Yvonne Welte, Diana Behrens, Iduna Fichtner, Dorothea Przybilla, Wasco Wruck, Marie–Laure Yaspo, Hans Lehrach, Reinhold Schäfer, Christian Regenbrecht
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0002987

Identification of Functional Networks of Estrogen- and c-Myc-Responsive Genes and Their Relationship to Response to Tamoxifen Therapy in Breast Cancer
Cited by: 90
Author(s): Elizabeth A. Musgrove, C. Marcelo Sergio, Sherene Loi, Claire K. Inman, Luke R. Anderson, M. Chehani Alles, Mark Pinese, C. Elizabeth Caldon, Judith Schütte, Margaret Gardiner-Garden, Christopher J. Ormandy, Grant A. McArthur, Alison J. Butt, Robert L. Sutherland
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0216898

Epstein-Barr virus (EBV) activates NKL homeobox gene HLX in DLBCL
Cited by: 14
Author(s): Stefan Nagel, Cord C. Uphoff, Wilhelm G. Dirks, Claudia Pommerenke, Corinna Meyer, Hans G. Drexler
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0163128

Activation of Ftz-F1-Responsive Genes through Ftz/Ftz-F1 Dependent Enhancers
Cited by: 8
Author(s): Amanda Field, Jie Xiang, W. Ray Anderson, Patricia L. Graham, Leslie Pick
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0076903

Genome-Wide Profiling of the Activity-Dependent Hippocampal Transcriptome
Cited by: 38
Author(s): Guido Hermey, Claudia Mahlke, Jakob J. Gutzmann, Jörg Schreiber, Nils Blüthgen, Dietmar Kuhl
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0013565

Ets-1 Regulates Energy Metabolism in Cancer Cells
Cited by: 48
Author(s): Meghan Verschoor, Leigh Wilson, Chris P. Verschoor, Gurmit Singh
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0118551

Overexpression of the Transcription Factor Sp1 Activates the OAS-RNAse L-RIG-I Pathway
Cited by: 17
Author(s): Valéryane Dupuis-Maurin, Lilia Brinza, Joël Baguet, Émilie Plantamura, Stéphane Schicklin, Solène Chambion, Claire Macari, Martine Tomkowiak, Emmanuelle Deniaud, Yann Leverrier, Jacqueline Marvel, M Michallet
Software Mentions: 3
Published: over 9 years ago

10.3390/cancers12010177

Contribution of mTOR and PTEN to Radioresistance in Sporadic and NF2-Associated Vestibular Schwannomas: A Microarray and Pathway Analysis
Cited by: 12
Author(s): Isabel Gugel, Florian Ebner, Florian Grimm, Stefan Czemmel, Frank Paulsen, Christian Hagel, Marcos Tatagiba, Sven Nahnsen, Ghazaleh Tabatabai
Software Mentions: 3
Published: almost 5 years ago

10.3390/cancers12061460

Omics Integration Analyses Reveal the Early Evolution of Malignancy in Breast Cancer
Cited by: 1
Author(s): Shamim Sarhadi, Ali Salehzadeh‐Yazdi, Mehdi Damaghi, Nosratollah Zarghami, Olaf Wolkenhauer, Hedayatollah Hosseini
Software Mentions: 3
Published: over 4 years ago

10.3390/cancers12010007

Overexpression of p62/IMP2 can Promote Cell Migration in Hepatocellular Carcinoma via Activation of the Wnt/β-Catenin Pathway
Cited by: 21
Author(s): Mengtao Xing, Pei Li, Xiao Wang, Jitian Li, Jianxiang Shi, Jiejie Qin, Xiaojun Zhang, Yangcheng Ma, Giulio Francia, Jianying Zhang
Software Mentions: 3
Published: almost 5 years ago

10.1038/s41419-020-02769-3

LEF1 mediates osteoarthritis progression through circRNF121/miR-665/MYD88 axis via NF-кB signaling pathway
Cited by: 31
Author(s): Tianfu Wang, Zhiyu Hao, Changcheng Liu, Lebin Yuan, Li Li, Menghong Yin, Qing Li, Zhiming Qi, Zi Wang
Software Mentions: 3
Published: over 4 years ago

Projects: bioconductor: affy

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