bioconductor: RankProd | Projects

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

10.1007/s10126-016-9704-x

Functional Genomic Analysis of the Impact of Camelina (Camelina sativa) Meal on Atlantic Salmon (Salmo salar) Distal Intestine Gene Expression and Physiology
Cited by: 20
Author(s): Tyler D. Brown, Tiago S. Hori, Xi Xue, Chang Lin Ye, D. M. Anderson, Matthew L. Rise
Software Mentions: 2
Published: over 8 years ago

10.1007/s11010-016-2776-0

Differential expression of store-operated calcium- and proliferation-related genes in hepatocellular carcinoma cells following TRPC1 ion channel silencing
Cited by: 14
Author(s): Çiğdem Selli, Dominic Pearce, Andrew H. Sims, Metiner Tosun
Software Mentions: 2
Published: over 8 years ago

10.1186/s13567-015-0286-9

Transcriptional analysis of porcine intestinal mucosa infected with Salmonella Typhimurium revealed a massive inflammatory response and disruption of bile acid absorption in ileum
Cited by: 28
Author(s): Júber Herrera-Uribe, Melania Collado-Romero, Sara Zaldívar‐López, Cristina Arce, Rocío Bautista, Ana Carvajal, Susanna Cirera, M. Gonzalo Claros, Juan J. Garrido
Software Mentions: 2
Published: almost 9 years ago

10.1186/s13071-016-1945-z

Immune and biochemical responses in skin differ between bovine hosts genetically susceptible and resistant to the cattle tick Rhipicephalus microplus
Cited by: 32
Author(s): Alessandra Mara Franzin, Sandra Regina Maruyama, Gustavo García, Rosane Oliveira, José M. C. Ribeiro, Richard P. Bishop, Antônio Augusto Mendes Maia, Daniela D. Moré, Beatriz Rossetti Ferreira, Isabel Kinney Ferreira de Miranda Santos
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12969-020-00483-0

Juvenile idiopathic arthritis fibroblast-like synoviocytes influence chondrocytes to alter BMP antagonist expression demonstrating an interaction between the two prominent cell types involved in endochondral bone formation
Cited by: 2
Author(s): Megan M. Simonds, A. Schlefman, Suzanne M. McCahan, Kathleen E. Sullivan, Carlos D. Rosé, AnneMarie C. Brescia
Software Mentions: 2
Published: about 4 years ago

10.1371/journal.pone.0152342

Identification of Differentially Expressed Genes through Integrated Study of Alzheimer’s Disease Affected Brain Regions
Cited by: 68
Author(s): Nisha Puthiyedth, Carlos Riveros, Regina Berretta, Pablo Moscato
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0068136

Genome-Wide Responses of Female Fruit Flies Subjected to Divergent Mating Regimes
Cited by: 8
Author(s): Dave T. Gerrard, Claudia Fricke, Dominic A. Edward, Dylan R. Edwards, Tracey Chapman
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0243715

The role of the MAD2-TLR4-MyD88 axis in paclitaxel resistance in ovarian cancer
Cited by: 7
Author(s): Mark Bates, Cathy Spillane, Michael Gallagher, Amanda McCann, Cara Martin, Gordon Blackshields, Helen Keegan, Luke Gubbins, Robert D. Brooks, Doug A. Brooks, Stavros Selemidis, Sharon O’Toole, John O’Leary
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0077261

Genes and Co-Expression Modules Common to Drought and Bacterial Stress Responses in Arabidopsis and Rice
Cited by: 93
Author(s): Shaik Rafi Ahamed, Wusirika Ramakrishna
Software Mentions: 2
Published: about 11 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.0091884

A microRNA Signature Associated with Early Recurrence in Breast Cancer
Cited by: 77
Author(s): Luis Gustavo Pérez-Rivas, José M. Jerez, Rosario Carmona, Vanessa de Luque, Luís Vicioso, M. Gonzalo Claros, Enrique Viguera, Bella Pajares, Alfonso Sánchez, Nuria Ribelles, Emilio Alba, José Lozano
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0027596

A Novel YY1-miR-1 Regulatory Circuit in Skeletal Myogenesis Revealed by Genome-Wide Prediction of YY1-miRNA Network
Cited by: 87
Author(s): Leina Lu, Liang Zhou, Eric Z. Chen, Kun Sun, Peiyong Jiang, Lijun Wang, Xiaoxi Su, Hao Sun, Huating Wang
Software Mentions: 2
Published: almost 13 years ago

10.1038/cddis.2016.148

A ribosome-related signature in peripheral blood CLL B cells is linked to reduced survival following treatment
Cited by: 24
Author(s): Thomas Sbarrato, Emilie Horvilleur, Tuija Pöyry, Kirsti Hill, L C Chaplin, R V Spriggs, Mark Stoneley, Lindsay A. Wilson, Sandrine Jayne, Tom Vulliamy, Daniel Beck, Inderjeet Dokal, Martin J. S. Dyer, Alison Yeomans, Graham Packham, Martin Bushell, Simon D. Wagner, Anne E. Willis
Software Mentions: 2
Published: over 8 years ago

10.1155/2016/2619828

Pathway Analysis Based on Attractor and Cross Talk in Colon Cancer
Cited by: 6
Author(s): Yanxia Liu, Lin Wang, Bingping Wang, Meng Yue, Yufeng Cheng
Software Mentions: 2
Published: almost 9 years ago

10.3389/fgene.2018.00457

Meta-Analysis Identification of Highly Robust and Differential Immune-Metabolic Signatures of Systemic Host Response to Acute and Latent Tuberculosis in Children and Adults
Cited by: 14
Author(s): Saikou Y. Bah, Thorsten Forster, Paul Dickinson, Beate Kampmann, Peter Ghazal
Software Mentions: 2
Published: about 6 years ago

10.3389/fnins.2016.00601

Variation in Gene Expression in Autism Spectrum Disorders: An Extensive Review of Transcriptomic Studies
Cited by: 62
Author(s): Ashley Ansel, Joshua P. Rosenzweig, Philip D. Zisman, Michal L. Melamed, Benjamin Gesundheit
Software Mentions: 2
Published: almost 8 years ago

10.3389/fnins.2016.00396

Comparative Gene Expression Analysis of Two Mouse Models of Autism: Transcriptome Profiling of the BTBR and En2−/− Hippocampus
Cited by: 27
Author(s): Giovanni Provenzano, Zelia Corradi, Katia Monsorno, Tarcisio Fedrizzi, Laura Ricceri, María Luisa Scattoni, Yuri Bozzi
Software Mentions: 2
Published: about 8 years ago

10.3389/fphys.2017.00753

Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference
Cited by: 9
Author(s): Tingting Zheng, Yueqiong Ni, Jun Li, Billy K. C. Chow, Gianni Panagiotou
Software Mentions: 2
Published: about 7 years ago

10.3389/fpls.2015.00118

Transcriptional profiling of Petunia seedlings reveals candidate regulators of the cold stress response
Cited by: 10
Author(s): Bei Li, Luyun Ning, Junwei Zhang, Manzhu Bao, Wei Zhang
Software Mentions: 2
Published: over 9 years ago

10.1186/gb-2009-10-1-r5

Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon
Cited by: 39
Author(s): Giselda Bucca, Emma Laing, Vassilis Mersinias, Nicholas E. E. Allenby, Douglas Hurd, Jolyon Holdstock, Volker Brenner, Marcus Harrison, Colin P. Smith
Software Mentions: 2
Published: almost 16 years ago

10.1111/jcmm.15432

Identification of castration‐resistant prostate cancer‐related hub genes using weighted gene co‐expression network analysis
Cited by: 17
Author(s): Yifei Cheng, Li Lü, Zongshi Qin, Xiao Li, Feng Qi
Software Mentions: 2
Published: over 4 years ago

10.1111/jcmm.15544

A three‐tiered integrative analysis of transcriptional data reveals the shared pathways related to heart failure from different aetiologies
Cited by: 6
Author(s): Zhenhong Jiang, Ninghong Guo, Kui Hong
Software Mentions: 2
Published: over 4 years ago

10.1038/srep14364

Translational compensation of genomic instability in neuroblastoma
Cited by: 10
Author(s): Erik Dassi, Valentina Greco, Viktoryia Sidarovich, Paola Zuccotti, Natalia Arseni, Paola Scaruffi, Gian Paolo Tonini, Alessandro Quattrone
Software Mentions: 2
Published: about 9 years ago

10.1038/srep09506

The effect of music performance on the transcriptome of professional musicians
Cited by: 36
Author(s): Chakravarthi Kanduri, Tuire Kuusi, Minna Ahvenainen, Anju K. Philips, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 2
Published: over 9 years ago

10.1038/s41598-018-34592-4

Integrative bioinformatics identifies postnatal lead (Pb) exposure disrupts developmental cortical plasticity
Cited by: 12
Author(s): Mary Patricia Smith, Priscilla Yevoo, Masato Sadahiro, Christine Austin, Chitra Amarasiriwardena, Mahmoud H. Awawda, Manish Arora, Joel T. Dudley, Hirofumi Morishita
Software Mentions: 2
Published: about 6 years ago

10.1128/mBio.02118-17

Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins
Cited by: 17
Author(s): Rosa Morra, Francesco Del Carratore, Howbeer Muhamadali, Luminita Gabriela Horga, Samantha Halliwell, Royston Goodacre, Rainer Breitling, Neil Dixon
Software Mentions: 2
Published: over 6 years ago

10.1128/mSystems.00014-16

OsdR of Streptomyces coelicolor and the Dormancy Regulator DevR of Mycobacterium tuberculosis Control Overlapping Regulons
Cited by: 28
Author(s): Mia Urem, Teunke van Rossum, Giselda Bucca, Geri F. Moolenaar, Emma Laing, Magda A. Świątek-Połatyńska, Joost Willemse, Elodie Tenconi, Sébastien Rigali, Nora Goosen, Colin P. Smith, Gilles P. van Wezel
Software Mentions: 2
Published: over 8 years ago

10.1038/onc.2015.526

A RelA(p65) Thr505 phospho-site mutation reveals an important mechanism regulating NF-κB-dependent liver regeneration and cancer
Cited by: 28
Author(s): Anna Moles, Jacqueline Butterworth, Ana M. Sánchez, Jill E. Hunter, Jack Leslie, Hélène Sellier, Dina Tiniakos, Simon Cockell, Derek A. Mann, Fiona Oakley, Neil D. Perkins
Software Mentions: 2
Published: almost 9 years ago

10.7554/eLife.61611

Temperature-dependent fasciation mutants provide a link between mitochondrial RNA processing and lateral root morphogenesis
Cited by: 4
Author(s): Kurataka Otsuka, Akihito Mamiya, Mineko Konishi, Mamoru Nozaki, Atsuko Kinoshita, Hiroaki Tamaki, Masaki Arita, Masato Saito, Keijiro Yamamoto, Takushi Hachiya, Ko Noguchi, Takashi Ueda, Yusuke Yagi, Takehito Kobayashi, Takahiro Nakamura, Yasushi Sato, Takashi Hirayama, Masaru Sugiyama
Software Mentions: 2
Published: almost 4 years ago

10.1111/jne.12387

Pre- and Post-Natal Stress Programming: Developmental Exposure to Glucocorticoids Causes Long-Term Brain-Region Specific Changes to Transcriptome in the Precocial Japanese Quail
Cited by: 26
Author(s): Valeria Marasco, Paweł Herzyk, Jane E. Robinson, Karen A. Spencer
Software Mentions: 2
Published: over 8 years ago

10.1186/s13048-018-0467-z

Identification of core genes in ovarian cancer by an integrative meta-analysis
Cited by: 15
Author(s): Wenyu Li, Zheran Liu, Bowen Liang, Siyang Chen, Xinping Zhang, Xiaoqin Tong, Weiming Lou, Lulu Le, Xiaoli Tang, Fang Fu
Software Mentions: 2
Published: about 6 years ago

10.18632/oncotarget.14253

MiR-21 as prognostic biomarker in head and neck squamous cell carcinoma patients undergoing an organ preservation protocol
Cited by: 45
Author(s): Lídia Maria Rebolho Batista Arantes, Ana Carolina Laus, Matias Eliseo Melendez, Ana Carolina de Carvalho, Bruna Pereira Sorroche, Pedro Rafael Martins De Marchi, Adriane Feijó Evangelista, Cristovam Scapulatempo‐Neto, Luciano de Souza Viana, André Lopes Carvalho
Software Mentions: 2
Published: almost 8 years ago

10.18632/oncotarget.27120

Transcriptome analysis of Sézary syndrome and lymphocytic-variant hypereosinophilic syndrome T cells reveals common and divergent genes
Cited by: 7
Author(s): Andrea Moerman-Herzog, Daniel Acheampong, A. Brooks, S. Blair, Ping-Ching Hsu, Henry K. Wong
Software Mentions: 2
Published: over 5 years ago

10.1186/s12967-017-1294-5

Transcriptomic meta-analysis identifies gene expression characteristics in various samples of HIV-infected patients with nonprogressive disease
Cited by: 16
Author(s): Lele Zhang, Zining Zhang, Xian Wang, Yongjun Jiang, Yajing Fu, Hong Shang
Software Mentions: 2
Published: about 7 years ago

10.1523/ENEURO.0240-16.2016

Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity
Cited by: 16
Author(s): Mary Patricia Smith, Poromendro Burman, Masato Sadahiro, Brian Kidd, Joel T. Dudley, Hirofumi Morishita
Software Mentions: 2
Published: about 8 years ago

10.7717/peerj.5285

Integrative machine learning analysis of multiple gene expression profiles in cervical cancer
Cited by: 24
Author(s): Mei Sze Tan, Siow-Wee Chang, Phaik Leng Cheah, Hwa Jen Yap
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2021.618089

Abiotic Stress-Responsive miRNA and Transcription Factor-Mediated Gene Regulatory Network in Oryza sativa: Construction and Structural Measure Study
Cited by: 11
Author(s): R.C. Sharma, Shashankaditya Upadhyay, Sitangshu Bhattacharya, Ashutosh Singh
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.5527

Comparison of gene expression profiles between human erythroid cells derived from fetal liver and adult peripheral blood
Cited by: 7
Author(s): Amornrat Tangprasittipap, Pavita Kaewprommal, Orapan Sripichai, Nuankanya Sathirapongsasuti, Chonthicha Satirapod, Philip Shaw, Jittima Piriyapongsa, Suradej Hongeng
Software Mentions: 1
Published: about 6 years ago

10.1038/onc.2014.269

A Cre-conditional MYCN-driven neuroblastoma mouse model as an improved tool for preclinical studies
Cited by: 100
Author(s): Kristina Althoff, Anneleen Beckers, Emma Bell, Maike Nortmeyer, Theresa Thor, Annika Sprüssel, Sven Lindner, Katleen De Preter, Alexandra Florin, Lukas C. Heukamp, Ludger Klein‐Hitpass, Kathy Astrahantseff, Candy Kumps, Franki Speleman, Angelika Eggert, Frank Westermann, Alexander Schramm, Johannes H. Schulte
Software Mentions: 1
Published: about 10 years ago

10.3389/fgene.2019.00181

Identification of Target Genes at Juvenile Idiopathic Arthritis GWAS Loci in Human Neutrophils
Cited by: 5
Author(s): Junyi Li, Xiucheng Yuan, Michael March, Xueming Yao, Yan Sun, Xiao Chang, Hákon Hákonarson, Qianghua Xia, Xinyi Meng, Jin Li
Software Mentions: 1
Published: over 5 years ago

10.1186/s12957-017-1125-4

Exploring the FGFR3-related oncogenic mechanism in bladder cancer using bioinformatics strategy
Cited by: 12
Author(s): Wei Cao, En-Guang Ma, Li Zhou, Tan Yuan, Chunying Zhang
Software Mentions: 1
Published: over 7 years ago

10.3389/fmicb.2019.01376

Quorum and Light Signals Modulate Acetoin/Butanediol Catabolism in Acinetobacter spp.
Cited by: 13
Author(s): Marisel R. Tuttobene, Laura Fernández-García, Lucía Blasco, Pamela Cribb, Antón Ambroa, Gabriela Müller, Felipe Fernández-Cuenca, Inés Bleriot, Ramiro E. Rodríguez, Beatriz G. V. Barbosa, Rafael López-Rojas, Rocío Trastoy, María López, Germán Bou, María Tomás, María Alejandra Mussi
Software Mentions: 1
Published: over 5 years ago

10.3390/nu10111719

Ursolic Acid Attenuates Hepatic Steatosis, Fibrosis, and Insulin Resistance by Modulating the Circadian Rhythm Pathway in Diet-Induced Obese Mice
Cited by: 27
Author(s): Eun‐Young Kwon, Su‐Kyung Shin, Myung‐Sook Choi
Software Mentions: 1
Published: about 6 years ago

10.1186/s12859-017-1794-6

A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification
Cited by: 0
Author(s): Xueping Xie, Yufeng Xie, Hongqiang Wang
Software Mentions: 1
Published: about 7 years ago

10.3389/fonc.2013.00254

Downregulation of 14q32 microRNAs in Primary Human Desmoplastic Medulloblastoma
Cited by: 21
Author(s): Danielle Ribeiro Lucon, Cristiane S. Rocha, Rogerio B. Craveiro, Dagmar Dilloo, Izilda Aparecida Cardinalli, Denise Pontes Cavalcanti, Simone dos Santos Aguiar, Cláudia Vianna Maurer-Morelli, José Andrés Yunes
Software Mentions: 1
Published: almost 12 years ago

10.3390/v10080414

Removal of the C6 Vaccinia Virus Interferon-β Inhibitor in the Hepatitis C Vaccine Candidate MVA-HCV Elicited in Mice High Immunogenicity in Spite of Reduced Host Gene Expression
Cited by: 11
Author(s): María Q. Marín, Patricia Pérez, Carmen Elena Gómez, Carlos Óscar S. Sorzano, Mariano Esteban, Juan García‐Arriaza
Software Mentions: 1
Published: over 6 years ago

10.1186/2040-2392-4-51

Transcriptome profiling in engrailed-2 mutant mice reveals common molecular pathways associated with autism spectrum disorders
Cited by: 28
Author(s): Paola Sgadó, Giovanni Provenzano, Erik Dassi, Valentina Adami, Giulia Zunino, Sacha Genovesi, Simona Casarosa, Yuri Bozzi
Software Mentions: 1
Published: almost 12 years ago

10.1155/2015/826316

Identification of Potential Transcriptomic Markers in Developing Ankylosing Spondylitis: A Meta-Analysis of Gene Expression Profiles
Cited by: 18
Author(s): Fang Fang, Jian Pan, Lixiao Xu, Gang Li, Jian Wang
Software Mentions: 1
Published: almost 10 years ago

10.3389/fphar.2015.00199

Systems pharmacology of adiposity reveals inhibition of EP300 as a common therapeutic mechanism of caloric restriction and resveratrol for obesity
Cited by: 22
Author(s): Yuhei Nishimura, Shota Sasagawa, Michiko Ariyoshi, Sayuri Ichikawa, Yasuhito Shimada, Koki Kawaguchi, Reiko Kawase, Reiko Yamamoto, Takuma Uehara, Takaaki Yanai, Ryoji Takata, Toshio Tanaka
Software Mentions: 1
Published: about 9 years ago

10.3389/fphar.2016.00057

DNA Damage Response Is Involved in the Developmental Toxicity of Mebendazole in Zebrafish Retina
Cited by: 20
Author(s): Shota Sasagawa, Yuhei Nishimura, Tetsuo Kon, Yukiko Yamanaka, Soichiro Murakami, Yoshifumi Ashikawa, Mizuki Yuge, Shiko Okabe, Koki Kawaguchi, Reiko Kawase, Toshio Tanaka
Software Mentions: 1
Published: over 8 years ago

10.1155/2017/7259097

Gastric Cancer Associated Genes Identified by an Integrative Analysis of Gene Expression Data
Cited by: 11
Author(s): Bing Jiang, Shuwen Li, Zhi Hong Jiang, Ping Shao
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-015-0847-y

A semi-parametric statistical model for integrating gene expression profiles across different platforms
Cited by: 16
Author(s): Yafei Lyu, Qunhua Li
Software Mentions: 1
Published: almost 9 years ago

10.3389/fpls.2015.00711

Tissue specific and abiotic stress regulated transcription of histidine kinases in plants is also influenced by diurnal rhythm
Cited by: 23
Author(s): Anupama Singh, Hemant R. Kushwaha, Praveen Soni, Himanshu Gupta, Sneh L. Singla‐Pareek, Ashwani Pareek
Software Mentions: 1
Published: about 9 years ago

10.3390/ijms14035214

Insight into Differential Responses of Upland and Paddy Rice to Drought Stress by Comparative Expression Profiling Analysis
Cited by: 38
Author(s): Xuezhi Ding, Xiaokai Li, Lizhong Xiong
Software Mentions: 1
Published: over 11 years ago

10.1093/bioinformatics/btx292

RankProd 2.0: a refactored bioconductor package for detecting differentially expressed features in molecular profiling datasets
Cited by: 96
Author(s): Francesco Del Carratore, Andris Jankevics, Rob Eisinga, Tom Heskes, Fangxin Hong, Rainer Breitling
Software Mentions: 1
Published: over 7 years ago

10.1186/1752-0509-5-138

Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair
Cited by: 26
Author(s): Vidhya Jagannathan, Marc Robinson‐Rechavi
Software Mentions: 1
Published: almost 14 years ago

10.3390/ijms21082716

Signaling Pathways Potentially Responsible for Foam Cell Formation: Cholesterol Accumulation or Inflammatory Response—What is First?
Cited by: 15
Author(s): Alexander N. Orekhov, Vasily N. Sukhorukov, Nikita G. Nikiforov, M. Kubekina, Igor A. Sobenin, Kathy Foxx, Sergey S. Pintus, Philip Stegmaier, Daria Stelmashenko, Alexander Kel, Anastasia V. Poznyak, Wei-Kai Wu, Artem S. Kasianov, Vsevolod J. Makeev, Ichiro Manabe, Yumiko Oishi
Software Mentions: 1
Published: over 4 years ago

10.1186/1752-0509-4-97

Evaluating diabetes and hypertension disease causality using mouse phenotypes
Cited by: 2
Author(s): Hong Yu, Jialiang Huang, Nan Qiao, Christopher D. Green, Jing–Dong Jackie Han
Software Mentions: 1
Published: over 14 years ago

10.1186/1756-0500-3-221

RankProdIt: A web-interactive Rank Products analysis tool
Cited by: 26
Author(s): Emma Laing, Colin P. Smith
Software Mentions: 1
Published: over 14 years ago

10.1111/jcmm.13228

Folate deficiency disturbs hsa-let-7 g level through methylation regulation in neural tube defects
Cited by: 12
Author(s): Li Wang, Shaofang Shangguan, Xuezhong Yu, Shaoyan Chang, Zhen Wang, Xiaolin Lü, Lihua Wu, Bo Niu, Ting Zhang
Software Mentions: 1
Published: over 7 years ago

10.1186/1756-0500-6-430

VAN: an R package for identifying biologically perturbed networks via differential variability analysis
Cited by: 7
Author(s): Vivek Jayaswal, Sarah-Jane Schramm, Graham J. Mann, Marc R. Wilkins, Jean Yee Hwa Yang
Software Mentions: 1
Published: about 11 years ago

10.1186/1471-2229-8-87

Transcriptional responses of Arabidopsis thaliana plants to As (V) stress
Cited by: 180
Author(s): Jason M. Abercrombie, Matthew D. Halfhill, Priya Ranjan, Murali Raghavendra Rao, Arnold M. Saxton, Joshua S. Yuan, C. Neal Stewart
Software Mentions: 1
Published: over 16 years ago

10.18632/oncotarget.16041

Mesenchymal stem cells differentially affect the invasion of distinct glioblastoma cell lines
Cited by: 58
Author(s): Barbara Breznik, Helena Motaln, Miloš Vittori, Ana Rotter, Tamara Lah Turnšek
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-12-438

Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior
Cited by: 8
Author(s): Lam C. Tsoi, Tingting Qin, Elizabeth H. Slate, W. Jim Zheng
Software Mentions: 1
Published: about 13 years ago

10.1186/2043-9113-4-2

Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference
Cited by: 15
Author(s): Claudia Cava, Italo Zoppis, Manuela Gariboldi, Isabella Castiglioni, Giancarlo Mauri
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.ppat.1004800

Novel Disease Susceptibility Factors for Fungal Necrotrophic Pathogens in Arabidopsis
Cited by: 30
Author(s): Albor Dobón, Juan Vicente Canet, Javier García-Andrade, Carlos Angulo, Lutz Neumetzler, Staffan Persson, Pablo Vera
Software Mentions: 1
Published: over 9 years ago

10.1186/1465-9921-10-92

Global gene expression patterns in the post-pneumonectomy lung of adult mice
Cited by: 24
Author(s): Julia Paxson, Christopher Parkin, Lakshmanan K. Iyer, Melissa R. Mazan, Edward P. Ingenito, Andrew M. Hoffman
Software Mentions: 1
Published: about 15 years ago

10.1186/1471-2229-10-221

Global transcript profiling of transgenic plants constitutively overexpressing the RNA-binding protein AtGRP7
Cited by: 54
Author(s): Corinna Streitner, Lars Hennig, Christin Korneli, Dorothee Staiger
Software Mentions: 1
Published: about 14 years ago

10.1186/1472-6793-10-21

Diet-induced obesity in zebrafish shares common pathophysiological pathways with mammalian obesity
Cited by: 286
Author(s): Takehiko Oka, Yuhei Nishimura, Liqing Zang, Minoru Hirano, Yasuhito Shimada, Zhipeng Wang, Noriko Umemoto, Junya Kuroyanagi, Norihiro Nishimura, Toshio Tanaka
Software Mentions: 1
Published: about 14 years ago

10.18632/oncotarget.22096

Meta-analysis identifies candidate key genes in endometrium as predictive biomarkers for clinical pregnancy in IVF
Cited by: 12
Author(s): Jingyu Li, Dongyun Liu, Jiang Wang, Huali Deng, Xiu Luo, Xiaoli Shen, Huan Ye, Gangliang Huang, Pengcheng Zhang
Software Mentions: 1
Published: about 7 years ago

10.1186/1741-7015-12-73

The endogenous and reactive depression subtypes revisited: integrative animal and human studies implicate multiple distinct molecular mechanisms underlying major depressive disorder
Cited by: 52
Author(s): Karim Malki, Robert Keers, Maria Grazia Tosto, Anbarasu Lourdusamy, Lucia Carboni, Enrico Domenici, Rudolf Uher, Peter McGuffin, Leonard C. Schalkwyk
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-9-571

Dissecting an alternative splicing analysis workflow for GeneChip®Exon 1.0 ST Affymetrix arrays
Cited by: 26
Author(s): Cristina Della Beffa, Francesca Cordero, Raffaele Calogero
Software Mentions: 1
Published: almost 16 years ago

10.1186/s12864-018-5188-6

Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed experimental diets based on terrestrial alternatives to fish meal and fish oil
Cited by: 44
Author(s): Albert Caballero‐Solares, Xi Xue, Christopher C. Parrish, Maryam Beheshti Foroutani, Richard G. Taylor, Matthew L. Rise
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.7478

X-linked <i>FHL1</i> as a novel therapeutic target for head and neck squamous cell carcinoma
Cited by: 11
Author(s): Wei Cao, Jiannan Liu, Ronghui Xia, Longnian Lin, Xu Wang, Meng Xiao, Chenping Zhang, Li Jiang, Tong Ji, Wantao Chen
Software Mentions: 1
Published: almost 9 years ago

10.1038/s41598-017-01432-w

Development of a Novel Zebrafish Model for Type 2 Diabetes Mellitus
Cited by: 103
Author(s): Liqing Zang, Yasuhito Shimada, Norihiro Nishimura
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-03056-6

A novel plant E3 ligase stabilizes Escherichia coli heat shock factor σ32
Cited by: 1
Author(s): Yulong Niu, Xingang Xu, Chengcheng Liu, Tao Wang, Ke Liang, Jianmei Wang, Zhibin Liu, Xufeng Li, Yi Yang
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-15867-8

Chemokines protect vascular smooth muscle cells from cell death induced by cyclic mechanical stretch
Cited by: 18
Author(s): Jing Zhao, Yuhei Nishimura, Akihiko Kimura, Kentaro Ozawa, Toshikazu Kondo, Toshio Tanaka, Masanori Yoshizumi
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-18137-9

Deep sequencing of blood and gut T-cell receptor β-chains reveals gluten-induced immune signatures in celiac disease
Cited by: 23
Author(s): Dawit A. Yohannes, Tobias Freitag, Andrea de Kauwe, Katri Kaukinen, Kalle Kurppa, Pirjo Wacklin, Markku Mäki, T. Petteri Arstila, Robert P. Anderson, Dario Greco, Päivi Saavalainen
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-20847-7

Evolution of the Quorum network and the mobilome (plasmids and bacteriophages) in clinical strains of Acinetobacter baumannii during a decade
Cited by: 24
Author(s): María López, Antonio Rueda, J. P. Florido, Lucía Blasco, Laura Fernández-García, Rocío Trastoy, Felipe Fernández-Cuenca, Luis Martı́nez-Martı́nez, Jordi Vila, Álvaro Pascual, Germán Bou, María Tomás
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-018-22884-8

System-wide coordinates of higher order functions in host-pathogen environment upon Mycobacterium tuberculosis infection
Cited by: 14
Author(s): P. V. Parvati Sai Arun, Sravan Kumar Miryala, Aarti Rana, Sreenivasulu Kurukuti, Yusuf Akhter, Sailu Yellaboina
Software Mentions: 1
Published: over 6 years ago

10.1186/1471-2105-14-368

Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline
Cited by: 111
Author(s): Lun‐Ching Chang, Hailong Lin, Etienne Sibille, George C. Tseng
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-019-39828-5

Cross-disease analysis of Alzheimer’s disease and type-2 Diabetes highlights the role of autophagy in the pathophysiology of two highly comorbid diseases
Cited by: 55
Author(s): Laura Caberlotto, Thanh Phương Nguyễn, Mario Lauria, Corrado Priami, Roberto Rimondini, Silvia Maioli, Ángel Cedazo-Minguez, Giulia Sita, Fabiana Morroni, Mauro Corsi, Lucia Carboni
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-020-65042-9

Circulating lymphocytes and monocytes transcriptomic analysis of patients with type 2 diabetes mellitus, dyslipidemia and periodontitis
Cited by: 18
Author(s): Sâmia Cruz Tfaile Corbi, Jaira F. de Vasconcellos, Alliny Souza Bastos, Diego Girotto Bussaneli, Bárbara Roque da Silva, Raquel Santos, Catarina Satie Takahashi, Cristiane S. Rocha, Benilton Carvalho, Cláudia Vianna Maurer-Morelli, Silvana Regina Perez Orrico, Silvana P. Barros, Raquel Mantuaneli Scarel‐Caminaga
Software Mentions: 1
Published: over 4 years ago

10.1186/1471-2164-8-261

New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures
Cited by: 58
Author(s): Andrew Hesketh, Giselda Bucca, Emma Laing, Fiona Flett, Graham Hotchkiss, Colin P. Smith, Keith F. Chater
Software Mentions: 1
Published: over 17 years ago

10.1002/stem.1761

Elevated <i>O</i>-GlcNAc Levels Activate Epigenetically Repressed Genes and Delay Mouse ESC Differentiation Without Affecting Naïve to Primed Cell Transition
Cited by: 50
Author(s): Christopher M. Speakman, Tanja Domke, Wikrom Wongpaiboonwattana, Kelly Sanders, Manikhandan Mudaliar, Daan M. F. van Aalten, Geoffrey J. Barton, Marios P. Stavridis
Software Mentions: 1
Published: about 10 years ago

10.3390/toxics7040050

Exposure of Larval Zebrafish to the Insecticide Propoxur Induced Developmental Delays that Correlate with Behavioral Abnormalities and Altered Expression of hspb9 and hspb11
Cited by: 6
Author(s): Jeremiah N. Shields, Eric C. Hales, Lillian E. Ranspach, Xixia Luo, Steven Orr, Donna L. Runft, Alan A. Dombkowski, Melody N. Neely, Larry H. Matherly, Jeffrey W. Taub, Tracie R. Baker, Ryan Thummel
Software Mentions: 1
Published: about 5 years ago

10.1038/tp.2015.15

Identification of genes and gene pathways associated with major depressive disorder by integrative brain analysis of rat and human prefrontal cortex transcriptomes
Cited by: 40
Author(s): Karim Malki, Oliver Pain, Maria Grazia Tosto, Ebba Du Rietz, Lucia Carboni, Leonard C. Schalkwyk
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0102466

Differential Transcriptional Effects of EGFR Inhibitors
Cited by: 12
Author(s): Miroslav Blumenberg
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0077430

Gene Expression Profiling Identifies Molecular Pathways Associated with Collagen VI Deficiency and Provides Novel Therapeutic Targets
Cited by: 22
Author(s): Sonia Paco, Susana G. Kalko, Cristina Jou, Maria Angels Rodríguez, J. Corbera, F. Muntoni, Lucy Feng, Eloy Rivas, Ferrán Torner, Francesca Gualandi, Anna M. Gómèz-Foix, Anna Ferrer, C. Ortez, A. Nascimento, J. Colomer, Cecilia Jiménez‐Mallebrera
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0148562

Meta-Analysis of Transcriptional Responses to Mastitis-Causing Escherichia coli
Cited by: 21
Author(s): Sidra Younis, Qamar Javed, Miroslav Blumenberg
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0010964

Human Endometrial Side Population Cells Exhibit Genotypic, Phenotypic and Functional Features of Somatic Stem Cells
Cited by: 164
Author(s): Irene Cervelló, Claudia Gil-Sanchís, Aymara Mas, Francisco Delgado-Rosas, José Antonio Martínez-Conejero, Amparo Galán, Alicia Martínez-Romero, Sebastián Martínez, Ismael Navarro, Jaime Ferro, José A. Horcajadas, Francisco J. Esteban, José Enrique O’Connor, António Pellicer, Carlos Simón
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0093046

A Meta Analysis of Pancreatic Microarray Datasets Yields New Targets as Cancer Genes and Biomarkers
Cited by: 43
Author(s): Nalin C. W. Goonesekere, Xiaosheng Wang, Lindsey Ludwig, Chittibabu Guda
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0056077

Transcriptomic Profiling of Human Peritumoral Neocortex Tissues Revealed Genes Possibly Involved in Tumor-Induced Epilepsy
Cited by: 20
Author(s): Charles E. Niesen, Jun Xu, Xuemo Fan, Xiaojin Li, Christopher J. Wheeler, Adam N. Mamelak, Charles Wang
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0031645

Transcriptome and Network Changes in Climbers at Extreme Altitudes
Cited by: 21
Author(s): Fang Chen, Wei Zhang, Yu Liang, Jialiang Huang, Kui Li, Christopher D. Green, Jiancheng Liu, Guojie Zhang, Bing Zhou, Xin Yi, Wei Wang, Huan Liu, Xiaohong Xu, Feng Shen, Ning Qu, Yading Wang, Guoyi Gao, Aye Mi San, Jiangbai Luosang, Hua Shi, Xiangdong Fang, Karsten Kristiansen, Huanming Yang, Jun Wang, Jing–Dong Jackie Han, Jian Wang
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0021260

Molecular Sub-Classification of Renal Epithelial Tumors Using Meta-Analysis of Gene Expression Microarrays
Cited by: 9
Author(s): Thomas Sanford, Paul H. Chung, Ariel Reinish, Vladimir Valera, Ramaprasad Srinivasan, W. Marston Linehan, Gennady Bratslavsky
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0031821

DNA Methylation Patterns in Cord Blood DNA and Body Size in Childhood
Cited by: 132
Author(s): Caroline L Relton, Alix Groom, Beaté St Pourcain, Adrian Sayers, Daniel Swan, Nicholas D. Embleton, Mark S. Pearce, Susan M. Ring, Kate Northstone, Jonathan H Tobias, Joseph Trakalo, Andy R Ness, Seif O. Shaheen, George Davey Smith
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0033254

The Role of TNF-α in Mice with Type 1- and 2- Diabetes
Cited by: 36
Author(s): Maria Koulmanda, Manoj Bhasin, Zuheir L. Awdeh, Andi Qipo, Zhipeng Fan, Dusan Hanidziar, Prabhakar Putheti, Hang Shi, Eva Csizuadia, Towia A. Libermann, Terry B. Strom
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0060439

Novel Molecular Pathways Elicited by Mutant FGFR2 May Account for Brain Abnormalities in Apert Syndrome
Cited by: 13
Author(s): Erika Yeh, Roberto Dalto Fanganiello, Daniele Yumi Sunaga, Xiaoli Zhou, Gregory Holmes, Kátia Maria da Rocha, Nivaldo Alonso, Hamilton Matushita, Yingli Wang, Ethylin Wang Jabs, Maria Rita Passos‐Bueno
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0022077

A Resource for Discovering Specific and Universal Biomarkers for Distributed Stem Cells
Cited by: 17
Author(s): Minsoo Noh, Janet L. Smith, Yang Hoon Huh, James L. Sherley
Software Mentions: 1
Published: over 13 years ago

Projects: bioconductor: RankProd

Papers Mentioning RankProd 213