bioconductor: limma | Projects | Ecosyste.ms: Papers

10.3390/nu7053370

Low Folate and Selenium in the Mouse Maternal Diet Alters Liver Gene Expression Patterns in the Offspring after Weaning
Cited by: 15
Author(s): Matthew P. G. Barnett, Emma N. Bermingham, Wayne Young, Shalome A. Bassett, John E. Hesketh, Anabel Maciel-Dominguez, Warren C. McNabb, Nicole C. Roy
Software Mentions: 2
Published: over 11 years ago

10.3390/nu9020116

Effects of an Encapsulated Fruit and Vegetable Juice Concentrate on Obesity-Induced Systemic Inflammation: A Randomised Controlled Trial
Cited by: 25
Author(s): Evan J. Williams, Katherine J. Baines, Bronwyn S. Berthon, Lisa G. Wood
Software Mentions: 2
Published: over 9 years ago

10.3390/nu11030639

Key Genes of Lipid Metabolism and WNT-Signaling Are Downregulated in Subcutaneous Adipose Tissue with Moderate Weight Loss
Cited by: 9
Author(s): Ruth Schübel, Disorn Sookthai, Judith Greimel, Theron Johnson, Mirja Grafetstätter, Romy Kirsten, Mario Kratz, Cornelia M. Ulrich, Rudolf Kaaks, Tilman Kühn
Software Mentions: 2
Published: over 7 years ago

10.3390/nu13051683

Methylation and Expression of FTO and PLAG1 Genes in Childhood Obesity: Insight into Anthropometric Parameters and Glucose–Lipid Metabolism
Cited by: 11
Author(s): Wojciech Czogała, Małgorzata Czogała, Wojciech Strojny, Gracjan Wątor, Paweł Wołkow, Małgorzata Wójcik, Mirosław Bik-Multanowski, Przemysław Tomasik, Andrzej Wędrychowicz, Wojciech Kowalczyk, Karol Miklusiak, Agnieszka Łazarczyk, Przemysław Hałubiec, Szymon Skoczeń
Software Mentions: 2
Published: over 5 years ago

10.1186/gm519

miR-638 regulates gene expression networks associated with emphysematous lung destruction
Cited by: 63
Author(s): Stephanie A. Christenson, Corry‐Anke Brandsma, Joshua D. Campbell, Darryl A. Knight, Dmitri V. Pechkovsky, James C. Hogg, Wim Timens, Dirkje S. Postma, Marc E. Lenburg, Avrum Spira
Software Mentions: 2
Published: over 13 years ago

10.1186/s12885-017-3897-x

Invasive micropapillary carcinoma of the breast overexpresses MUC4 and is associated with poor outcome to adjuvant trastuzumab in HER2-positive breast cancer
Cited by: 18
Author(s): María F. Mercogliano, Gloria Inurrigarro, Mara De Martino, Leandro Venturutti, Martín A. Rivas, Rosalía Cordo Russo, Cecilia J. Proietti, Elmer Fernández, Isabel Frahm, Sabrina Barchuk, Daniel H. Allemand, Silvina Figurelli, Ernesto Gil Deza, Sandra Ares, Felipe G. Gercovich, E Cortese, Matías Amasino, Pablo Guzmán, Juan Carlos Roa, Patricia V. Elizalde, Roxana Schillaci
Software Mentions: 2
Published: almost 9 years ago

10.1186/gm550

Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity
Cited by: 10
Author(s): Nadia M. Penrod, Casey S. Greene, Jason H. Moore
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2407-13-175

Systematic antibody generation and validation via tissue microarray technology leading to identification of a novel protein prognostic panel in breast cancer
Cited by: 45
Author(s): Patrick C O ́Leary, Sarah Penny, Roisin T. Dolan, Catherine M. Kelly, Stephen F. Madden, Elton Rexhepaj, Donal J. Brennan, Amanda McCann, Fredrik Pontén, Mathias Uhlén, Radosław Zagożdżon, Michael J. Duffy, Malcolm R. Kell, Karin Jirström, William M. Gallagher
Software Mentions: 2
Published: over 13 years ago

10.1186/s13073-014-0075-5

Alteration in basal and depolarization induced transcriptional network in iPSC derived neurons from Timothy syndrome
Cited by: 72
Author(s): Yuan Tian, Irina Voineagu, Sergiu P. Pașca, Hyejung Won, Vijayendran Chandran, Steve Horvath, Ricardo E. Dolmetsch, Daniel H. Geschwind
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13073-014-0097-z

Linking hypothetical knowledge patterns to disease molecular signatures for biomarker discovery in Alzheimer’s disease
Cited by: 7
Author(s): Ashutosh Malhotra, Erfan Younesi, Shweta Bagewadi, Martin Hofmann‐Apitius
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13148-015-0112-2

DNA methylation signature in peripheral blood reveals distinct characteristics of human X chromosome numerical aberrations
Cited by: 59
Author(s): Ingo G. H. Schmidt‐Wolf, Muhammad Ahmer Jamil, Nicole Nuesgen, Felix Schreiner, Lutz Priebe, Per Hoffmann, Stefan Herns, Markus M. Nöthen, Holger Fröhlich, Johannes Oldenburg, Joachim Woelfle, Osman El‐Maarri
Software Mentions: 2
Published: about 11 years ago

10.1186/1755-8794-3-44

Molecular signature of response and potential pathways related to resistance to the HSP90 inhibitor, 17AAG, in breast cancer
Cited by: 26
Author(s): Magdalena Zając, Gonzalo Vázquez Gómez, Javier Benı́tez, Beatriz Martı́nez-Delgado
Software Mentions: 2
Published: almost 16 years ago

10.3390/cells10010101

MiR-26a-5p as a Reference to Normalize MicroRNA qRT-PCR Levels in Plasma Exosomes of Pediatric Hematological Malignancies
Cited by: 18
Author(s): Carlotta C. Damanti, Enrico Gaffo, Federica Lovisa, Anna Garbin, Piero Di Battista, Ilaria Gallingani, Anna Tosato, Marta Pillon, Elisa Carraro, Maurizio Mascarin, Caterina Elia, Alessandra Biffi, Stefania Bortoluzzi, Lara Mussolin
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2407-14-552

E-cadherin loss alters cytoskeletal organization and adhesion in non-malignant breast cells but is insufficient to induce an epithelial-mesenchymal transition
Cited by: 105
Author(s): Augustine Chen, Henry Beetham, Michael A. Black, Rashmi Priya, Bryony J. Telford, Joanne Guest, George A. R. Wiggins, Tanis Godwin, Alpha S. Yap, Parry Guilford
Software Mentions: 2
Published: about 12 years ago

10.1186/1755-8794-4-29

Sex hormones and gene expression signatures in peripheral blood from postmenopausal women - the NOWAC postgenome study
Cited by: 10
Author(s): Marit Waaseth, Karina Standahl Olsen, Charlotta Rylander, Eiliv Lund, Vanessa Dumeaux
Software Mentions: 2
Published: over 15 years ago

10.18632/aging.103547

FGF2-induced PI3K/Akt signaling evokes greater proliferation and adipogenic differentiation of human adipose stem cells from breast than from abdomen or thigh
Cited by: 3
Author(s): Guan-Ming Lu, Yong-Xian Rong, Zheng Liang, Dong-Lin Hunag, Fengyao Wu, Yuju Ma, Zhizhai Luo, Xinheng Liu, Steven Mo, Hong-Mian Li
Software Mentions: 2
Published: about 6 years ago

10.1186/s13148-020-00884-8

meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes
Cited by: 19
Author(s): Diana‐Maria Ciuculete, Sarah Voisin, Lara Kular, Jan‐Ingvar Jönsson, Mathias Rask‐Andersen, Jessica Mwinyi, Helgi B. Schiöth
Software Mentions: 2
Published: about 6 years ago

10.1186/s12885-021-07857-x

ETV4 plays a role on the primary events during the adenoma-adenocarcinoma progression in colorectal cancer
Cited by: 8
Author(s): Aline Simoneti Fonseca, Anelisa Ramão, Matheus Carvalho Bürger, Jorge Estefano Santana de Souza, Dalila Lucíola Zanette, Greice Andreotti de Molfetta, Luíza Ferreira de Araújo, Rafaela de Barros e Lima Bueno, Graziela Moura Aguiar, Jéssica Rodrigues Plaça, Cleidson de Pádua Alves, Anemari Ramos Dinarte dos Santos, Daniel Onofre Vidal, Gyl Eanes Barros Silva, Rodrigo Alexandre Panepucci, Fernanda Maris Peria, Omar Féres, José Joaquim Ribeiro da Rocha, Marco Antônio Zago, Wilson A. Silva
Software Mentions: 2
Published: over 5 years ago

10.1186/s12885-020-07075-x

Immune-related genes in tumor-specific CD4+ and CD8+ T cells in colon cancer
Cited by: 15
Author(s): Yang Xi, Wei Wu, Yuefen Pan, Qing Zhou, Jingying Xu, Shuwen Han
Software Mentions: 2
Published: about 6 years ago

10.1186/s13073-016-0345-5

Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation
Cited by: 3
Author(s): Peter Humburg, Narelle J. Maugeri, Wanseon Lee, Bert Mohr, Julian C. Knight
Software Mentions: 2
Published: about 10 years ago

10.1186/s13073-016-0347-3

Genomic analysis of the molecular neuropathology of tuberous sclerosis using a human stem cell model
Cited by: 34
Author(s): Nils Grabole, Jitao David Zhang, Stefan Aigner, Nadine Ruderisch, Veronica Costa, Felix Weber, Michel Theron, Nikolaos Berntenis, Olivia Spleiss, Martin Ebeling, G Yeo, Ravi Jagasia, Anna Kiialainen
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12885-015-1953-y

Consistent gene expression profiles in MexTAg transgenic mouse and wild type mouse asbestos-induced mesothelioma
Cited by: 12
Author(s): Cleo Robinson, Ian M. Dick, Michael J. Wise, Andrew Holloway, Dileepa S. Diyagama, B. W. Robinson, Jenette Creaney, Richard Lake
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13073-016-0381-1

Allele-specific expression in the human heart and its application to postoperative atrial fibrillation and myocardial ischemia
Cited by: 6
Author(s): Martin I. Sigurdsson, Louis A. Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary F. Aranki, Gregory S. Couper, Stanton K. Shernan, J. G. Seidman, Simon C. Body, Jochen D. Muehlschlegel
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12920-020-00745-6

Genome-wide identification of methylated CpG sites in nongenital cutaneous warts
Cited by: 3
Author(s): Laith N. AL-Eitan, Mansour A. Alghamdi, Amneh H. Tarkhan, Firas Al‐Qarqaz
Software Mentions: 2
Published: about 6 years ago

10.1186/s13073-017-0443-z

DNA methylation-based chromatin compartments and ChIP-seq profiles reveal transcriptional drivers of prostate carcinogenesis
Cited by: 15
Author(s): Poppy Simmonds, Erick Loomis, Ed Curry
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms20143444

Long Non-coding RNAs as Important Biomarkers in Laryngeal Cancer and Other Head and Neck Tumours
Cited by: 61
Author(s): Alessia Maria Cossu, Laura Mosca, Silvia Zappavigna, Gabriella Misso, Marco Bocchetti, Federica De Micco, Lucio Quagliuolo, Marina Porcelli, Michele Caraglia, Mariarosaria Boccellino
Software Mentions: 2
Published: about 7 years ago

10.3390/ijms20153651

MicroRNA Profiling During Neural Differentiation of Induced Pluripotent Stem Cells
Cited by: 21
Author(s): Katarzyna Kulcenty, Joanna Wróblewska, Marcin Ruciński, Emilia Kozłowska, Karol Jopek, Wiktoria Maria Suchorska
Software Mentions: 2
Published: about 7 years ago

10.18632/aging.103192

Identification of potential novel differentially-expressed genes and their role in invasion and migration in renal cell carcinoma
Cited by: 3
Author(s): Shen-Nan Shi, Xia Qin, Shuo Wang, Wenfu Wang, Yao Zhu, Yu Lin, Zhou Zhang, Benkang Shi, Xigao Liu
Software Mentions: 2
Published: over 6 years ago

10.1289/ehp.1205963

MicroRNA Expression in Response to Controlled Exposure to Diesel Exhaust: Attenuation by the Antioxidant <i>N</i> -Acetylcysteine in a Randomized Crossover Study
Cited by: 88
Author(s): Masatsugu Yamamoto, Amrit Singh, Francesco Sava, Mandy Pui, Scott J. Tebbutt, Christopher Carlsten
Software Mentions: 2
Published: over 13 years ago

10.1186/s13073-020-00759-w

Cytokine-induced molecular responses in airway smooth muscle cells inform genome-wide association studies of asthma
Cited by: 14
Author(s): Emma E. Thompson, Quynh Dang, Blair Mitchell-Handley, Kavitha Rajendran, Sumati Ram-Mohan, Julian Solway, Carole Ober, Ramaswamy Krishnan
Software Mentions: 2
Published: about 6 years ago

10.7554/eLife.04506

Heterochromatin assembly and transcriptome repression by Set1 in coordination with a class II histone deacetylase
Cited by: 25
Author(s): David R. Lorenz, Lauren F Meyer, Patrick J. R. Grady, Michelle M. Meyer, Hugh P. Cam
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12896-014-0091-y

Comparison of intracellular and secretion-based strategies for production of human α-galactosidase A in the filamentous fungus Trichoderma reesei
Cited by: 11
Author(s): Wesley Smith, Jussi Jäntti, Merja Oja, Markku Saloheimo
Software Mentions: 2
Published: almost 12 years ago

10.1186/1741-7007-10-16

Imbalance of heterologous protein folding and disulfide bond formation rates yields runaway oxidative stress
Cited by: 70
Author(s): Keith E.J. Tyo, Zihe Liu, Dina Petranović, Jens Nielsen
Software Mentions: 2
Published: over 14 years ago

10.1186/s13073-020-00808-4

Identification of epigenome-wide DNA methylation differences between carriers of APOE ε4 and APOE ε2 alleles
Cited by: 18
Author(s): Richard M Martin, Kadi Vaher, Mairead Lesley Bermingham, Stewart W. Morris, Andrew D. Bretherick, Yanni Zeng, Konrad Rawlik, Carmen Amador, Archie Campbell, Chris Haley, Caroline Hayward, David J. Porteous, Andrew M. McIntosh, Riccardo E. Marioni, Kathryn Evans
Software Mentions: 2
Published: over 5 years ago

10.1186/s12915-015-0186-5

Systems-level organization of yeast methylotrophic lifestyle
Cited by: 110
Author(s): Hannes Rußmayer, Markus Buchetics, Clemens Gruber, Minoska Valli, Karlheinz Grillitsch, Gerda Modarres, Raffaele Guerrasio, Kristaps Klavins, Stefan Neubauer, H. Drexler, Matthias G. Steiger, Christina Troyer, Ali Al Chalabi, Guido Krebiehl, Denise Sonntag, Günther Zellnig, Günther Daum, Alexandra B. Graf, Friedrich Altmann, Gunda Koellensperger, Stephan Hann, Michael Sauer, Diethard Mattanovich, Brigitte Gasser
Software Mentions: 2
Published: almost 11 years ago

10.1186/s13148-019-0790-2

The effects of bariatric surgery on clinical profile, DNA methylation, and ageing in severely obese patients
Cited by: 18
Author(s): Eliza Fraszczyk, Mirjam Luijten, Annemieke M.W. Spijkerman, Harold Snieder, Paul Wackers, Vincent W. Bloks, Carolina Ferreira Nicoletti, Carla Barbosa Nonino, Ana B. Crujeiras, Wim A. Buurman, Jan Greve, Sander S. Rensen, Bruce H. R. Wolffenbuttel, Jana V. van Vliet-Ostaptchouk
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2021.651619

A Comprehensive View on the Human Antibody Repertoire Against Staphylococcus aureus Antigens in the General Population
Cited by: 18
Author(s): Tanja Meyer, Stephan Michalik, Silva Holtfreter, Stefan Weiß, Nele Friedrich, Henry Völzke, Thomas Kocher, Christian Köhler, Frank Schmidt, Barbara M. Bröker, Uwe Völker
Software Mentions: 2
Published: over 5 years ago

10.1186/1755-8794-4-30

Identification of SERPINA1 as single marker for papillary thyroid carcinoma through microarray meta analysis and quantification of its discriminatory power in independent validation
Cited by: 41
Author(s): Klemens Vierlinger, Markus Mansfeld, Oskar Koperek, Christa Nöhammer, Klaus Kaserer, Friedrich Leisch
Software Mentions: 2
Published: over 15 years ago

10.1186/s12915-021-00959-9

A brain cyst load-associated antigen is a Toxoplasma gondii biomarker for serodetection of persistent parasites and chronic infection
Cited by: 5
Author(s): Céline Dard, Christopher Swale, Marie-Pierre Brenier-Pinchart, Dayana C Farhat, Valeria Bellini, M Robert, Dominique Cannella, H Pelloux, Isabelle Tardieux, Mohamed‐Ali Hakimi
Software Mentions: 2
Published: over 5 years ago

10.1016/j.gpb.2020.02.002

CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma
Cited by: 14
Author(s): Ziyi Li, Binbin Wang, Shengqing Gu, Peng Jiang, Avinash Sahu, Chen-Hao Chen, Tong Han, Sailing Shi, Xiaoqing Wang, Nicole Traugh, Hailing Liu, Yin Liu, Qiu Liang Wu, Myles Brown, Tengfei Xiao, Genevieve M. Boland, X. Shirley Liu
Software Mentions: 2
Published: over 6 years ago

10.1186/1741-7007-7-1

Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration
Cited by: 147
Author(s): James R. Monaghan, Leonard G. Epp, Srikrishna Putta, Robert B. Page, John Walker, Chris K Beachy, Wei Zhu, Gerald M. Pao, Inder M. Verma, Tony Hunter, Susan V. Bryant, David M. Gardiner, Tim Harkins, S. Randal Voss
Software Mentions: 2
Published: over 17 years ago

10.1186/1741-7007-9-29

Lack of global meiotic sex chromosome inactivation, and paucity of tissue-specific gene expression on the Drosophila X chromosome
Cited by: 67
Author(s): Lyudmila Mikhaylova, Dmitry I. Nurminsky
Software Mentions: 2
Published: over 15 years ago

10.1128/MCB.00145-13

Epigenetic Functions of Smchd1 Repress Gene Clusters on the Inactive X Chromosome and on Autosomes
Cited by: 96
Author(s): Anne-Valérie Gendrel, Y. Amy Tang, Masako Suzuki, Jonathan Godwin, Tatyana B. Nesterova, John M. Greally, Edith Heard, Neil Brockdorff
Software Mentions: 2
Published: about 13 years ago

10.1186/s12915-020-00791-7

Multi-omics analysis delineates the distinct functions of sub-cellular acetyl-CoA pools in Toxoplasma gondii
Cited by: 31
Author(s): Joachim Kloehn, Rebecca Oppenheim, Ghizal Siddiqui, Pieter Jan De Bock, Sunil Kumar Dogga, Yohann Couté, Mohamed‐Ali Hakimi, Darren J. Creek, Dominique Soldati‐Favre
Software Mentions: 2
Published: over 6 years ago

10.1186/s12915-016-0334-6

Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway
Cited by: 32
Author(s): Deborah L. McEwan, Rhonda Feinbaum, Nicholas Stroustrup, Wilhelm Haas, Annie L. Conery, Anthony Anselmo, Ruslan I. Sadreyev, Frederick M. Ausubel
Software Mentions: 2
Published: almost 10 years ago

10.3389/fimmu.2019.00261

Aberrant Expressions of Co-stimulatory and Co-inhibitory Molecules in Autoimmune Diseases
Cited by: 11
Author(s): Wei He, Bin Wang, Qian Li, Qiuming Yao, Xi Jia, Ronghua Song, Sheli Li, Jinan Zhang
Software Mentions: 2
Published: over 7 years ago

10.1186/s12935-020-01572-6

Integrated analysis of immune-related genes in endometrial carcinoma
Cited by: 9
Author(s): Yiru Wang, Yunduo Liu, Yue Guan, Hao Li, Yuan Liu, Mengjun Zhang, Ping Cui, Dan Kong, Xiuwei Chen, Hang Yin
Software Mentions: 2
Published: almost 6 years ago

10.3390/cells9020448

A System Based-Approach to Examine Host Response during Infection with Influenza A Virus Subtype H7N9 in Human and Avian Cells
Cited by: 2
Author(s): Biruhalem Taye, Hui Chen, David Yeo, Shirley Gek Kheng Seah, Michelle Wong, Richard J. Sugrue, Boon Huan Tan
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2105-12-228

Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics
Cited by: 24
Author(s): Tracy L. Bergemann, Jason Wilson
Software Mentions: 2
Published: over 15 years ago

10.1080/19490976.2019.1651596

Mucosal IgG in inflammatory bowel disease – a question of (sub)class?
Cited by: 10
Author(s): Tomas Castro‐Dopico, Menna R. Clatworthy
Software Mentions: 2
Published: about 7 years ago

10.18632/oncotarget.16437

Promoter DNA methylation analysis reveals a combined diagnosis of CpG-based biomarker for prostate cancer
Cited by: 10
Author(s): Yuanyuan Tang, Sanyuan Jiang, Yinmin Gu, Weidong Li, Zengnan Mo, Yuanjie Huang, Tianyu Li, Yanling Hu
Software Mentions: 2
Published: over 9 years ago

10.1080/15592294.2020.1827713

Birth weight associations with DNA methylation differences in an adult population
Cited by: 15
Author(s): Rebecca A Madden, Daniel L. McCartney, Richard M Martin, Robert F. Hillary, Mairead Lesley Bermingham, Konrad Rawlik, Stewart W. Morris, Archie Campbell, David J. Porteous, Ian J. Deary, Kathryn Evans, Jonathan D. Hafferty, Andrew M. McIntosh, Riccardo E. Marioni
Software Mentions: 2
Published: almost 6 years ago

10.1002/hsr2.202

A prognostic risk model based on immune‐related genes predicts overall survival of patients with hepatocellular carcinoma
Cited by: 2
Author(s): Banglun Pan, Lin Liu, Wei Li
Software Mentions: 2
Published: almost 6 years ago

10.3389/fimmu.2021.709164

Defining a Methylation Signature Associated With Operational Tolerance in Kidney Transplant Recipients
Cited by: 5
Author(s): Ramón María Alvargonzález Rodríguez, María P. Hernández-Fuentes, Viviana Corte-Iglesias, María Laura Sáiz, Juan José Lozano, Ana R. Cortázar, Isabel Mendizabal, María Luisa Suárez-Fernández, Eliécer Coto, Antonio López-Vázquez, Carmen Díaz‐Corte, Ana M. Aransay, Carlos López‐Larrea, Beatriz Suárez-Álvarez
Software Mentions: 2
Published: about 5 years ago

10.7554/eLife.63326

The mTORC1-mediated activation of ATF4 promotes protein and glutathione synthesis downstream of growth signals
Cited by: 80
Author(s): Margaret E. Torrence, Michael R. MacArthur, Aaron M. Hosios, Alexander J. Valvezan, John M. Asara, James R. Mitchell, Brendan D. Manning
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-015-0712-z

Seq-ing improved gene expression estimates from microarrays using machine learning
Cited by: 5
Author(s): Paul K. Korir, Paul Geeleher, Cathal Seoighe
Software Mentions: 2
Published: about 11 years ago

10.1002/hep.29877

Impact of Interferon Lambda 4 Genotype on Interferon‐Stimulated Gene Expression During Direct‐Acting Antiviral Therapy for Hepatitis C
Cited by: 17
Author(s): Narayan Ramamurthy, Emanuele Marchi, Azim Ansari, Vincent Pedergnana, Angela R. McLean, Emma Hudson, Rory Bowden, Chris C. A. Spencer, Eleanor Barnes, Paul Klenerman
Software Mentions: 2
Published: about 8 years ago

10.1186/1755-8794-1-34

Influence of monolayer, spheroid, and tumor growth conditions on chromosome 3 gene expression in tumorigenic epithelial ovarian cancer cell lines
Cited by: 22
Author(s): Neal Cody, Magdalena Zietarska, Ali Filali‐Mouhim, Diane Provencher, Anne-Marie Mes-Masson, Patricia N. Tonin
Software Mentions: 2
Published: about 18 years ago

10.1186/1756-8935-5-8

The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner
Cited by: 81
Author(s): Frank Sleutels, Widia Soochit, Marek Bartkuhn, Helen Heath, Sven Dienstbach, Philipp Bergmaier, Vedran Franke, Manuel Rosa‐Garrido, Suzanne van de Nobelen, Lisa Caesar, Michael I.J.A. van der Reijden, Jan Christian Bryne, Wilfred F. J. van IJcken, J. Anton Grootegoed, M. Dolores Delgado, Boris Lenhard, Rainer Renkawitz, Frank Grosveld, Niels Galjart
Software Mentions: 2
Published: over 14 years ago

10.7554/eLife.66608

KSR1- and ERK-dependent translational regulation of the epithelial-to-mesenchymal transition
Cited by: 10
Author(s): C. Mallikarjuna Rao, Danielle E. Frodyma, Siddesh Southekal, Robert A. Svoboda, Adrian R. Black, Chittibabu Guda, Tomohiro Mizutani, Hans Clevers, Keith R. Johnson, Kurt W. Fisher, Robert E. Lewis
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2105-12-413

Impact of the spotted microarray preprocessing method on fold-change compression and variance stability
Cited by: 26
Author(s): Jérôme Ambroise, Bertrand Bearzatto, Annie Robert, Bernadette Govaerts, Benoı̂t Macq, Jean‐Luc Gala
Software Mentions: 2
Published: almost 15 years ago

10.1186/s13148-018-0491-2

Global DNA methylation changes spanning puberty are near predicted estrogen-responsive genes and enriched for genes involved in endocrine and immune processes
Cited by: 38
Author(s): Emma E. Thompson, Jessie Nicodemus‐Johnson, Kyung Won Kim, James E. Gern, Daniel J. Jackson, Robert F. Lemanske, Carole Ober
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-6-65

Cited by: 21
Author(s): Mayte Suárez‐Fariñas, Asifa Haider, Knut M. Wittkowski
Software Mentions: 2
Published: over 21 years ago

10.3389/fimmu.2017.00489

Heterogeneity of Phenotype and Function Reflects the Multistage Development of T Follicular Helper Cells
Cited by: 18
Author(s): Marta Trüb, Tom A. Barr, Vicky L. Morrison, Sheila Brown, Stefano Caserta, Jordan Rixon, Alasdair Ivens, David Gray
Software Mentions: 2
Published: over 9 years ago

10.3389/fimmu.2021.636614

Integrative Transcriptomic, Proteomic and Functional Analysis Reveals ATP1B3 as a Diagnostic and Potential Therapeutic Target in Hepatocellular Carcinoma
Cited by: 12
Author(s): Shanshan Lu, Shenglan Cai, Peng Xu, Ruochan Cheng, Yiya Zhang
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.202494

Identification of novel candidate biomarkers for pancreatic adenocarcinoma based on TCGA cohort
Cited by: 5
Author(s): Jie Yang, Peng Wang, Yuanyuan Li
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0203468

Particulate metal exposures induce plasma metabolome changes in a commuter panel study
Cited by: 34
Author(s): Chandresh N Ladva, Rachel Golan, Donghai Liang, Roby Greenwald, Douglas I. Walker, Karan Uppal, Amit U. Raysoni, ViLinh Tran, Tianwei Yu, W. Dana Flanders, Gary W. Miller, Dean P. Jones, Jeremy A. Sarnat
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12859-017-1925-0

Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling
Cited by: 38
Author(s): Daniel Castillo, Juan Manuel Gálvez, José Benavente Herrera, Belén San Román, Fernando Rojas, Ignacio Rojas
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2105-11-556

Assessment and optimisation of normalisation methods for dual-colour antibody microarrays
Cited by: 23
Author(s): Martin Sill, Christoph Schröder, Jörg D. Hoheisel, Axel Benner, Manuela Zucknick
Software Mentions: 2
Published: almost 16 years ago

10.1038/s41438-019-0119-5

What makes turnips: anatomy, physiology and transcriptome during early stages of its hypocotyl-tuber development
Cited by: 23
Author(s): Mengyang Li, Niccolò Bassetti, Stefan Petrasch, Ningwen Zhang, Johan Bucher, Shuxing Shen, Zhao Jian-jun, Guusje Bonnema
Software Mentions: 2
Published: over 7 years ago

10.1038/s41438-019-0212-9

Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage (Brassica rapa)
Cited by: 10
Author(s): Xiaoxue Sun, Ram Kumar Basnet, Zhichun Yan, Johan Bucher, Chengcheng Cai, Jianjun Zhao, Guusje Bonnema
Software Mentions: 2
Published: almost 7 years ago

10.18632/aging.102667

Systematic analysis of lncRNA and microRNA dynamic features reveals diagnostic and prognostic biomarkers of myocardial infarction
Cited by: 6
Author(s): Hang Shi, Haoran Sun, Jiayao Li, Ziyi Bai, Jie Wu, Xiuhong Li, Yingli Lv, Guangde Zhang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-021-01085-9

Identification of seven novel ferroptosis-related long non-coding RNA signatures as a diagnostic biomarker for acute myeloid leukemia
Cited by: 15
Author(s): Zhiyuan Zheng, Wei Wu, Zehang Lin, Shuhan Liu, Qiaoqian Chen, Xiandong Jiang, Yu Xue, Lin Dong
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12920-021-00894-2

Integrated analysis of differentially expressed genes and construction of a competing endogenous RNA network in human Huntington neural progenitor cells
Cited by: 3
Author(s): Xiaoping Tan, Yang Liu, Taiming Zhang, Shuyan Cong
Software Mentions: 2
Published: over 5 years ago

10.1186/1755-8794-2-54

MicroRNA-125a is over-expressed in insulin target tissues in a spontaneous rat model of Type 2 Diabetes
Cited by: 111
Author(s): Blanca Herrera, Helen Lockstone, Jennifer Taylor, Quin F. Wills, Pamela J. Kaisaki, Amy Barrett, Carme Camps, Christina Fernández, Jiannis Ragoussis, Dominique Guyader, Mark I. McCarthy, Cecilia M. Lindgren
Software Mentions: 2
Published: about 17 years ago

10.1186/s12859-019-2893-3

JCD-DEA: a joint covariate detection tool for differential expression analysis on tumor expression profiles
Cited by: 3
Author(s): Yi Li, Yanan Liu, Yiming Wu, Xudong Zhao
Software Mentions: 2
Published: about 7 years ago

10.7554/eLife.04525

Mucosal effects of tenofovir 1% gel
Cited by: 40
Author(s): Florian Hladik, Adam Burgener, Lamar Ballweber, Raphaël Gottardo, Lucia Vojtech, Slim Fourati, Jiyan Dai, Mark J. Cameron, Johanna Strobl, Sean M. Hughes, Craig Hoesley, P. Andrew, Sherri Johnson, Jeanna Piper, David R. Friend, T. Blake Ball, Ross D. Cranston, Kenneth H. Mayer, M. Juliana McElrath, Ian McGowan
Software Mentions: 2
Published: over 11 years ago

10.1186/1756-8935-6-42

Murine esBAF chromatin remodeling complex subunits BAF250a and Brg1 are necessary to maintain and reprogram pluripotency-specific replication timing of select replication domains
Cited by: 28
Author(s): Shin‐ichiro Takebayashi, Ienglam Lei, Tyrone Ryba, Takayo Sasaki, Vishnu Dileep, Dana Battaglia, Xiaolin Gao, Fang Peng, Yong Fan, Miguel A. Esteban, Jianfeng Tang, Robert H. Crabtree, Zhong Wang, David M. Gilbert
Software Mentions: 2
Published: almost 13 years ago

10.3390/cells9030676

Loss of Cx43 in Murine Sertoli Cells Leads to Altered Prepubertal Sertoli Cell Maturation and Impairment of the Mitosis-Meiosis Switch
Cited by: 10
Author(s): Erika Hilbold, O. Distl, Martina Hoedemaker, S. Wilkening, Rüdiger Behr, Aleksandar Rajkovic, Marion Langeheine, Kristina Rode, Klaus Jung, Julia Metzger, Ralph Brehm
Software Mentions: 2
Published: over 6 years ago

10.1186/s13148-015-0128-7

Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma
Cited by: 19
Author(s): Pablo Conesa‐Zamora, José García‐Solano, María del Carmen Turpin, Patricia Sebastián-León, Daniel Torres-Moreno, Eduardo Estrada, Anne Tuomisto, Jamie Wilce, Markus J. Mäkinen, Miguel Pérez‐Guillermo, Ana Conesa
Software Mentions: 2
Published: about 11 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: almost 6 years ago

10.1186/s12859-019-2756-y

Leveraging the effects of chloroquine on resistant malaria parasites for combination therapies
Cited by: 5
Author(s): Ana M. Untaroiu, Maureen A. Carey, Jennifer L. Guler, Jason A. Papin
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-10-409

An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation)
Cited by: 89
Author(s): Martin J. Aryee, José A. Gutiérrez‐Pabello, Igor Kramnik, Tapabrata Maiti, John Quackenbush
Software Mentions: 2
Published: almost 17 years ago

10.1111/imcb.12399

GPR43 regulates marginal zone B‐cell responses to foreign and endogenous antigens
Cited by: 9
Author(s): Leona Rohrbeck, Mónika Ádori, Shan Wang, Chenfei He, Christopher Andrew Tibbitt, Mark Chernyshev, Madle Sirel, Ulf Ribacke, Ben Murrell, Mohammad Bohlooly‐Y, Mikael C. I. Karlsson, Gunilla B. Karlsson Hedestam, Jonathan M. Coquet
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12920-020-0672-7

Pathway mapping of leukocyte transcriptome in influenza patients reveals distinct pathogenic mechanisms associated with progression to severe infection
Cited by: 12
Author(s): Yoann Zerbib, Emily Jenkins, Maryam Shojaei, Adrienne F. A. Meyers, John Ho, T. Blake Ball, Yoav Keynan, Amarnath Pisipati, Aseem Kumar, Anand Kumar, Marek Nalos, Benjamin Tang, Klaus Schughart, Anthony S. McLean
Software Mentions: 2
Published: over 6 years ago

10.1007/s00592-019-01464-w

Metabolite profiling paradoxically reveals favorable levels of lipids, markers of oxidative stress and unsaturated fatty acids in a diabetes susceptible group of Middle Eastern immigrants
Cited by: 6
Author(s): Mahmoud Al-Majdoub, Peter Sartipy, Louise Bennet
Software Mentions: 2
Published: over 6 years ago

10.1186/s12920-020-00741-w

Construction and analysis of a lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in oral cancer
Cited by: 22
Author(s): Jian Yin, Xiaoli Zeng, Zexin Ai, Miao Yu, Yang’ou Wu, Shengjiao Li
Software Mentions: 2
Published: about 6 years ago

10.1007/s00401-019-02056-2

MYCN amplification drives an aggressive form of spinal ependymoma
Cited by: 87
Author(s): David R. Ghasemi, Martin Sill, Konstantin Okonechnikov, Andrey Korshunov, Stephen Yip, Peter W. Schütz, David Scheie, Andreas Kruse, Patrick N. Harter, Marina Kastelan, Marlies Wagner, Christian Hartmann, Julia Benzel, Kendra K. Maaß, Mustafa Khasraw, Ronald Sträter, Christian Thomas, Werner Paulus, Christian P. Kratz, Hendrik Witt, Daisuke Kawauchi, Christel Herold‐Mende, Felix Sahm, Sebastian Brandner, Marcel Kool, David Jones, Andreas von Deimling, Stefan M. Pfister, David Reuß, Kristian W. Pajtler
Software Mentions: 2
Published: about 7 years ago

10.3389/fimmu.2021.634441

ERAP2 Increases the Abundance of a Peptide Submotif Highly Selective for the Birdshot Uveitis-Associated HLA-A29
Cited by: 16
Author(s): Wouter J. Venema, Sanne Hiddingh, Joke H. de Boer, Frans H.J. Claas, Arend Mulder, Anneke I. den Hollander, Efstratios Stratikos, Siranush Sarkizova, Lars T. van der Veken, George M.C. Janssen, Peter A. van Veelen, Jonas J.W. Kuiper
Software Mentions: 2
Published: over 5 years ago

10.18632/aging.102610

The correlation and role analysis of COL4A1 and COL4A2 in hepatocarcinogenesis
Cited by: 21
Author(s): Yanli Li, Jiaye Zhang, Yan Chen, Mahmodul Hasan Sohel, Xinrong Ke, Jingqi Chen, Yin‐Xiong Li
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2021.682415

Integrative Analysis of Neuregulin Family Members-Related Tumor Microenvironment for Predicting the Prognosis in Gliomas
Cited by: 16
Author(s): Wenjin Zhao, Guan‐Yong Ou, Wen–Jen Lin
Software Mentions: 2
Published: over 5 years ago

10.1186/s12935-021-01797-z

MicroRNA-1182 and let-7a exert synergistic inhibition on invasion, migration and autophagy of cholangiocarcinoma cells through down-regulation of NUAK1
Cited by: 16
Author(s): Xin Pan, Gang Wang, Baoming Wang
Software Mentions: 2
Published: over 5 years ago

10.7554/eLife.50670

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling
Cited by: 29
Author(s): Rachel K. Lex, Zhicheng Ji, Kristin N. Falkenstein, Weiqiang Zhou, Joanna L Henry, Hongkai Ji, Steven A. Vokes
Software Mentions: 2
Published: over 6 years ago

10.1186/s12859-021-04100-z

Strain-specific behavior of Mycobacterium tuberculosis in A549 lung cancer cell line
Cited by: 4
Author(s): Shima Hadifar, Shayan Mostafaei, Ava Behrouzi, Abolfazl Fateh, Parisa Riahi, Seyed Davar Siadat, Farzam Vaziri
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2019.01661

Lnc-C/EBPβ Modulates Differentiation of MDSCs Through Downregulating IL4i1 With C/EBPβ LIP and WDR5
Cited by: 22
Author(s): Yuan Gao, Wencong Shang, Dan Zhang, Shiwu Zhang, Xipeng Zhang, Yuan Zhang, Rongcun Yang
Software Mentions: 2
Published: about 7 years ago

10.1186/s12920-020-00856-0

A predictive model for assessing prognostic risks in gastric cancer patients using gene expression and methylation data
Cited by: 1
Author(s): Dan Luo, Qingling Yang, Haibo Wang, Mao Tan, Yanlei Zou, Jian Liu
Software Mentions: 2
Published: over 5 years ago

10.1172/jci.insight.93739

Neonatal and adult recent thymic emigrants produce IL-8 and express complement receptors CR1 and CR2
Cited by: 43
Author(s): Marcin Ł. Pękalski, Arcadio Rubio Garćıa, Ricardo C. Ferreira, Daniel B. Rainbow, Deborah J. Smyth, Meghavi Mashar, Jane Brady, Natalia Savinykh, Xaquín Castro Dopico, Sumiyya Mahmood, Simon Duley, Helen Stevens, Neil Walker, Antony J. Cutler, Frank Waldron‐Lynch, David B. Dunger, Claire Shannon-Lowe, Alasdair Coles, Joanne L. Jones, Chris Wallace, John A. Todd, Linda S. Wicker
Software Mentions: 2
Published: about 9 years ago

10.1186/s12935-020-1140-3

Identification of molecular markers associated with the progression and prognosis of endometrial cancer: a bioinformatic study
Cited by: 12
Author(s): Jinhui Liu, Mingming Feng, Siyue Li, Song Nie, Hui Wang, Shan Wu, Jiangnan Qiu, Jie Zhang, Wenjun Cheng
Software Mentions: 2
Published: over 6 years ago

10.18632/aging.101737

BCL2L10/BECN1 modulates hepatoma cells autophagy by regulating PI3K/AKT signaling pathway
Cited by: 10
Author(s): Jiafa He, Li Deng, Heping Li, Taiying Chen, Shengying Chen, Shangzhou Xia, Yubin Liu
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.ppat.1008468

Human papillomavirus E7 binds Oct4 and regulates its activity in HPV-associated cervical cancers
Cited by: 13
Author(s): Theofano Panayiotou, Stella Michael, Apostolos Zaravinos, Ece Demirag, Charis Achilleos, Katerina Strati
Software Mentions: 2
Published: over 6 years ago

Projects: bioconductor: limma

Science Score: 78/100

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Papers Mentioning limma 7,776