bioconductor: vsn | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: over 15 years ago

MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data
Cited by: 11
Author(s): Guy Brock, Partha Mukhopadhyay, Vasyl Pihur, Cynthia L. Webb, Robert M. Greene, M. Michele Pisano
Software Mentions: 24
Published: over 11 years ago

10.1186/1756-0500-3-277

EMA - A R package for Easy Microarray data analysis
Cited by: 45
Author(s): Nicolas Servant, Eléonore Gravier, Pierre Gestraud, Cécile Laurent, Caroline Paccard, Anne Biton, Isabel Martínez Brito, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupé
Software Mentions: 20
Published: over 13 years ago

10.1186/s12859-017-1994-0

PIVOT: platform for interactive analysis and visualization of transcriptomics data
Cited by: 30
Author(s): Qin Zhu, Stephen Fisher, Hannah Dueck, Sarah A. Middleton, Mugdha Khaladkar, Junhyong Kim
Software Mentions: 15
Published: over 6 years ago

10.26508/lsa.202000766

Egr2 and 3 control inflammation, but maintain homeostasis, of PD-1<sup>high</sup> memory phenotype CD4 T cells
Cited by: 6
Author(s): Alistair L. J. Symonds, Wei Zheng, Tizong Miao, Ang Li, Tieshang Wang, Ruth Kiome, Xiaofeng Hou, Suling Li, Ping Wang
Software Mentions: 15
Published: about 4 years ago

10.1093/bib/bbz158

Toward a gold standard for benchmarking gene set enrichment analysis
Cited by: 74
Author(s): Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Software Mentions: 13
Published: over 4 years ago

10.1038/s41598-020-69239-w

Neural innervation as a potential trigger of morphological color change and sexual dimorphism in cichlid fish
Cited by: 14
Author(s): Yipeng Liang, Axel Meyer, Claudius F. Kratochwil
Software Mentions: 12
Published: about 4 years ago

10.1186/1471-2105-11-194

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data
Cited by: 32
Author(s): Benedikt Zacher, Pei Fen Kuan, Achim Tresch
Software Mentions: 12
Published: over 14 years ago

10.1084/jem.20160553

Egr2 and 3 control adaptive immune responses by temporally uncoupling expansion from T cell differentiation
Cited by: 46
Author(s): Tizong Miao, Alistair L. J. Symonds, Randeep Singh, Janine D. Symonds, Ane Ogbe, Becky Omodho, Bo Zhu, Suling Li, Ping Wang
Software Mentions: 12
Published: about 7 years ago

10.1016/j.cels.2018.09.003

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency
Cited by: 56
Author(s): Aleksandra Pękowska, Bernd Klaus, Wanqing Xiang, Jacqueline Severino, Nathalie Daigle, Felix A. Klein, Małgorzata Oleś, Rafael Casellas, Jan Ellenberg, Lars M. Steinmetz, Paul Bertone, Wolfgang Huber
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0256016

Integration of chronological omics data reveals mitochondrial regulatory mechanisms during the development of hepatocellular carcinoma
Cited by: 2
Author(s): J. Noé García-Chávez, Verónica Rocío Vásquez-Garzón, Mercedes G. López, Saúl Villa‐Treviño, Rafaél Montiel
Software Mentions: 10
Published: almost 3 years ago

10.1016/j.ebiom.2015.09.027

Distinct Transcriptional and Anti-Mycobacterial Profiles of Peripheral Blood Monocytes Dependent on the Ratio of Monocytes: Lymphocytes
Cited by: 58
Author(s): Vivek Naranbhai, Helen A. Fletcher, Rachel Tanner, Matthew K. O’Shea, Helen McShane, Benjamin P. Fairfax, Julian C. Knight, Adrian V. S. Hill
Software Mentions: 9
Published: over 8 years ago

10.1186/1471-2105-8-221

Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
Cited by: 156
Author(s): Joern Toedling, Oleg Sklyar, Wolfgang Huber
Software Mentions: 9
Published: about 17 years ago

10.3390/cells9030786

Systematic Identification of Housekeeping Genes Possibly Used as References in Caenorhabditis elegans by Large-Scale Data Integration
Cited by: 13
Author(s): Jingxin Tao, Youjin Hao, Xudong Li, Huachun Yin, Xiner Nie, Jie Zhang, Bo-Ying Xu, Chen Qiao, Bo Li
Software Mentions: 8
Published: over 4 years ago

10.3390/ijms19102903

Identification of a Prognostic Hypoxia-Associated Gene Set in IDH-Mutant Glioma
Cited by: 27
Author(s): Philip Dao Trong, Saskia Rösch, Heimo Mairbäurl, Stefan Pusch, Andreas Unterberg, Christel Herold‐Mende, Rolf Warta
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0159138

Technical Advances of the Recombinant Antibody Microarray Technology Platform for Clinical Immunoproteomics
Cited by: 26
Author(s): Payam Delfani, Linda Dexlin Mellby, Malin Nordström, Andreas Holmér, Mattias Ohlsson, Carl Borrebaeck, Christer Wingren
Software Mentions: 7
Published: about 8 years ago

10.1186/1471-2164-11-349

Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3
Cited by: 70
Author(s): RM Schmid, Patrick Baum, Carina Ittrich, Katrin Fundel‐Clemens, Wolfgang Huber, Benedikt Brors, Roland Eils, Andreas Weith, Detlev Mennerich, Karsten Quast
Software Mentions: 7
Published: about 14 years ago

10.1016/j.celrep.2020.107930

Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras
Cited by: 17
Author(s): Nele Merret Hollmann, Pravin Kumar Ankush Jagtap, Paweł Masiewicz, Tanit Guitart, Bernd Simon, Jan Provazník, Frank Stein, Per Haberkant, Lara Sweetapple, Laura Villacorta, Dylan Mooijman, Vladimı́r Beneš, Mikhail M. Savitski, Fátima Gebauer, Janosch Hennig
Software Mentions: 7
Published: about 4 years ago

10.1136/gutjnl-2019-318343

A blood-based prognostic biomarker in IBD
Cited by: 125
Author(s): Daniele Biasci, James C. Lee, Nurulamin M Noor, Diana R Pombal, Monica Hou, Nina Lewis, Tariq Ahmad, Ailsa Hart, Miles Parkes, Eoín McKinney, Paul Lyons, Kenneth G. C. Smith
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0012657

A Comprehensive and Universal Method for Assessing the Performance of Differential Gene Expression Analyses
Cited by: 13
Author(s): Mikhail G. Dozmorov, Joel M. Guthridge, Robert E. Hurst, Igor Dozmorov
Software Mentions: 6
Published: almost 14 years ago

10.1371/journal.pone.0132798

Partial Hepatectomy Induced Long Noncoding RNA Inhibits Hepatocyte Proliferation during Liver Regeneration
Cited by: 20
Author(s): Lulu Huang, Sagar S. Damle, Sheri Booten, Priyam Singh, Mahyar Sabripour, Jeff Hsu, Minji Jo, Melanie Katz, Andy Watt, Christopher E. Hart, Susan M. Freier, Brett P. Monia, Shuling Guo
Software Mentions: 6
Published: about 9 years ago

10.1186/s12915-018-0547-y

Species comparison of liver proteomes reveals links to naked mole-rat longevity and human aging
Cited by: 52
Author(s): Ivonne Heinze, Martin Bens, Enrico Calzia, Susanne Holtze, Oleksandr Dakhovnik, Arne Sahm, Joanna Kirkpatrick, Karol Szafranski, Natalie Romanov, Sai Nagender Sama, Kerstin Hölzer, Stephan Singer, Maria A. Ermolaeva, Matthias Platzer, Thomas B. Hildebrandt, Alessandro Ori
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pone.0053033

Differences in Transcription Patterns between Induced Pluripotent Stem Cells Produced from the Same Germ Layer Are Erased upon Differentiation
Cited by: 2
Author(s): Iryna Pirozhkova, Ana Barat, Petr Dmitriev, Elena Kim, Robert Thomas, Justine Guégan, Chrystèle Bilhou‐Nabera, Florence Busato, Jörg Tost, Gilles Carnac, Dalila Laoudj-Chenivesse, Marc Lipinski, Yegor S. Vassetzky
Software Mentions: 5
Published: over 11 years ago

10.1371/journal.pgen.1000302

The Chromosomal High-Affinity Binding Sites for the Drosophila Dosage Compensation Complex
Cited by: 171
Author(s): Tobias Straub, Charlotte Grimaud, Gregor D. Gilfillan, Angelika Mitterweger, Peter B. Becker
Software Mentions: 5
Published: over 15 years ago

10.1186/1471-2164-10-63

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes
Cited by: 16
Author(s): Steven P. Wilder, Pamela J. Kaisaki, Karène Argoud, Anita Salhan, Jiannis Ragoussis, Marie-Thérèse Bihoreau, Dominique Guyader
Software Mentions: 5
Published: over 15 years ago

10.1186/1756-0500-7-302

Assessment of a novel multi-array normalization method based on spike-in control probes suitable for microRNA datasets with global decreases in expression
Cited by: 9
Author(s): Alain Sewer, Sylvain Gubian, Ulrike Kogel, Emilija Veljkovic, Wanjiang Han, Arnd Hengstermann, Manuel C. Peitsch, Julia Hoeng
Software Mentions: 5
Published: about 10 years ago

10.3389/fimmu.2021.657162

Host Transcriptome and Microbiota Signatures Prior to Immunization Profile Vaccine Humoral Responsiveness
Cited by: 3
Author(s): Eléna Gonçalves, Yolanda Guillén, Javier R. Lama, Jorge Sánchez, Christian Berthou, Roger Paredes, Béhazine Combadière
Software Mentions: 5
Published: about 3 years ago

10.7717/peerj.4584

Empirical evaluation of data normalization methods for molecular classification
Cited by: 12
Author(s): Hsin‐Chieh Huang, Li‐Xuan Qin
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-016-1097-7

Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery
Cited by: 64
Author(s): Andrée Delahaye‐Duriez, Prashant K. Srivastava, Kirill Shkura, Sarah R. Langley, Liisi Laaniste, Aida Moreno‐Moral, Bénédicte Danis, Manuela Mazzuferi, Patrik Foerch, Elena V. Gazina, Kay Richards, Steven Petrou, Rafał M. Kamiński, Enrico Petretto, Michael R. Johnson
Software Mentions: 5
Published: over 7 years ago

10.1186/1471-2164-15-132

Major aging-associated RNA expressions change at two distinct age-positions
Cited by: 17
Author(s): Marius Gheorghe, M.M.J. Snoeck, Michael Emmerich, Thomas Bäck, Jelle J. Goeman, Vered Raz
Software Mentions: 5
Published: over 10 years ago

10.1186/1471-2164-11-32

Integrative analysis of the heat shock response in Aspergillus fumigatus
Cited by: 76
Author(s): Daniela Albrecht, Reinhard Guthke, Axel A. Brakhage, Olaf Kniemeyer
Software Mentions: 5
Published: over 14 years ago

10.1186/1471-2164-9-124

Can subtle changes in gene expression be consistently detected with different microarray platforms?
Cited by: 48
Author(s): Paola Pedotti, Peter A C ‘t Hoen, Erno Vreugdenhil, Geert J. Schenk, Rolf H. A. M. Vossen, Yavuz Ariyürek, Mattias de Hollander, Rowan Kuiper, G.J.B. van Ommen, Johan T. den Dunnen, Judith M. Boer, Renée X. de Menezes
Software Mentions: 5
Published: over 16 years ago

10.1371/journal.pone.0151335

Activation of Myenteric Glia during Acute Inflammation In Vitro and In Vivo
Cited by: 59
Author(s): Corinna Rosenbaum, Martin Alexander Schick, Jakob Wollborn, Andreas Heider, Claus‐Jürgen Scholz, Alexander Cecil, Beate Niesler, Johannes Hirrlinger, Heike Walles, Marco Metzger
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0035035

MAPK Signaling Determines Anxiety in the Juvenile Mouse Brain but Depression-Like Behavior in Adults
Cited by: 37
Author(s): Benedikt Wefers, Christiane Hitz, Sabine M. Hölter, Dietrich Trümbach, Jens Hansen, Peter Weber, Benno Pütz, Jan M. Deussing, Martin Hrabě de Angelis, Till Roenneberg, Fang Zheng, Christian Alzheimer, Alcino Silva, Wolfgang Wurst, Ralf Kühn
Software Mentions: 4
Published: over 12 years ago

10.1186/s13071-015-0974-3

Autophagic digestion of Leishmania major by host macrophages is associated with differential expression of BNIP3, CTSE, and the miRNAs miR-101c, miR-129, and miR-210
Cited by: 58
Author(s): Benjamin Frank, Ana Marcu, Antônio Luis de Oliveira Almeida Petersen, Heike Weber, Christian Stigloher, Jeremy C. Mottram, Claus‐Jürgen Scholz, Uta Schurigt
Software Mentions: 4
Published: almost 9 years ago

10.1186/s40246-019-0247-x

Transcriptomic analysis of monocytes from HIV-positive men on antiretroviral therapy reveals effects of tobacco smoking on interferon and stress response systems associated with depressive symptoms
Cited by: 6
Author(s): David R. Lorenz, Vikas Misra, Dana Gabuzda
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.22423

Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome
Cited by: 2
Author(s): Shana Claeys, Geertrui Denecker, Robrecht Cannoodt, Candy Kumps, Kaat Durinck, Franki Speleman, Katleen De Preter
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0034534

MicroRNA Dysregulation in the Spinal Cord following Traumatic Injury
Cited by: 113
Author(s): Mónica Yunta, Manuel Nieto‐Díaz, Francisco J. Esteban, Marcos Caballero-López, Rosa Navarro-Ruíz, David Reigada, D. Wolfgang Pita-Thomas, Ángela del Águila, Teresa Muñoz‐Galdeano, Rodrigo M. Maza
Software Mentions: 4
Published: over 12 years ago

10.1186/s12859-017-1501-7

Mixture model normalization for non-targeted gas chromatography/mass spectrometry metabolomics data
Cited by: 31
Author(s): Anna C. Reisetter, Michael J. Muehlbauer, James R. Bain, Michael Nodzenski, Robert Stevens, Olga Ilkayeva, Boyd E. Metzger, Christopher B. Newgard, William L. Lowe
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-021-87137-7

Distinct SARS-CoV-2 antibody reactivity patterns in coronavirus convalescent plasma revealed by a coronavirus antigen microarray
Cited by: 10
Author(s): Rafael de Assis, Aarti Jain, Rie Nakajima, Algis Jasinskas, Saahir Khan, Huw Davies, Laurence Corash, Larry J. Dumont, Kathleen Kelly, Graham Simmons, Mars Stone, Clara Di Germanio, Michael P. Busch, Philip L. Felgner
Software Mentions: 4
Published: over 3 years ago

10.15252/emmm.201505344

Characterization and quantification of proteins secreted by single human embryos prior to implantation
Cited by: 34
Author(s): Maurizio Poli, Alessandro Ori, Tim Child, S. Jaroudi, K Spath, Martin Beck, Dagan Wells
Software Mentions: 4
Published: almost 9 years ago

10.1186/1475-2859-10-18

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli
Cited by: 157
Author(s): Jeremy J. Minty, Ann A Lesnefsky, Fengming Lin, Yu Chen, Ted A. Zaroff, Artur Veloso, Bin Xie, Catie A McConnell, Rebecca J Ward, Donald R. Schwartz, Jean-Marie Rouillard, Yuan Gao, Erdogan Gülari, Xiaoxia Lin
Software Mentions: 4
Published: over 13 years ago

10.1074/mcp.RA117.000189

Spatial Tissue Proteomics Quantifies Inter- and Intratumor Heterogeneity in Hepatocellular Carcinoma (HCC)
Cited by: 63
Author(s): Katarzyna Buczak, Alessandro Ori, Joanna Kirkpatrick, Kerstin Hölzer, Daniel Dauch, Stephanie Roessler, Volker Endris, Felix Lasitschka, Luca Parca, Alexander Schmidt, Lars Zender, Peter Schirmacher, Jeroen Krijgsveld, Stephan Singer, Martin Beck
Software Mentions: 4
Published: over 6 years ago

10.15252/embj.2019102246

Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi‐enzyme complexes in <i>Escherichia coli</i>
Cited by: 61
Author(s): Manuel Banzhaf, Hamish C. L. Yau, Jolanda Verheul, Adam Lodge, George Kritikos, André Mateus, Baptiste Cordier, Ann Kristin Hov, Frank Stein, Morgane Wartel, Manuel Pazos, Alexandra S Solovyova, Eefjan Breukink, Sven van Teeffelen, Mikhail M. Savitski, Tanneke den Blaauwen, Athanasios Typas, Waldemar Vollmer
Software Mentions: 3
Published: over 4 years ago

10.1186/1756-0500-5-1

Peripheral blood gene expression: it all boils down to the RNA collection tubes
Cited by: 128
Author(s): Andreas Menke, Monika Rex‐Haffner, Torsten Klengel, Elisabeth B. Binder, Divya Mehta
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2105-6-265

Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
Cited by: 206
Author(s): Patrick Warnat, Roland Eils, Benedikt Brors
Software Mentions: 3
Published: over 18 years ago

10.1371/journal.pbio.2002690

Common genes associated with antidepressant response in mouse and man identify key role of glucocorticoid receptor sensitivity
Cited by: 26
Author(s): Tania Carrillo-Roa, Christiana Labermaier, Peter Weber, David P. Herzog, Caleb A. Lareau, Sara Santarelli, Klaus V. Wagner, Monika Rex‐Haffner, D. Harbich, Sebastian H. Scharf, Charles B. Nemeroff, Boadie W. Dunlop, W. Edward Craighead, Helen S. Mayberg, Mathias Schmidt, Manfred Uhr, Florian Holsboer, Inge Sillaber, Elisabeth B. Binder, Marianne B. Müller
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pgen.1007096

Role of co-repressor genomic landscapes in shaping the Notch response
Cited by: 13
Author(s): Stephen Kk Chan, Gustavo Cerda-Moya, Robert Stojnic, Kat Millen, Bettina Fischer, Silvie Fexová, Lenka Skalska, Maria J. Gomez-Lamarca, Zoe Pillidge, Steven Russell, Sarah Bray
Software Mentions: 3
Published: over 6 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: over 13 years ago

10.1371/journal.pone.0028402

Influence of 17β-Estradiol on Gene Expression of Paracoccidioides during Mycelia-to-Yeast Transition
Cited by: 40
Author(s): Jata Shankar, Thomas D. Wu, Karl V. Clemons, J. P. Monteiro, Laurence F. Mirels, David A. Stevens
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0051562

Prophylactic Valproic Acid Treatment Prevents Schizophrenia-Related Behaviour in Disc1-L100P Mutant Mice
Cited by: 23
Author(s): Tatiana V. Lipina, F. Nipa Haque, Alexander McGirr, Paul C. Boutros, Thorsten Berger, Tak W. Mak, John Roder, Albert H.C. Wong
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0011447

Identification of the Feline Humoral Immune Response to Bartonella henselae Infection by Protein Microarray
Cited by: 34
Author(s): Adam Vigil, Rocio Ortega, Aarti Jain, Rie Nakajima-Sasaki, Xiaolin Tan, Bruno B Chomel, Rickie W. Kasten, Jane E. Koehler, Philip L. Felgner
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0096615

Analysis of the Effects of Five Factors Relevant to In Vitro Chondrogenesis of Human Mesenchymal Stem Cells Using Factorial Design and High Throughput mRNA-Profiling
Cited by: 38
Author(s): Rune Bruhn Jakobsen, Esben Østrup, Xiaolan Zhang, Tarjei S. Mikkelsen, Jan E. Brinchmann
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0211180

Effect of Sec61 interaction with Mpd1 on endoplasmic reticulum-associated degradation
Cited by: 8
Author(s): Фернандо Лобо Перейра, Mandy Rettel, Frank Stein, Mikhail M. Savitski, Ian Collinson, Karin Römisch
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1003986

Alcohol-Induced Histone Acetylation Reveals a Gene Network Involved in Alcohol Tolerance
Cited by: 48
Author(s): Alfredo Ghezzi, Harish R. Krishnan, Linda Lew, Francisco J. Prado, Darryl S. Ong, Nigel S. Atkinson
Software Mentions: 2
Published: over 10 years ago

10.1038/s41598-018-24232-2

Translational study identifies XPF and MUS81 as predictive biomarkers for oxaliplatin-based peri-operative chemotherapy in patients with esophageal adenocarcinoma
Cited by: 8
Author(s): Thomas P. MacGregor, R Carter, Richard Gillies, John M. Findlay, Christiana Kartsonaki, Francesc Castro-Giner, Natasha Sahgal, L M Wang, Runjan Chetty, Nicholas Maynard, Jean‐Baptiste Cazier, Francesca M. Buffa, Peter J. McHugh, Ian Tomlinson, Mark R. Middleton, Ricky A. Sharma
Software Mentions: 2
Published: about 6 years ago

10.1186/1756-3305-7-290

Discovery of novel Schistosoma japonicum antigens using a targeted protein microarray approach
Cited by: 24
Author(s): Hamish E G McWilliam, Patrick Driguez, David Piedrafita, Donald P. McManus, Elza Nicole Theresia Meeusen
Software Mentions: 2
Published: over 10 years ago

10.1016/j.omtn.2018.11.017

Posttranscriptional Regulation of 14q32 MicroRNAs by the CIRBP and HADHB during Vascular Regeneration after Ischemia
Cited by: 21
Author(s): Angela Downie Ruiz Velasco, S. Welten, Eveline A. C. Goossens, Paul H.A. Quax, Juri Rappsilber, Gracjan Michlewski, A. Yaël Nossent
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0146570

Increased Skin Tumor Incidence and Keratinocyte Hyper-Proliferation in a Mouse Model of Down Syndrome
Cited by: 5
Author(s): Annan Yang, Duane Currier, Jennifer L. Poitras, Roger H. Reeves
Software Mentions: 2
Published: over 8 years ago

10.1186/1746-6148-9-12

Detection and comparison of microRNA expression in the serum of Doberman Pinschers with dilated cardiomyopathy and healthy controls
Cited by: 28
Author(s): Carola Steudemann, Stefan Bauersachs, Karin Weber, Gerhard Wess
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-7-59

Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays
Cited by: 280
Author(s): Yulei Wang, Cátálin Bárbácioru, Fiona Hyland, Wenming Xiao, Kathryn Hunkapiller, Julie Blake, Felix Hon-Wai Chan, C. Gonzalez, Lu Zhang, Raymond R. Samaha
Software Mentions: 2
Published: over 18 years ago

10.1186/1471-2164-15-460

Identification of candidate long non-coding RNAs in response to myocardial infarction
Cited by: 98
Author(s): Jennifer Zangrando, Lu Zhang, Mélanie Vausort, Fatiha Maskali, Pierre-Yves Marie, Daniel R. Wagner, Yvan Devaux
Software Mentions: 2
Published: about 10 years ago

10.1186/s12864-017-3641-6

Tissue and time specific expression pattern of interferon regulated genes in the chicken
Cited by: 17
Author(s): Susanne Röll, Stefan Härtle, Thomas Lütteke, Bernd Kaspers, Sonja Härtle
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2407-12-22

RNA expression patterns in serum microvesicles from patients with glioblastoma multiforme and controls
Cited by: 166
Author(s): Mikkel Noerholm, Leonora Balaj, Tobias Limperg, Afshin Salehi, Lin Zhu, Fred H. Hochberg, Xandra O. Breakefield, Bob S. Carter, Johan Skog
Software Mentions: 2
Published: over 12 years ago

10.18632/oncotarget.14683

Identification of microRNAs implicated in the late differentiation stages of normal B cells suggests a central role for miRNA targets ZEB1 and TP53
Cited by: 11
Author(s): Giorgio Malpeli, Stefano Barbi, Simona Zupo, Gabriele Tosadori, Giovanni Scardoni, Anna Bertolaso, Silvia Sartoris, Stefano Ugel, Caterina Vicentini, Matteo Fassan, Annalisa Adamo, Mauro Krampera, Maria Teresa Scupoli, Carlo M. Croce, Aldo Scarpa
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-46359-6

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

10.1186/s12974-015-0393-6

Fingolimod induces neuroprotective factors in human astrocytes
Cited by: 67
Author(s): Franziska Hoffmann, Johann Hofereiter, Heike Rübsamen, Johannes C. Melms, Sigrid C. Schwarz, Hans von Faber, Peter Weber, Benno Pütz, Verena Loleit, Frank Weber, Reinhard Hohlfeld, Edgar Meinl, Markus Krumbholz
Software Mentions: 2
Published: almost 9 years ago

10.15252/embr.201947723

Centriolar satellites are required for efficient ciliogenesis and ciliary content regulation
Cited by: 62
Author(s): Ezgi Odabasi, Şeref Gül, İbrahim Halil Kavaklı, Elif Nur Firat‐Karalar
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-213X-9-54

Smad4-dependent pathways control basement membrane deposition and endodermal cell migration at early stages of mouse development
Cited by: 48
Author(s): Ita Costello, Christine A. Biondi, Jennifer Taylor, Elizabeth K. Bikoff, Elizabeth J. Robertson
Software Mentions: 2
Published: almost 15 years ago

10.3390/ijms140611190

Angiotensin II Regulates microRNA-132/-212 in Hypertensive Rats and Humans
Cited by: 107
Author(s): Tilde V Eskildsen, Pia Jeppesen, Mikael Schneider, A. Yaël Nossent, Maria Boysen Sandberg, Pernille Hansen, Charlotte Harken Jensen, Morten Hartvig Hansen, Niels Marcussen, Lars Melholt Rasmussen, Peter Bie, Ditte Caroline Andersen, Søren Paludan Sheikh
Software Mentions: 2
Published: about 11 years ago

10.3389/fimmu.2021.599530

Dietary Inclusion of Black Soldier Fly (Hermetia Illucens) Larvae Meal and Paste Improved Gut Health but Had Minor Effects on Skin Mucus Proteome and Immune Response in Atlantic Salmon (Salmo Salar)
Cited by: 30
Author(s): Pabodha Weththasinghe, Leidy Lagos, Marcos Cortés, Jon Øvrum Hansen, Margareth Øverland
Software Mentions: 2
Published: over 3 years ago

10.1128/mSystems.00808-19

Systematic Localization of Escherichia coli Membrane Proteins
Cited by: 20
Author(s): Anna Sueki, Frank Stein, Mikhail M. Savitski, Joel Selkrig, Athanasios Typas
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-020-80941-7

Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients
Cited by: 8
Author(s): Teresa Rubio, Vicente Felipo, Sonia Tarazona, Roberta Pastorelli, Desamparados Escudero‐García, Joan Tosca, Amparo Urios, Ana Conesa, Carmina Montoliú
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-020-66713-3

Epstein-Barr virus reactivation in sepsis due to community-acquired pneumonia is associated with increased morbidity and an immunosuppressed host transcriptomic endotype
Cited by: 12
Author(s): Cyndi Goh, Katie L Burnham, Azim Ansari, Mariateresa de Cesare, Tanya Golubchik, Paula Hutton, Lauren Overend, Emma E Davenport, C. J. Hinds, Rory Bowden, Julian C. Knight
Software Mentions: 2
Published: about 4 years ago

10.1186/1471-2105-6-114

Cited by: 6
Author(s): Jianhua Ruan, Weixiong Zhang
Software Mentions: 2
Published: over 19 years ago

10.35248/0974-276x.19.12.496

Standardizing Proteomics Workflow for Liquid Chromatography-Mass Spectrometry: Technical and Statistical Considerations
Cited by: 12
Author(s): Sudhir Srivastava, Michael L. Merchant, Anil Rai, N. Shesh
Software Mentions: 1
Published: over 5 years ago

10.1186/1471-2105-6-234

Quality determination and the repair of poor quality spots in array experiments
Cited by: 5
Author(s): Brian D. M. Tom, Walter R. Gilks, Elizabeth T. Brooke‐Powell, James W. Ajioka
Software Mentions: 1
Published: almost 19 years ago

10.1186/1471-2105-11-207

G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
Cited by: 20
Author(s): Mario Fasold, Peter F. Stadler, Hans Binder
Software Mentions: 1
Published: over 14 years ago

10.1186/1471-2105-8-124

A full Bayesian hierarchical mixture model for the variance of gene differential expression
Cited by: 7
Author(s): Samuel Manda, Rebecca E. Walls, Mark S. Gilthorpe
Software Mentions: 1
Published: over 17 years ago

10.1186/1755-8794-7-4

Kinome and mRNA expression profiling of high-grade osteosarcoma cell lines implies Akt signaling as possible target for therapy
Cited by: 55
Author(s): Marieke L. Kuijjer, Brendy E.W.M. van den Akker, Riet Hilhorst, Monique Mommersteeg, Emilie P. Buddingh, Massimo Serra, Horst Bürger, Pancras C.W. Hogendoorn, Anne Marie Cleton-Jansen
Software Mentions: 1
Published: over 10 years ago

10.1186/s12874-015-0088-9

A measure of the impact of CV incompleteness on prediction error estimation with application to PCA and normalization
Cited by: 16
Author(s): Roman Hornung, Christoph Bernau, Caroline Truntzer, Rory Wilson, Thomas Städler, Anne‐Laure Boulesteix
Software Mentions: 1
Published: over 8 years ago

10.1042/BCJ20200627

Temporal modulation of the NF-κB RelA network in response to different types of DNA damage
Cited by: 10
Author(s): Amy E. Campbell, Catarina Franco, Ling-I Su, Emma K. Corbin, Simon Perkins, Anton Kalyuzhnyy, Andrew R. Jones, Philip Brownridge, Neil D. Perkins, Patrick A. Eyers
Software Mentions: 1
Published: over 3 years ago

10.1186/1756-3305-3-4

Schistosomiasis vaccine discovery using immunomics
Cited by: 60
Author(s): Patrick Driguez, Denise L. Doolan, Alex Loukas, Philip L. Felgner, Donald P. McManus
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0148173

Osteogenic Differentiation of MSC through Calcium Signaling Activation: Transcriptomics and Functional Analysis
Cited by: 92
Author(s): Federica Viti, Martina Landini, Alessandra Mezzelani, Loredana Petecchia, Luciano Milanesi, Silvia Scaglione
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0114617

Transcriptional Consequence and Impaired Gametogenesis with High-Grade Aneuploidy in Arabidopsis thaliana
Cited by: 6
Author(s): Kuan‐Lin Lo, Long‐Chi Wang, I-Ju Chen, Yuchen Liu, Mei‐Chu Chung, Wen Lo
Software Mentions: 1
Published: over 9 years ago

10.3390/cancers12113270

Integration and Comparison of Transcriptomic and Proteomic Data for Meningioma
Cited by: 7
Author(s): Jemma Dunn, Vasileios Panagiotis Lenis, David A. Hilton, Rolf Warta, Christel Herold‐Mende, C. Oliver Hanemann, Matthias E. Futschik
Software Mentions: 1
Published: over 3 years ago

10.1186/s12014-018-9218-9

Identification of Cytauxzoon felis antigens via protein microarray and assessment of expression library immunization against cytauxzoonosis
Cited by: 9
Author(s): Megan E. Schreeg, Henry S. Marr, Jaime L. Tarigo, Meredith K. Sherrill, Hilton Outi, Elizabeth H. Scholl, David Bird, Adam Vigil, Christopher Hung, Rie Nakajima, Li Liang, Angela Trieu, Denise L. Doolan, Jennifer E. Thomas, Michael G. Levy, Mason V. Reichard, Phil Felgner, Leah A. Cohn, Adam J. Birkenheuer
Software Mentions: 1
Published: over 5 years ago

10.1186/1756-8935-2-1

High-resolution mapping of heterochromatin redistribution in a Drosophila position-effect variegation model
Cited by: 41
Author(s): Maartje J. Vogel, Ludo Pagie, Wendy Talhout, Marja Nieuwland, Ron Kerkhoven, Bas van Steensel
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2005-6-11-r96

Cited by: 37
Author(s): Francis D. Gibbons, Markus Proft, Kevin Struhl, Frederick P. Roth
Software Mentions: 1
Published: over 19 years ago

10.18632/oncotarget.25707

MYC-related microRNAs signatures in non-Hodgkin B-cell lymphomas and their relationships with core cellular pathways
Cited by: 11
Author(s): Giorgio Malpeli, Stefano Barbi, Gabriele Tosadori, Corinna Greco, Simona Zupo, Serena Pedron, Matteo Brunelli, Anna Bertolaso, Maria Teresa Scupoli, Mauro Krampera, Paul Takam Kamga, Carlo M. Croce, George A. Calin, Aldo Scarpa, Alberto Zamò
Software Mentions: 1
Published: about 6 years ago

10.1152/ajpendo.00637.2012

A role for thioredoxin-interacting protein (Txnip) in cellular creatine homeostasis
Cited by: 12
Author(s): Sevasti Zervou, Tanmoy Ray, Natasha Sahgal, Liam Sebag-Montefiore, Rebecca Cross, Debra J. Medway, Philip J. Ostrowski, Stefan Neubauer, Craig A. Lygate
Software Mentions: 1
Published: about 11 years ago

Projects: bioconductor: vsn

Papers Mentioning vsn 91