bioconductor: AnnotationDbi | Projects

10.12688/f1000research.17824.2

Enhancing gene set enrichment using networks
Cited by: 2
Author(s): Michael Prummer
Software Mentions: 51
Published: over 5 years ago

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: almost 16 years ago

BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Cited by: 20
Author(s): Andrea Komljenović, Julien Roux, Julien Wollbrett, Marc Robinson‐Rechavi, Frederic Bastian
Software Mentions: 33
Published: over 6 years ago

10.3390/biology3010085

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms
Cited by: 17
Author(s): Frank Krämer, Michaela Bayerlová, Tim Beißbarth
Software Mentions: 28
Published: almost 11 years ago

10.1016/j.xcrm.2020.100096

Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV Infection
Cited by: 11
Author(s): Sean M. Hughes, Claire Levy, Fernanda Calienes, Joanne D. Stekler, Urvashi Pandey, Lucia Vojtech, Alicia R. Berard, Kenzie Birse, Laura Noël‐Romas, Brian Richardson, Jackelyn B. Golden, Michael Cartwright, Ann C. Collier, Claire E. Stevens, Marcel E. Curlin, Timothy H. Holtz, Nelly Mugo, Elizabeth Irungu, Elly Katabira, Timothy Muwonge, Javier R. Lama, Jared M. Baeten, Adam Burgener, Jairam R. Lingappa, M. Juliana McElrath, Romel D. Mackelprang, Ian McGowan, Ross D. Cranston, Mark J. Cameron, Florian Hladik
Software Mentions: 21
Published: about 4 years ago

10.3389/fgene.2019.00499

ABioTrans: A Biostatistical Tool for Transcriptomics Analysis
Cited by: 6
Author(s): Zou Yutong, Thuy Tien Bui, Kumar Selvarajoo
Software Mentions: 17
Published: over 5 years ago

10.1186/s12864-021-07370-2

GCSscore: an R package for differential gene expression analysis in Affymetrix/Thermo-Fisher whole transcriptome microarrays
Cited by: 3
Author(s): Guy M. Harris, Shahroze Abbas, Michael F. Miles
Software Mentions: 17
Published: almost 4 years ago

10.1186/s12859-015-0453-z

MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis
Cited by: 41
Author(s): Koki Tsuyuzaki, Gota Morota, Manabu Ishii, Takeru Nakazato, Satoru Miyazaki, Itoshi Nikaido
Software Mentions: 13
Published: almost 10 years ago

10.12688/f1000research.19236.3

Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures
Cited by: 11
Author(s): Dharmesh D. Bhuva, Momeneh Foroutan, Yi Xie, Ruqian Lyu, Joseph Cursons, Melissa J. Davis
Software Mentions: 13
Published: about 5 years ago

10.3389/fgene.2018.00278

RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses (Equus caballus) and Cattle (Bos taurus)
Cited by: 11
Author(s): Carolina N. Correia, Kirsten E. McLoughlin, Nicolas C. Nalpas, David A. Magee, John A. Browne, Kévin Rue-Albrecht, Stephen V. Gordon, David E. MacHugh
Software Mentions: 12
Published: over 6 years ago

10.1186/1756-0500-3-10

A collection of bioconductor methods to visualize gene-list annotations
Cited by: 46
Author(s): Gang Feng, Pan Du, Nancy L. Krett, Michael A. Tessel, Steven T. Rosen, Warren A. Kibbe, Simon Lin
Software Mentions: 11
Published: almost 15 years ago

10.12688/f1000research.7035.1

RNA-Seq workflow: gene-level exploratory analysis and differential expression
Cited by: 253
Author(s): Michael I. Love, Simon Anders, Vladislav Kim, Wolfgang Huber
Software Mentions: 9
Published: about 9 years ago

10.1038/s41598-021-98542-3

A differential DNA methylome signature of pulmonary immune cells from individuals converting to latent tuberculosis infection
Cited by: 11
Author(s): Lovisa Karlsson, Jyotirmoy Das, Moa Nilsson, Amanda Tyrén, Isabelle Pehrson, Nina Idh, Shumaila Sayyab, Jakob Paues, César Ugarte-Gil, Melissa Méndez-Aranda, Maria Lerm
Software Mentions: 9
Published: about 3 years ago

10.18632/aging.202956

Gene expression profiles for an immunoscore model in bone and soft tissue sarcoma
Cited by: 5
Author(s): Jingyuan Fan, Xinyi Qin, Rong‐Quan He, Jie Ma, Qingjun Wei
Software Mentions: 9
Published: over 3 years ago

10.3389/fendo.2020.554922

Chenodeoxycholic Acid Modulates Bile Acid Synthesis Independent of Fibroblast Growth Factor 19 in Primary Human Hepatocytes
Cited by: 6
Author(s): H Johansson, Jonas Nørskov Søndergaard, Carl Jorns, Claudia Kutter, Ewa Ellis
Software Mentions: 9
Published: almost 4 years ago

10.1186/s12859-020-03910-x

multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data
Cited by: 48
Author(s): Sebastian Canzler, Jörg Hackermüller
Software Mentions: 9
Published: almost 4 years ago

10.7554/eLife.64919

Tissue-autonomous immune response regulates stress signaling during hypertrophy
Cited by: 11
Author(s): Robert Krautz, Dilan Khalili, Ulrich Theopold
Software Mentions: 8
Published: almost 4 years ago

10.1186/1471-2164-12-507

Chipster: user-friendly analysis software for microarray and other high-throughput data
Cited by: 294
Author(s): M Aleksi Kallio, Jarno Tuimala, Taavi Hupponen, Petri Klemelä, Massimiliano Gentile, Ilari Scheinin, M.K. Koski, Janne Käki, Eija Korpelainen
Software Mentions: 8
Published: about 13 years ago

10.1038/srep38411

Distinct epigenomes in CD4+ T cells of newborns, middle-ages and centenarians
Cited by: 34
Author(s): Ming Zhao, Jian Qin, Hang Yin, Yixin Tan, Wei Liao, Qian Liu, Shuangyan Luo, Min He, Gongping Liang, Yajing Shi, Qing Zhang, Wenjun Cai, Guangliang Yin, Yin Zhou, Jing Wang, Mengying Li, Yi Huang, Aiyun Liu, Haijian Wu, Zhiyong Zhang, Qianjin Lu
Software Mentions: 8
Published: almost 8 years ago

10.1093/bioinformatics/btz031

ensembldb: an R package to create and use Ensembl-based annotation resources
Cited by: 76
Author(s): Johannes Michael Rainer, Laurent Gatto, Christian X. Weichenberger
Software Mentions: 7
Published: almost 6 years ago

10.1038/s41598-021-92036-y

Capitalizing on transcriptome profiling to optimize and identify targets for promoting early murine folliculogenesis in vitro
Cited by: 6
Author(s): Andrea Jones, Beatriz Peñalver Bernabé, Vasantha Padmanabhan, Jun Li, Ariella Shikanov
Software Mentions: 7
Published: over 3 years ago

10.1186/1471-2164-15-452

Gene co-expression network analysis identifies porcine genes associated with variation in Salmonella shedding
Cited by: 52
Author(s): Arun Kommadath, Hua Bao, Adriano S. Arantes, Graham Plastow, Christopher K. Tuggle, Shawn M. D. Bearson, Le Luo Guan, Paul Stothard
Software Mentions: 7
Published: over 10 years ago

10.1038/s41598-017-05927-4

Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity
Cited by: 35
Author(s): Handan Melike Dönertaş, Hamit İzgi, Altuğ Kamacıoğlu, Zhisong He, Philipp Khaitovich, Mehmet Somel
Software Mentions: 7
Published: over 7 years ago

10.3389/fimmu.2021.729217

Timing of Transcriptomic Peripheral Blood Mononuclear Cell Responses of Sheep to Fasciola hepatica Infection Differs From Those of Cattle, Reflecting Different Disease Phenotypes
Cited by: 4
Author(s): Dagmara A. Niedziela, Amalia Naranjo‐Lucena, Verónica Molina-Hernández, John A. Browne, Á. Martínez-Moreno, J. Pérez, David E. MacHugh, Grace Mulcahy
Software Mentions: 6
Published: about 3 years ago

10.1186/s12859-019-2840-3

m6Acomet: large-scale functional prediction of individual m6A RNA methylation sites from an RNA co-methylation network
Cited by: 30
Author(s): Xiangyu Wu, Zhen Wei, Kunqi Chen, Qing Zhang, Jionglong Su, Hui Liu, Lin Zhang, Jia Meng
Software Mentions: 6
Published: over 5 years ago

10.1186/s12885-021-08711-w

Construction of a ceRNA network of hub genes affecting immune infiltration in ovarian cancer identified by WGCNA
Cited by: 12
Author(s): Rongjia Su, Chengjuan Jin, Lina Zhou, Yannan Cao, Menghua Kuang, Linxia Li, Jianbin Xiang
Software Mentions: 6
Published: about 3 years ago

10.1186/s12918-018-0620-8

Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin
Cited by: 11
Author(s): Theresia Conrad, Olaf Kniemeyer, Sebastian Henkel, Thomas Krüger, Derek J. Mattern, Vito Valiante, Reinhard Guthke, Ilse D. Jacobsen, Axel A. Brakhage, Sebastian Vlaic, Jörg Linde
Software Mentions: 6
Published: about 6 years ago

10.3390/v11010053

Proteogenomics Uncovers Critical Elements of Host Response in Bovine Soft Palate Epithelial Cells Following In Vitro Infection with Foot-And-Mouth Disease Virus
Cited by: 13
Author(s): Florian Pfaff, Sara Hägglund, Martina Zoli, Sandra Blaise‐Boisseau, Eve Laloy, Susanne Koethe, Daniela Zühlke, Katharina Riedel, Stéphan Zientara, Labib Bakkali‐Kassimi, J. F. Valarcher, Dirk W. Höper, Martin Beer, Michael Eschbaumer
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.pgen.1009737

Corticosterone pattern-dependent glucocorticoid receptor binding and transcriptional regulation within the liver
Cited by: 9
Author(s): Benjamin P. Flynn, Matthew T. Birnie, Yvonne M. Kershaw, Audrys G Pauža, Sohyoung Kim, Songjoon Baek, Mark F. Rogers, Alex Paterson, Diana A. Stavreva, David Murphy, Gordon L. Hager, Stafford Lightman, Becky Conway-Campbell
Software Mentions: 6
Published: over 3 years ago

10.3389/fimmu.2020.606338

Specific Induction of Double Negative B Cells During Protective and Pathogenic Immune Responses
Cited by: 33
Author(s): Christoph Ruschil, Gisela Gabernet, Gildas Lepennetier, Simon Heumos, Miriam Kaminski, Zsuzsanna Hracskó, Martin Irmler, Johannes Beckers, Ulf Ziemann, Sven Nahnsen, Gregory P. Owens, Jeffrey L. Bennett, Bernhard Hemmer, Markus C. Kowarik
Software Mentions: 6
Published: almost 4 years ago

10.1016/j.stemcr.2017.09.018

Laser Capture and Deep Sequencing Reveals the Transcriptomic Programmes Regulating the Onset of Pancreas and Liver Differentiation in Human Embryos
Cited by: 33
Author(s): Rachel Jennings, Andrew Berry, Dave T. Gerrard, Stephen J. Wearne, James Strutt, Sarah Withey, Mariya Chhatriwala, Karen Piper Hanley, Ludovic Vallier, Nicoletta Bobola, Neil A. Hanley
Software Mentions: 6
Published: about 7 years ago

10.3390/cancers12102769

Identification of Genes Whose Expression Overlaps Age Boundaries and Correlates with Risk Groups in Paediatric and Adult Acute Myeloid Leukaemia
Cited by: 6
Author(s): Lindsay Davis, Ken Mills, Kim Orchard, Barbara Guinn
Software Mentions: 5
Published: about 4 years ago

10.1186/s12864-015-1820-x

PhosphOrtholog: a web-based tool for cross-species mapping of orthologous protein post-translational modifications
Cited by: 19
Author(s): Rima Chaudhuri, Arash Sadrieh, Nolan J. Hoffman, Benjamin L. Parker, Sean J. Humphrey, Jacqueline Stöckli, Adam P. Hill, David E. James, Jean Yee Hwa Yang
Software Mentions: 5
Published: over 9 years ago

10.18632/oncotarget.23748

Use of deep neural network ensembles to identify embryonic-fetal transition markers: repression of <i>COX7A1</i> in embryonic and cancer cells
Cited by: 27
Author(s): Michael West, Ivan Labat, Hal Sternberg, Dana Larocca, Igor O. Nasonkin, Karen Chapman, Ratnesh Singh, Eugene Makarev, Alex Aliper, Andrey Kazennov, Andrey Alekseenko, Nikolai Shuvalov, Evgenia Cheskidova, Aleksandr Alekseev, Artemov Av, Evgeny Putin, Polina Mamoshina, Nikita Pryanichnikov, Jacob Larocca, Karen A. F. Copeland, Evgeny Izumchenko, Mikhail Korzinkin, Alex Zhavoronkov
Software Mentions: 5
Published: almost 7 years ago

10.3390/ijms21020471

The Influence of Met Receptor Level on HGF-Induced Glycolytic Reprogramming in Head and Neck Squamous Cell Carcinoma
Cited by: 17
Author(s): Verena Boschert, Nicola Klenk, Alexander Abt, Sudha Janaki Raman, Markus Fischer, Roman C. Brands, Axel Seher, Christian Linz, Urs Müller‐Richter, Thorsten Bischler, Stefan Hartmann
Software Mentions: 5
Published: almost 5 years ago

10.1016/j.devcel.2018.10.004

SETDB1 Links the Meiotic DNA Damage Response to Sex Chromosome Silencing in Mice
Cited by: 60
Author(s): Takayuki Hirota, Paul Blakeley, Mahesh N. Sangrithi, Shantha K. Mahadevaiah, Vesela Encheva, Ambrosius P. Snijders, Elias ElInati, Obah A. Ojarikre, Dirk G. de Rooij, Kathy K. Niakan, James M. A. Turner
Software Mentions: 5
Published: almost 6 years ago

10.3390/genes11121430

Distinct Myocardial Transcriptomic Profiles of Cardiomyopathies Stratified by the Mutant Genes
Cited by: 7
Author(s): Katharina Sielemann, Zaher Elbeck, Anna Gärtner, Hendrik Milting, Caroline Stanasiuk, Henrik Fox, Lech Paluszkiewicz, Jens Tiesmeier, Stefan Wlost, Jan Gummert, Stefan P. Albaum, Janik Sielemann, Ralph Knöll
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12864-016-2851-7

The application of transcriptomic data in the authentication of beef derived from contrasting production systems
Cited by: 6
Author(s): T. Sweeney, Alexandre Lejeune, A.P. Moloney, Frank J. Monahan, Paul M Gettigan, Gérard Downey, Stephen D. E. Park, M. F. Ryan
Software Mentions: 5
Published: about 8 years ago

10.3390/cancers13010027

Inflammatory Proteins HMGA2 and PRTN3 as Drivers of Vulvar Squamous Cell Carcinoma Progression
Cited by: 12
Author(s): Agnieszka Fatalska, Natalia Rusetska, Elwira Bakuła‐Zalewska, Artur Kowalik, Sebastian Zięba, Agnieszka Wroblewska, Kamil Zalewski, Krzysztof Goryca, Dominik Domański, Magdalena Kowalewska
Software Mentions: 5
Published: almost 4 years ago

10.1186/s40709-020-00118-1

Genome wide meta-analysis of cDNA datasets reveals new target gene signatures of colorectal cancer based on systems biology approach
Cited by: 11
Author(s): Umair Ilyas, Shahiq uz Zaman, Reem Altaf, Humaira Nadeem, Syed Aun Muhammad
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0014782

Genome-Wide Footprints of Pig Domestication and Selection Revealed through Massive Parallel Sequencing of Pooled DNA
Cited by: 122
Author(s): Andreia J. Amaral, Luca Ferretti, Hendrik‐Jan Megens, R.P.M.A. Crooijmans, Haisheng Nie, Sebastián E. Ramos-Onsins, Miguel Pérez‐Enciso, Lawrence B. Schook, Martien A. M. Groenen
Software Mentions: 4
Published: over 13 years ago

10.1186/1471-2229-14-97

ARACNe-based inference, using curated microarray data, of Arabidopsis thaliana root transcriptional regulatory networks
Cited by: 35
Author(s): Ricardo A. Chávez Montes, Gerardo Coello, Karla L. González-Aguilera, Nayelli Marsch-Martínez, Stefan de Folter, Elena Álvarez-Buylla
Software Mentions: 4
Published: over 10 years ago

10.3389/fpls.2019.00603

Analysis of Key Genes Involved in Potato Anthocyanin Biosynthesis Based on Genomics and Transcriptomics Data
Cited by: 13
Author(s): Nie Tengkun, Dongdong Wang, Xiaoyan Ma, Yue Chen, Qin Chen
Software Mentions: 4
Published: over 5 years ago

10.15252/msb.20145141

Intercellular network structure and regulatory motifs in the human hematopoietic system
Cited by: 56
Author(s): Wenlian Qiao, Weijia Wang, Elisa Laurenti, Andrei L. Turinsky, Shoshana J. Wodak, Gary D. Bader, John E. Dick, Peter W. Zandstra
Software Mentions: 4
Published: over 10 years ago

10.3389/fnins.2017.00112

Antidyskinetic Effects of MEK Inhibitor Are Associated with Multiple Neurochemical Alterations in the Striatum of Hemiparkinsonian Rats
Cited by: 21
Author(s): Guiqin Chen, Shuke Nie, Chao Han, Kai Ma, Xu Yan, Zhentao Zhang, Stella M. Papa, Xin Cao
Software Mentions: 4
Published: over 7 years ago

10.3389/fphar.2021.618773

Combination of Ginsenosides Rb2 and Rg3 Promotes Angiogenic Phenotype of Human Endothelial Cells via PI3K/Akt and MAPK/ERK Pathways
Cited by: 12
Author(s): Ran Joo Choi, Siti Zuraidah Mohamad Zobir, Benjamin Alexander-Dann, Naomi L. Sharma, Kenneth L. Marcella, Brian Lam, Giles S.H. Yeo, Guoqing Zhang, Tai-Ping Fan, Andreas Bender
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-019-2656-1

Gsslasso Cox: a Bayesian hierarchical model for predicting survival and detecting associated genes by incorporating pathway information
Cited by: 13
Author(s): Zaixiang Tang, Shu‐Feng Lei, Xinyan Zhang, Zixuan Yi, Boyi Guo, Jake Y. Chen, Yueping Shen, Nengjun Yi
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms17091426

Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs
Cited by: 26
Author(s): Julia Welzenbach, Christiane Neuhoff, Hanna Heidt, Mehmet Ulaş Çınar, Christian Looft, K. Schellander, Ernst Tholen, Christine Große‐Brinkhaus
Software Mentions: 4
Published: about 8 years ago

10.1186/1471-2164-10-373

Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers
Cited by: 170
Author(s): Xinxia Peng, Li Yu, Kathie–Anne Walters, Elizabeth Rosenzweig, Sharon Lederer, Lauri Aicher, Sean Proll, Michael G. Katze
Software Mentions: 4
Published: over 15 years ago

10.1371/journal.pone.0183679

Multidimensional pooled shRNA screens in human THP-1 cells identify candidate modulators of macrophage polarization
Cited by: 31
Author(s): Ewa Surdziel, Ieuan Clay, Florian Nigsch, Anke Thiemeyer, Cyril Allard, Gregory R. Hoffman, John S. Reece‐Hoyes, Tanushree Phadke, Romain Gambert, Caroline Gubser Keller, Marie-Gabrielle Ludwig, Birgit Baumgarten, Mathias Frederiksen, Dirk Schübeler, Klaus Seuwen, Tewis Bouwmeester, Barna D. Fodor
Software Mentions: 4
Published: over 7 years ago

10.1186/1753-6561-3-S4-S9

Microarray data mining using Bioconductor packages
Cited by: 8
Author(s): Haisheng Nie, Pieter Neerincx, Jan van der Poel, Francesco Ferrari, Silvio Bicciato, Jack A. M. Leunissen, Martien A. M. Groenen
Software Mentions: 4
Published: over 15 years ago

10.15252/msb.156240

Extensive allele‐specific translational regulation in hybrid mice
Cited by: 30
Author(s): Jingyi Hou, Xi Wang, Erik McShane, Henrik Zauber, Wei Sun, Matthias Selbach, Wei Chen
Software Mentions: 3
Published: over 9 years ago

10.1242/dev.161034

Neural stem cell quiescence and stemness are molecularly distinct outputs of the Notch3 signaling cascade in the vertebrate adult brain
Cited by: 61
Author(s): Emmanuel Than‐Trong, Sara Ortica-Gatti, Sébastien Mella, Chirag Nepal, Alessandro Alunni, Laure Bally‐Cuif
Software Mentions: 3
Published: almost 7 years ago

10.1042/BSR20202346

Identification of novel biomarkers involved in pulmonary arterial hypertension based on multiple-microarray analysis
Cited by: 18
Author(s): Yi Ma, Shu Shu Chen, Yan Feng, Huan Liang Wang
Software Mentions: 3
Published: about 4 years ago

10.3389/fendo.2020.00138

Developmentally Driven Changes in Adipogenesis in Different Fat Depots Are Related to Obesity
Cited by: 10
Author(s): Jana Breitfeld, Stephanie Kehr, Luise Müller, Peter F. Stadler, Yvonne Böttcher, Matthias Blüher, Michael Stümvoll, Peter Kovacs
Software Mentions: 3
Published: over 4 years ago

10.1186/s12916-015-0282-y

Multi-omic signature of body weight change: results from a population-based cohort study
Cited by: 58
Author(s): Simone Wahl, Susanne Vogt, Ferdinand Stückler, Jan Krumsiek, Jörg Bartel, Tim Kacprowski, Katharina Schramm, Maren Carstensen, Wolfgang Rathmann, Michael Roden, Carolin Jourdan, Antti J. Kangas, Pasi Soininen, Mika Ala‐Korpela, Ute Nöthlings, Heiner Boeing, Fabian J. Theis, Christa Meisinger, Mélanie Waldenberger, Karsten Suhre, Georg Homuth, Christian Gieger, Gabi Kastenmüller, Thomas Illig, Jakob Linseisen, Annette Peters, Holger Prokisch, Christian Herder, Barbara Thorand, Harald Grallert
Software Mentions: 3
Published: over 9 years ago

10.1186/s40709-019-0094-x

A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in alopecia
Cited by: 10
Author(s): Syed Aun Muhammad, Nighat Fatima, Rehan Zafar Paracha, Amjad Ali, Jake Y. Chen
Software Mentions: 3
Published: over 5 years ago

10.1186/s40709-021-00136-7

Genome-scale meta-analysis of breast cancer datasets identifies promising targets for drug development
Cited by: 5
Author(s): Reem Altaf, Humaira Nadeem, Mustafeez Mujtaba Babar, Umair Ilyas, Syed Aun Muhammad
Software Mentions: 3
Published: almost 4 years ago

10.1038/srep26020

The N-end rule pathway regulates pathogen responses in plants
Cited by: 37
Author(s): Rémi de Marchi, Maud Sorel, Brian Mooney, Isabelle Fudal, Kevin Goslin, Kamila Kwaśniewska, Patrick T. Ryan, Marina Pfalz, Juergen Kroymann, Stephan Pollmann, Angela Feechan, Frank Wellmer, Susana Rivas, Emmanuelle Graciet
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.46711

Embryo polarity in moth flies and mosquitoes relies on distinct old genes with localized transcript isoforms
Cited by: 23
Author(s): Yoseop Yoon, Jeff Klomp, Inés Martín-Martín, Frank Criscione, Eric Calvo, José M. C. Ribeiro, Urs Schmidt‐Ott
Software Mentions: 3
Published: about 5 years ago

10.1074/mcp.TIR119.001481

Nonparametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-binding Proteins*
Cited by: 63
Author(s): Dorothee Childs, Karsten Bach, Holger Franken, Simon Anders, Nils Kurzawa, Marcus Bantscheff, Mikhail M. Savitski, Wolfgang Huber
Software Mentions: 2
Published: almost 5 years ago

10.1186/1471-2105-11-214

Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis
Cited by: 38
Author(s): Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Mizutani, Kazuki Saito, Masanori Arita
Software Mentions: 2
Published: over 14 years ago

10.26508/lsa.201900495

Conservation of cell-intrinsic immune responses in diverse nonhuman primate species
Cited by: 6
Author(s): Jenna M. Gaska, Lance Parsons, Metodi Balev, Ann Cirincione, Wei Wang, Robert E. Schwartz, Alexander Ploß
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0021503

siRNA Off-Target Effects Can Be Reduced at Concentrations That Match Their Individual Potency
Cited by: 75
Author(s): Daniel R. Caffrey, Juan Zhao, Zhili Song, Michael Schäffer, Steven Haney, Romesh R. Subramanian, Albert B. Seymour, Jason D. Hughes
Software Mentions: 2
Published: over 13 years ago

10.15252/msb.20166941

Pervasive isoform‐specific translational regulation via alternative transcription start sites in mammals
Cited by: 78
Author(s): Xi Wang, Jingyi Hou, Claudia Quedenau, Wei Chen
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2014.00331

Characterizing the human hematopoietic CDome
Cited by: 8
Author(s): Mike Bogetofte Barnkob, Christian Simon, Lars Rønn Olsen
Software Mentions: 1
Published: about 10 years ago

10.1186/1753-6561-3-S4-S1

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis
Cited by: 7
Author(s): Pieter Neerincx, Pierrot Casel, Dennis Prickett, Haisheng Nie, Michael Watson, Jack A. M. Leunissen, Martien A. M. Groenen, Christophe Klopp
Software Mentions: 1
Published: over 15 years ago

10.3389/fbioe.2020.00255

Mining Data From Plasma Cell Differentiation Identified Novel Genes for Engineering of a Yeast Antibody Factory
Cited by: 2
Author(s): Essi V. Koskela, Alina Gonzalez Salcedo, Mari A. Piirainen, Heidi A. Iivonen, Heidi Salminen, Alexander D. Frey
Software Mentions: 1
Published: over 4 years ago

10.1186/s13040-021-00263-w

Personalized single-cell networks: a framework to predict the response of any gene to any drug for any patient
Cited by: 2
Author(s): Haripriya Harikumar, Thomas P. Quinn, Santu Rana, Sunil Gupta, Svetha Venkatesh
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-14-242

GOParGenPy: a high throughput method to generate Gene Ontology data matrices
Cited by: 5
Author(s): Ajay Kumar, Liisa Holm, Petri Törönen
Software Mentions: 1
Published: over 11 years ago

10.1038/s41419-020-2253-2

Frataxin deficiency induces lipid accumulation and affects thermogenesis in brown adipose tissue
Cited by: 41
Author(s): Riccardo Turchi, Flavia Tortolici, Giulio Guidobaldi, Federico Iacovelli, Mattia Falconi, Stefano Rufini, Raffaella Faraonio, Viviana Casagrande, Massimo Federici, L. De Angelis, Simone Carotti, Maria Francesconi, Maria Zingariello, Sergio Morini, Roberta Bernardini, Maurizio Mattei, Piergiorgio La Rosa, Fiorella Piemonte, Daniele Lettieri Barbato, Katia Aquilano
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0098237

Fetal Exposure to Maternal Inflammation Does Not Affect Postnatal Development of Genetically-Driven Ileitis and Colitis
Cited by: 6
Author(s): Jana Hemmerling, Katharina Heller, Gabriele Hörmannsperger, Monika Bazanella, Thomas Clavel, George Kollias, Dirk Haller
Software Mentions: 1
Published: over 10 years ago

Projects: bioconductor: AnnotationDbi

Papers Mentioning AnnotationDbi 73