Venkata Satagopam - Publications

Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 

48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Alper P, Dĕd V, Herzinger S, Grouès V, Peter S, Lebioda J, Ebermann L, Popleteeva M, Barry ND, Welter D, Ghosh S, Becker R, Schneider R, Gu W, Trefois C, ... Satagopam V, et al. DS-PACK: Tool assembly for the end-to-end support of controlled access human data sharing. Scientific Data. 11: 501. PMID 38750048 DOI: 10.1038/s41597-024-03326-9  0.47
2024 Vega C, Ostaszewski M, Grouès V, Schneider R, Satagopam V. BioKC: a collaborative platform for curation and annotation of molecular interactions. Database : the Journal of Biological Databases and Curation. 2024. PMID 38537198 DOI: 10.1093/database/baae013  0.475
2024 Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, ... ... Satagopam V, et al. Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology. 14: 1282859. PMID 38414974 DOI: 10.3389/fimmu.2023.1282859  0.421
2023 Acencio ML, Ostaszewski M, Mazein A, Rosenstiel P, Aden K, Mishra N, Andersen V, Sidiropoulos P, Banos A, Filia A, Rahmouni S, Finckh A, Gu W, Schneider R, Satagopam V. The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease. Frontiers in Immunology. 14: 1257321. PMID 38022524 DOI: 10.3389/fimmu.2023.1257321  0.444
2023 Gawron P, Hoksza D, Piñero J, Peña-Chilet M, Esteban-Medina M, Fernandez-Rueda JL, Colonna V, Smula E, Heirendt L, Ancien F, Groues V, Satagopam VP, Schneider R, Dopazo J, Furlong LI, et al. Visualization of automatically combined disease maps and pathway diagrams for rare diseases. Frontiers in Bioinformatics. 3: 1101505. PMID 37502697 DOI: 10.3389/fbinf.2023.1101505  0.485
2023 Mazein A, Acencio ML, Balaur I, Rougny A, Welter D, Niarakis A, Ramirez Ardila D, Dogrusoz U, Gawron P, Satagopam V, Gu W, Kremer A, Schneider R, Ostaszewski M. A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance. Frontiers in Bioinformatics. 3: 1197310. PMID 37426048 DOI: 10.3389/fbinf.2023.1197310  0.467
2023 Vega C, Schneider R, Satagopam V. Analysis: Flawed Datasets of Monkeypox Skin Images. Journal of Medical Systems. 47: 37. PMID 36933065 DOI: 10.1007/s10916-023-01928-1  0.385
2022 Vega C, Gawron P, Lebioda J, Grouès V, Matyjaszczyk P, Pauly C, Smula E, Krüger R, Schneider R, Satagopam V. Smart Scheduling (SMASCH): multi-appointment scheduling system for longitudinal clinical research studies. Jamia Open. 5: ooac038. PMID 35651522 DOI: 10.1093/jamiaopen/ooac038  0.384
2021 Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, ... ... Satagopam V, et al. COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology. 17: e10851. PMID 34939300 DOI: 10.15252/msb.202110851  0.401
2021 Kratochvíl M, Heirendt L, Wilken SE, Pusa T, Arreckx S, Noronha A, van Aalst M, Satagopam VP, Ebenhöh O, Schneider R, Trefois C, Gu W. COBREXA.jl: constraint-based reconstruction and exascale analysis. Bioinformatics (Oxford, England). PMID 34791064 DOI: 10.1093/bioinformatics/btab782  0.414
2021 Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, ... ... Satagopam V, et al. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Molecular Systems Biology. 17: e10387. PMID 34664389 DOI: 10.15252/msb.202110387  0.481
2021 Chowdhary A, Satagopam V, Schneider R. Long Non-coding RNAs: Mechanisms, Experimental, and Computational Approaches in Identification, Characterization, and Their Biomarker Potential in Cancer. Frontiers in Genetics. 12: 649619. PMID 34276764 DOI: 10.3389/fgene.2021.649619  0.403
2021 Bernhofer M, Dallago C, Karl T, Satagopam V, Heinzinger M, Littmann M, Olenyi T, Qiu J, Schütze K, Yachdav G, Ashkenazy H, Ben-Tal N, Bromberg Y, Goldberg T, Kajan L, et al. PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Research. PMID 33999203 DOI: 10.1093/nar/gkab354  0.401
2021 Badimon L, Robinson EL, Jusic A, Carpusca I, de Windt LJ, Emanueli C, Ferdinandy P, Gu W, Gyöngyösi M, Hackl M, Karaduzovic-Hadziabdic K, Lustrek M, Martelli F, Nham E, Potočnjak I, ... Satagopam V, et al. Cardiovascular rna markers and artificial intelligence may improve covid-19 outcome: position paper from the eu-cardiorna cost action ca17129. Cardiovascular Research. PMID 33839767 DOI: 10.1093/cvr/cvab094  0.395
2020 Kratochvíl M, Hunewald O, Heirendt L, Verissimo V, Vondrášek J, Satagopam VP, Schneider R, Trefois C, Ollert M. GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets. Gigascience. 9. PMID 33205814 DOI: 10.1093/gigascience/giaa127  0.463
2020 Lebioda J, Heirendt L, Jarosz Y, Trefois C, Guerard E, Duarte D, Gu W, Satagopam V, Schneider R. Reproducible websites: a state-of-the-art ecosystem F1000research. 9. DOI: 10.7490/F1000Research.1117956.1  0.41
2020 Satagopam V, Trefois C, Alper P, Becker R, Ostaszewski M, Krause R, Lebioda J, Toukourou N, Gu W, Schneider R. ELIXIR-LU: Overview and updates on activities F1000research. 9. DOI: 10.7490/F1000Research.1117949.1  0.418
2019 Becker R, Alper P, Grouès V, Munoz S, Jarosz Y, Lebioda J, Rege K, Trefois C, Satagopam V, Schneider R. DAISY: A Data Information System for accountability under the General Data Protection Regulation. Gigascience. 8. PMID 31800037 DOI: 10.1093/Gigascience/Giz140  0.53
2019 Gu W, Yildirimman R, Van der Stuyft E, Verbeeck D, Herzinger S, Satagopam V, Barbosa-Silva A, Schneider R, Lange B, Lehrach H, Guo Y, Henderson D, Rowe A. Data and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium. Bmc Bioinformatics. 20: 164. PMID 30935364 DOI: 10.1186/S12859-019-2748-Y  0.478
2019 Alper P, Becker R, Grouès V, Munoz S, Jarosz Y, Lebioda J, Rege K, Trefois C, Satagopam V, Schneider R. DAISY: A tool to document biomedical research data processing for accountability under the GDPR F1000research. 8. DOI: 10.7490/F1000Research.1117085.1  0.51
2018 Barbosa-Silva A, Bratfalean D, Gu W, Satagopam V, Houston P, Becnel LB, Eifes S, Richard F, Tielmann A, Herzinger S, Rege K, Balling R, Peeters P, Schneider R. Presenting and Sharing Clinical Data using the eTRIKS Standards Master Tree for tranSMART. Bioinformatics (Oxford, England). PMID 30256906 DOI: 10.1093/Bioinformatics/Bty809  0.513
2018 Herzinger S, Grouès V, Gu W, Satagopam V, Banda P, Trefois C, Schneider R. Fractalis: A scalable open-source service for platform-independent interactive visual analysis of biomedical data. Gigascience. PMID 30165440 DOI: 10.1093/Gigascience/Giy109  0.526
2018 Schneider R, Gerloff D, Satagopam V, Krause R, Trefois C, Gu W, Lebioda J, Toukourou N, Alper P, Becker R. ELIXIR-LU : Current node activities F1000research. 7. DOI: 10.7490/F1000Research.1115781.1  0.409
2018 Alper P, Becker R, Satagopam V, Grouès V, Lebioda J, Jarosz Y, Trefois C, Krause R, Munoz S, Schneider R. Provenance-enabled stewardship of human data in the GDPR era F1000research. 7. DOI: 10.7490/F1000Research.1115768.1  0.486
2017 van Rijswijk M, Beirnaert C, Caron C, Cascante M, Dominguez V, Dunn WB, Ebbels TMD, Giacomoni F, Gonzalez-Beltran A, Hankemeier T, Haug K, Izquierdo-Garcia JL, Jimenez RC, Jourdan F, Kale N, ... ... Satagopam V, et al. The future of metabolomics in ELIXIR. F1000research. 6. PMID 29043062 DOI: 10.12688/F1000Research.12342.2  0.321
2017 Roomp K, Kristinsson H, Schvartz D, Ubhayasekera K, Sargsyan E, Manukyan L, Chowdhury A, Manell H, Satagopam V, Groebe K, Schneider R, Bergquist J, Sanchez JC, Bergsten P. Combined lipidomic and proteomic analysis of isolated human islets exposed to palmitate reveals time-dependent changes in insulin secretion and lipid metabolism. Plos One. 12: e0176391. PMID 28448538 DOI: 10.1371/Journal.Pone.0176391  0.454
2017 Herzinger S, Gu W, Satagopam V, Eifes S, Rege K, Barbosa Da Silva A, Schneider R. SmartR: An open-source platform for interactive visual analytics for translational research data. Bioinformatics (Oxford, England). PMID 28334291 DOI: 10.1093/Bioinformatics/Btx137  0.535
2016 Gawron P, Ostaszewski M, Satagopam V, Gebel S, Mazein A, Kuzma M, Zorzan S, McGee F, Otjacques B, Balling R, Schneider R. MINERVA-a platform for visualization and curation of molecular interaction networks. Npj Systems Biology and Applications. 2: 16020. PMID 28725475 DOI: 10.1038/npjsba.2016.20  0.457
2016 Satagopam V, Gu W, Eifes S, Gawron P, Ostaszewski M, Gebel S, Barbosa-Silva A, Balling R, Schneider R. Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. Big Data. 4: 97-108. PMID 27441714 DOI: 10.1089/big.2015.0057  0.496
2015 Jimenez-Sanchez M, Lam W, Hannus M, Sönnichsen B, Imarisio S, Fleming A, Tarditi A, Menzies F, Ed Dami T, Xu C, Gonzalez-Couto E, Lazzeroni G, Heitz F, Diamanti D, Massai L, ... Satagopam VP, et al. siRNA screen identifies QPCT as a druggable target for Huntington's disease. Nature Chemical Biology. 11: 347-54. PMID 25848931 DOI: 10.1038/Nchembio.1790  0.395
2015 Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I. BioTextQuest+: a knowledge integration platform for literature mining and concept discovery. Bioinformatics (Oxford, England). 31: 979. PMID 25673338 DOI: 10.7490/F1000Research.1096805.1  0.421
2014 Davey NE, Satagopam VP, Santiago-Mozos S, Villacorta-Martin C, Bharat TA, Schneider R, Briggs JA. The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data. Plos Computational Biology. 10: e1003951. PMID 25474213 DOI: 10.1371/Journal.Pcbi.1003951  0.385
2014 Papanikolaou N, Pavlopoulos GA, Pafilis E, Theodosiou T, Schneider R, Satagopam VP, Ouzounis CA, Eliopoulos AG, Promponas VJ, Iliopoulos I. BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery. Bioinformatics (Oxford, England). 30: 3249-56. PMID 25100685 DOI: 10.1093/Bioinformatics/Btu524  0.493
2014 Fujita KA, Ostaszewski M, Matsuoka Y, Ghosh S, Glaab E, Trefois C, Crespo I, Perumal TM, Jurkowski W, Antony PM, Diederich N, Buttini M, Kodama A, Satagopam VP, Eifes S, et al. Integrating pathways of Parkinson's disease in a molecular interaction map. Molecular Neurobiology. 49: 88-102. PMID 23832570 DOI: 10.1007/S12035-013-8489-4  0.395
2014 Trefois C, Jarosz Y, Gu W, Satagopam V, Coronado S, Schneider R. Reproducible Research Results R3 F1000research. 6. DOI: 10.7490/F1000Research.1097472.1  0.423
2013 Bali KK, Venkataramani V, Satagopam VP, Gupta P, Schneider R, Kuner R. Transcriptional mechanisms underlying sensitization of peripheral sensory neurons by granulocyte-/granulocyte-macrophage colony stimulating factors. Molecular Pain. 9: 48. PMID 24067145 DOI: 10.1186/1744-8069-9-48  0.377
2013 Bali KK, Selvaraj D, Satagopam VP, Lu J, Schneider R, Kuner R. Genome-wide identification and functional analyses of microRNA signatures associated with cancer pain. Embo Molecular Medicine. 5: 1740-58. PMID 24039159 DOI: 10.1002/Emmm.201302797  0.383
2013 Chowdhury A, Satagopam VP, Manukyan L, Artemenko KA, Fung YM, Schneider R, Bergquist J, Bergsten P. Signaling in insulin-secreting MIN6 pseudoislets and monolayer cells. Journal of Proteome Research. 12: 5954-62. PMID 24006944 DOI: 10.1021/pr400864w  0.382
2013 Simonetti M, Hagenston AM, Vardeh D, Freitag HE, Mauceri D, Lu J, Satagopam VP, Schneider R, Costigan M, Bading H, Kuner R. Nuclear calcium signaling in spinal neurons drives a genomic program required for persistent inflammatory pain. Neuron. 77: 43-57. PMID 23312515 DOI: 10.1016/J.Neuron.2012.10.037  0.36
2013 Pafilis E, Pavlopoulos GA, Satagopam VP, Papanikolaou N, Horn H, Arvanitidis C, Jensen LJ, Schneider R, Iliopoulos I. OnTheFly 2.0: A tool for automatic annotation of files and biological information extraction 13th Ieee International Conference On Bioinformatics and Bioengineering, Ieee Bibe 2013. DOI: 10.1109/BIBE.2013.6701679  0.398
2012 Soldatos TG, O'Donoghue SI, Satagopam VP, Barbosa-Silva A, Pavlopoulos GA, Wanderley-Nogueira AC, Soares-Cavalcanti NM, Schneider R. Caipirini: using gene sets to rank literature. Biodata Mining. 5: 1. PMID 22297131 DOI: 10.1186/1756-0381-5-1  0.45
2010 Satagopam VP, Theodoropoulou MC, Stampolakis CK, Pavlopoulos GA, Papandreou NC, Bagos PG, Schneider R, Hamodrakas SJ. GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. Database : the Journal of Biological Databases and Curation. 2010: baq019. PMID 20689020 DOI: 10.1093/Database/Baq019  0.44
2010 Marji J, O'Donoghue SI, McClintock D, Satagopam VP, Schneider R, Ratner D, Worman HJ, Gordon LB, Djabali K. Defective lamin A-Rb signaling in Hutchinson-Gilford Progeria Syndrome and reversal by farnesyltransferase inhibition. Plos One. 5: e11132. PMID 20559568 DOI: 10.1371/Journal.Pone.0011132  0.378
2010 Neumann B, Walter T, Hériché JK, Bulkescher J, Erfle H, Conrad C, Rogers P, Poser I, Held M, Liebel U, Cetin C, Sieckmann F, Pau G, Kabbe R, Wünsche A, ... Satagopam V, et al. Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes. Nature. 464: 721-7. PMID 20360735 DOI: 10.1038/Nature08869  0.499
2010 Soldatos TG, O'Donoghue SI, Satagopam VP, Jensen LJ, Brown NP, Barbosa-Silva A, Schneider R. Martini: using literature keywords to compare gene sets. Nucleic Acids Research. 38: 26-38. PMID 19858102 DOI: 10.1093/Nar/Gkp876  0.429
2010 O'Donoghue SI, Horn H, Pafilis E, Haag S, Kuhn M, Satagopam VP, Schneider R, Jensen LJ. Reflect: A practical approach to web semantics Journal of Web Semantics. 8: 182-189. DOI: 10.1016/J.Websem.2010.03.003  0.417
2008 Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R. Arena3D: visualization of biological networks in 3D. Bmc Systems Biology. 2: 104. PMID 19040715 DOI: 10.1186/1752-0509-2-104  0.436
2008 Barbosa-Silva A, Satagopam VP, Schneider R, Ortega JM. Clustering of cognate proteins among distinct proteomes derived from multiple links to a single seed sequence. Bmc Bioinformatics. 9: 141. PMID 18321373 DOI: 10.1186/1471-2105-9-141  0.4
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