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Reinhard Schneider, PhD - Publications

Affiliations: 
2004-2012 Structural and Computational Biology European Molecular Biology Laboratory (EMBL), Heidelberg, Baden-Württemberg, Germany 
 2011- Luxembourg Centre for Systems Biomedicine University of Luxembourg 
Area:
data integration, data management, parallel computing, visualisation
Website:
https://wwwfr.uni.lu/lcsb/people/reinhard_schneider
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118 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 Hemedan AA, Satagopam V, Schneider R, Ostaszewski M. Cohort-specific boolean models highlight different regulatory modules during Parkinson's disease progression. Iscience. 27: 110956. PMID 39429779 DOI: 10.1016/j.isci.2024.110956  0.579
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, 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  0.615
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  0.636
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, ... ... Schneider R, 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  0.654
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  0.612
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  0.638
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  0.625
2023 Kokoli M, Karatzas E, Baltoumas FA, Schneider R, Pafilis E, Paragkamian S, Doncheva NT, Jensen LJ, Pavlopoulos GA. Arena3D: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration. Nar Genomics and Bioinformatics. 5: lqad053. PMID 37260509 DOI: 10.1093/nargab/lqad053  0.751
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  0.567
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  0.557
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, ... ... Schneider R, 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  0.761
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  0.588
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, ... ... Schneider R, 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  0.792
2021 Baltoumas FA, Zafeiropoulou S, Karatzas E, Paragkamian S, Thanati F, Iliopoulos I, Eliopoulos AG, Schneider R, Jensen LJ, Pafilis E, Pavlopoulos GA. OnTheFly: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. Nar Genomics and Bioinformatics. 3: lqab090. PMID 34632381 DOI: 10.1093/nargab/lqab090  0.779
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  0.586
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, ... ... Schneider R, et al. PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Research. PMID 33999203 DOI: 10.1093/nar/gkab354  0.793
2021 Karatzas E, Baltoumas FA, Panayiotou NA, Schneider R, Pavlopoulos GA. Arena3Dweb: interactive 3D visualization of multilayered networks. Nucleic Acids Research. PMID 33885790 DOI: 10.1093/nar/gkab278  0.61
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, ... ... Schneider R, 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  0.571
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  0.62
2020 Piereck B, Oliveira-Lima M, Benko-Iseppon AM, Diehl S, Schneider R, Brasileiro-Vidal AC, Barbosa-Silva A. LAITOR4HPC: A text mining pipeline based on HPC for building interaction networks. Bmc Bioinformatics. 21: 365. PMID 32838742 DOI: 10.1186/S12859-020-03620-4  0.374
2020 Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, ... ... Schneider R, et al. Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data. 7: 247. PMID 32678106 DOI: 10.1038/S41597-020-00589-W  0.459
2020 Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, ... ... Schneider R, et al. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms. Scientific Data. 7: 136. PMID 32371892 DOI: 10.1038/S41597-020-0477-8  0.454
2020 Hoksza D, Gawron P, Ostaszewski M, Hasenauer J, Schneider R. Closing the gap between formats for storing layout information in systems biology. Briefings in Bioinformatics. PMID 32083642 DOI: 10.1093/Bib/Bbaa030  0.337
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  0.574
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  0.578
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  0.647
2019 Hoksza D, Gawron P, Ostaszewski M, Smula E, Schneider R. MINERVA API and plugins: opening molecular network analysis and visualization to the community. Bioinformatics (Oxford, England). PMID 31074494 DOI: 10.1093/Bioinformatics/Btz286  0.354
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  0.655
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  0.629
2018 Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Daníelsdóttir AD, Krecke M, Merten D, Haraldsdóttir HS, Heinken A, Heirendt L, Magnúsdóttir S, Ravcheev DA, Sahoo S, ... ... Schneider R, et al. The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Research. PMID 30371894 DOI: 10.1093/Nar/Gky992  0.315
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  0.639
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  0.655
2018 Ostaszewski M, Kieffer E, Danoy G, Schneider R, Bouvry P. Clustering approaches for visual knowledge exploration in molecular interaction networks. Bmc Bioinformatics. 19: 308. PMID 30157777 DOI: 10.1186/S12859-018-2314-Z  0.359
2018 Hoksza D, Gawron P, Ostaszewski M, Schneider R. MolArt: A molecular structure annotation and visualization tool. Bioinformatics (Oxford, England). PMID 29931246 DOI: 10.1093/Bioinformatics/Bty489  0.36
2018 Ostaszewski M, Gebel S, Kuperstein I, Mazein A, Zinovyev A, Dogrusoz U, Hasenauer J, Fleming RMT, Le Novère N, Gawron P, Ligon T, Niarakis A, Nickerson D, Weindl D, Balling R, ... ... Schneider R, et al. Community-driven roadmap for integrated disease maps. Briefings in Bioinformatics. PMID 29688273 DOI: 10.1093/Bib/Bby024  0.326
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  0.574
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  0.617
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  0.611
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  0.662
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  0.636
2016 Noronha A, Daníelsdóttir AD, Gawron P, Jóhannsson F, Jónsdóttir S, Jarlsson S, Gunnarsson JP, Brynjólfsson S, Schneider R, Thiele I, Fleming RM. ReconMap: an interactive visualization of human metabolism. Bioinformatics (Oxford, England). PMID 27993782 DOI: 10.1093/Bioinformatics/Btw667  0.308
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  0.637
2016 Auffray C, Balling R, Barroso I, Bencze L, Benson M, Bergeron J, Bernal-Delgado E, Blomberg N, Bock C, Conesa A, Del Signore S, Delogne C, Devilee P, Di Meglio A, Eijkemans M, ... ... Schneider R, et al. Making sense of big data in health research: Towards an EU action plan. Genome Medicine. 8: 71. PMID 27338147 DOI: 10.1186/S13073-016-0323-Y  0.311
2016 Mazein A, Meulder BD, Lefaudeux D, Knowles RG, Wheelock C, Dahlen S, Chung F, Adcock I, Openshaw P, Roberts G, Djukanovic R, Gawron P, Ostaszewski M, Touré V, Kuzma M, ... ... Schneider R, et al. LSC Abstract – The AsthmaMap: Towards a community-driven reconstruction of asthma-relevant pathways and networks European Respiratory Journal. 48: 204. DOI: 10.1183/13993003.Congress-2016.Pp204  0.323
2015 Hofmann-Apitius M, Ball G, Gebel S, Bagewadi S, de Bono B, Schneider R, Page M, Kodamullil AT, Younesi E, Ebeling C, Tegnér J, Canard L. Bioinformatics Mining and Modeling Methods for the Identification of Disease Mechanisms in Neurodegenerative Disorders. International Journal of Molecular Sciences. 16: 29179-206. PMID 26690135 DOI: 10.3390/Ijms161226148  0.343
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, ... ... Schneider R, 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  0.612
2015 Glaab E, Schneider R. RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis. Bioinformatics (Oxford, England). PMID 25717197 DOI: 10.1093/Bioinformatics/Btv127  0.345
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  0.77
2014 Krishna A, Biryukov M, Trefois C, Antony PM, Hussong R, Lin J, Heinäniemi M, Glusman G, Köglsberger S, Boyd O, van den Berg BH, Linke D, Huang D, Wang K, Hood L, ... ... Schneider R, et al. Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease. Bmc Genomics. 15: 1154. PMID 25528190 DOI: 10.1186/1471-2164-15-1154  0.303
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  0.602
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  0.804
2014 Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, ... Schneider R, et al. PredictProtein--an open resource for online prediction of protein structural and functional features. Nucleic Acids Research. 42: W337-43. PMID 24799431 DOI: 10.1093/Nar/Gku366  0.694
2014 Binder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O'Donoghue SI, Schneider R, Jensen LJ. COMPARTMENTS: unification and visualization of protein subcellular localization evidence. Database : the Journal of Biological Databases and Curation. 2014: bau012. PMID 24573882 DOI: 10.1093/Database/Bau012  0.615
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, ... ... Schneider R, 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  0.609
2014 Secrier M, Schneider R. Visualizing time-related data in biology, a review. Briefings in Bioinformatics. 15: 771-82. PMID 23585583 DOI: 10.1093/Bib/Bbt021  0.692
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  0.574
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  0.596
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  0.601
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  0.574
2013 Secrier M, Schneider R. PhenoTimer: software for the visual mapping of time-resolved phenotypic landscapes. Plos One. 8: e72361. PMID 23951317 DOI: 10.1371/Journal.Pone.0072361  0.7
2013 Pavlopoulos GA, Oulas A, Iacucci E, Sifrim A, Moreau Y, Schneider R, Aerts J, Iliopoulos I. Unraveling genomic variation from next generation sequencing data. Biodata Mining. 6: 13. PMID 23885890 DOI: 10.1186/1756-0381-6-13  0.663
2013 Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, ... ... Schneider R, et al. iAnn: an event sharing platform for the life sciences. Bioinformatics (Oxford, England). 29: 1919-21. PMID 23742982 DOI: 10.1093/Bioinformatics/Btt306  0.307
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  0.588
2013 Pavlopoulos GA, Pafilis E, Satagopam VP, Horn H, Arvanitidis C, Jensen L, Iliopoulos I, Schneider R. OnTheFly 2.0 beta: automated annotation of scientific documents F1000research. 4. DOI: 10.7490/F1000Research.1093964.1  0.734
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  0.772
2012 Iacucci E, Tranchevent LC, Popovic D, Pavlopoulos GA, De Moor B, Schneider R, Moreau Y. ReLiance: a machine learning and literature-based prioritization of receptor--ligand pairings. Bioinformatics (Oxford, England). 28: i569-i574. PMID 22962483 DOI: 10.1093/Bioinformatics/Bts391  0.611
2012 Glaab E, Baudot A, Krasnogor N, Schneider R, Valencia A. EnrichNet: network-based gene set enrichment analysis. Bioinformatics (Oxford, England). 28: i451-i457. PMID 22962466 DOI: 10.1093/Bioinformatics/Bts389  0.546
2012 Rost B, Gaasterland T, Lengauer T, Linial M, Markel S, Morrison McKay BJ, Schneider R, Horton P, Kelso J. Paving the future: finding suitable ISMB venues. Bioinformatics (Oxford, England). 28: 2556-9. PMID 22796959 DOI: 10.1093/Bioinformatics/Bts420  0.469
2012 Michalopoulos I, Pavlopoulos GA, Malatras A, Karelas A, Kostadima MA, Schneider R, Kossida S. Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes. Bmc Research Notes. 5: 265. PMID 22672625 DOI: 10.1186/1756-0500-5-265  0.624
2012 Secrier M, Pavlopoulos GA, Aerts J, Schneider R. Arena3D: visualizing time-driven phenotypic differences in biological systems. Bmc Bioinformatics. 13: 45. PMID 22439608 DOI: 10.1186/1471-2105-13-45  0.786
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  0.788
2012 Glaab E, Schneider R. PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data. Bioinformatics (Oxford, England). 28: 446-7. PMID 22123829 DOI: 10.1093/Bioinformatics/Btr656  0.344
2012 Glaab E, Schneider R. Analyzing gene and protein expression variance in cellular pathways using high-throughput experimental data F1000research. 3. DOI: 10.7490/F1000Research.1089698.1  0.322
2011 Moschopoulos CN, Pavlopoulos GA, Iacucci E, Aerts J, Likothanassis S, Schneider R, Kossida S. Which clustering algorithm is better for predicting protein complexes? Bmc Research Notes. 4: 549. PMID 22185599 DOI: 10.1186/1756-0500-4-549  0.633
2011 Pavlopoulos GA, Hooper SD, Sifrim A, Schneider R, Aerts J. Medusa: A tool for exploring and clustering biological networks. Bmc Research Notes. 4: 384. PMID 21978489 DOI: 10.1186/1756-0500-4-384  0.654
2011 Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J, Schneider R, Bagos PG. Using graph theory to analyze biological networks. Biodata Mining. 4: 10. PMID 21527005 DOI: 10.1186/1756-0381-4-10  0.756
2011 Joosten RP, te Beek TA, Krieger E, Hekkelman ML, Hooft RW, Schneider R, Sander C, Vriend G. A series of PDB related databases for everyday needs. Nucleic Acids Research. 39: D411-9. PMID 21071423 DOI: 10.1093/Nar/Gkq1105  0.628
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  0.75
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  0.706
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, ... ... Schneider R, 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  0.643
2010 Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin AC. Visualization of omics data for systems biology. Nature Methods. 7: S56-68. PMID 20195258 DOI: 10.1038/Nmeth.1436  0.611
2010 Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R. A reference guide for tree analysis and visualization. Biodata Mining. 3: 1. PMID 20175922 DOI: 10.1186/1756-0381-3-1  0.671
2010 Barbosa-Silva A, Soldatos TG, Magalhães IL, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM. LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships. Bmc Bioinformatics. 11: 70. PMID 20122157 DOI: 10.1186/1471-2105-11-70  0.732
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  0.729
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  0.778
2009 Moschopoulos CN, Pavlopoulos GA, Schneider R, Likothanassis SD, Kossida S. GIBA: a clustering tool for detecting protein complexes. Bmc Bioinformatics. 10: S11. PMID 19534736 DOI: 10.1186/1471-2105-10-S6-S11  0.651
2009 Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R. Reflect: augmented browsing for the life scientist. Nature Biotechnology. 27: 508-10. PMID 19513049 DOI: 10.1038/Nbt0609-508  0.764
2009 Pavlopoulos GA, Moschopoulos CN, Hooper SD, Schneider R, Kossida S. jClust: a clustering and visualization toolbox. Bioinformatics (Oxford, England). 25: 1994-6. PMID 19454618 DOI: 10.1093/Bioinformatics/Btp330  0.615
2009 Bromberg Y, Yachdav G, Ofran Y, Schneider R, Rost B. New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'. Current Opinion in Drug Discovery & Development. 12: 408-19. PMID 19396742  0.52
2009 Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R. OnTheFly: a tool for automated document-based text annotation, data linking and network generation. Bioinformatics (Oxford, England). 25: 977-8. PMID 19223449 DOI: 10.1093/Bioinformatics/Btp081  0.797
2008 Pavlopoulos GA, Wegener AL, Schneider R. A survey of visualization tools for biological network analysis. Biodata Mining. 1: 12. PMID 19040716 DOI: 10.1186/1756-0381-1-12  0.658
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  0.783
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  0.655
2007 Barbosa-Silva A, Pafilis E, Ortega JM, Schneider R. Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases. Genetics and Molecular Research : Gmr. 6: 1142-50. PMID 18273808  0.693
2006 Erhardt RA, Schneider R, Blaschke C. Status of text-mining techniques applied to biomedical text. Drug Discovery Today. 11: 315-25. PMID 16580973 DOI: 10.1016/J.Drudis.2006.02.011  0.328
2005 Ofran Y, Punta M, Schneider R, Rost B. Beyond annotation transfer by homology: novel protein-function prediction methods to assist drug discovery. Drug Discovery Today. 10: 1475-82. PMID 16243268 DOI: 10.1016/S1359-6446(05)03621-4  0.534
2005 Kremer A, Schneider R, Terstappen GC. A bioinformatics perspective on proteomics: data storage, analysis, and integration. Bioscience Reports. 25: 95-106. PMID 16222422 DOI: 10.1007/S10540-005-2850-4  0.401
1998 Dodge C, Schneider R, Sander C. The HSSP database of protein structure-sequence alignments and family profiles. Nucleic Acids Research. 26: 313-5. PMID 9399862 DOI: 10.1093/Nar/26.1.313  0.613
1997 Andrade MA, Daruvar A, Casari G, Schneider R, Termier M, Sander C. Characterization of new proteins found by analysis of short open reading frames from the full yeast genome. Yeast (Chichester, England). 13: 1363-74. PMID 9392081 DOI: 10.1002/(Sici)1097-0061(199711)13:14<1363::Aid-Yea182>3.0.Co;2-8  0.614
1997 Andrade M, Casari G, de Daruvar A, Sander C, Schneider R, Tamames J, Valencia A, Ouzounis C. Sequence analysis of the Methanococcus jannaschii genome and the prediction of protein function. Computer Applications in the Biosciences : Cabios. 13: 481-3. PMID 9283767 DOI: 10.1093/Bioinformatics/13.4.481  0.656
1997 Rost B, Schneider R, Sander C. Protein fold recognition by prediction-based threading. Journal of Molecular Biology. 270: 471-80. PMID 9237912 DOI: 10.1006/Jmbi.1997.1101  0.673
1997 Schneider R, de Daruvar A, Sander C. The HSSP database of protein structure-sequence alignments. Nucleic Acids Research. 25: 226-30. PMID 9016541 DOI: 10.1093/Nar/25.1.226  0.615
1996 Casari G, De Daruvar A, Sander C, Schneider R. Bioinformatics and the discovery of gene function. Trends in Genetics : Tig. 12: 244-5. PMID 8763493 DOI: 10.1016/0168-9525(96)30057-7  0.568
1996 Schneider R, Sander C. The HSSP database of protein structure-sequence alignments. Nucleic Acids Research. 24: 201-5. PMID 8594579 DOI: 10.1093/nar/24.1.201  0.576
1995 Casari G, Andrade MA, Bork P, Boyle J, Daruvar A, Ouzounis C, Schneider R, Tamames J, Valencia A, Sander C. Challenging times for bioinformatics. Nature. 376: 647-8. PMID 7651513 DOI: 10.1038/376647A0  0.617
1995 Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM. Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Molecular Microbiology. 16: 955-67. PMID 7476192 DOI: 10.1111/J.1365-2958.1995.Tb02321.X  0.592
1994 Rost B, Sander C, Schneider R. Redefining the goals of protein secondary structure prediction. Journal of Molecular Biology. 235: 13-26. PMID 8289237 DOI: 10.1016/S0022-2836(05)80007-5  0.665
1994 Göbel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins. 18: 309-17. PMID 8208723 DOI: 10.1002/Prot.340180402  0.66
1994 Rost B, Sander C, Schneider R. PHD--an automatic mail server for protein secondary structure prediction. Computer Applications in the Biosciences : Cabios. 10: 53-60. PMID 8193956 DOI: 10.1093/Bioinformatics/10.1.53  0.682
1994 Sander C, Schneider R. The HSSP database of protein structure-sequence alignments. Nucleic Acids Research. 22: 3597-9. PMID 7937066  0.571
1994 Scharf M, Schneider R, Casari G, Bork P, Valencia A, Ouzounis C, Sander C. GeneQuiz: a workbench for sequence analysis. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 2: 348-53. PMID 7584411  0.598
1993 Rost B, Schneider R, Sander C. Progress in protein structure prediction? Trends in Biochemical Sciences. 18: 120-3. PMID 8493721 DOI: 10.1016/0968-0004(93)90017-H  0.67
1993 Ouzounis C, Sander C, Scharf M, Schneider R. Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. Journal of Molecular Biology. 232: 805-25. PMID 8355272 DOI: 10.1006/Jmbi.1993.1433  0.611
1993 Sander C, Schneider R. The HSSP data base of protein structure-sequence alignments. Nucleic Acids Research. 21: 3105-9. PMID 8332531  0.573
1992 Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. What's in a genome? Nature. 358: 287. PMID 1641000 DOI: 10.1038/358287A0  0.546
1992 Bork P, Ouzounis C, Sander C, Scharf M, Schneider R, Sonnhammer E. Comprehensive sequence analysis of the 182 predicted open reading frames of yeast chromosome III. Protein Science : a Publication of the Protein Society. 1: 1677-90. PMID 1304897 DOI: 10.1002/Pro.5560011216  0.614
1992 Hobohm U, Scharf M, Schneider R, Sander C. Selection of representative protein data sets. Protein Science : a Publication of the Protein Society. 1: 409-17. PMID 1304348 DOI: 10.1002/Pro.5560010313  0.62
1991 Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 9: 56-68. PMID 2017436 DOI: 10.1002/Prot.340090107  0.607
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