Visualization of omics data for systems biology

Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, Kitano H, Kohlbacher O, Neuweger H, Schneider R, Tenenbaum D, Gavin A-C (2010)
Nat Methods 7(3s): S56-S68.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Gehlenborg, Nils; O'Donoghue, Sean I; Baliga, Nitin S; Goesmann, AlexanderUniBi ; Hibbs, Matthew A; Kitano, Hiroaki; Kohlbacher, Oliver; Neuweger, Heiko; Schneider, Reinhard; Tenenbaum, Dan; Gavin, Anne-Claude
Einrichtung
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Abstract / Bemerkung
High-throughput studies of biological systems are rapidly accumulating a wealth of 'omics'-scale data. Visualization is a key aspect of both the analysis and understanding of these data, and users now have many visualization methods and tools to choose from. The challenge is to create clear, meaningful and integrated visualizations that give biological insight, without being overwhelmed by the intrinsic complexity of the data. In this review, we discuss how visualization tools are being used to help interpret protein interaction, gene expression and metabolic profile data, and we highlight emerging new directions.
Erscheinungsjahr
2010
Zeitschriftentitel
Nat Methods
Band
7
Ausgabe
3s
Seite(n)
S56-S68
ISSN
1548-7091
eISSN
1548-7105
Page URI
https://pub.uni-bielefeld.de/record/1990186

Zitieren

Gehlenborg N, O'Donoghue SI, Baliga NS, et al. Visualization of omics data for systems biology. Nat Methods. 2010;7(3s):S56-S68.
Gehlenborg, N., O'Donoghue, S. I., Baliga, N. S., Goesmann, A., Hibbs, M. A., Kitano, H., Kohlbacher, O., et al. (2010). Visualization of omics data for systems biology. Nat Methods, 7(3s), S56-S68. https://doi.org/10.1038/NMETH.1436
Gehlenborg, Nils, O'Donoghue, Sean I, Baliga, Nitin S, Goesmann, Alexander, Hibbs, Matthew A, Kitano, Hiroaki, Kohlbacher, Oliver, et al. 2010. “Visualization of omics data for systems biology”. Nat Methods 7 (3s): S56-S68.
Gehlenborg, N., O'Donoghue, S. I., Baliga, N. S., Goesmann, A., Hibbs, M. A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D., et al. (2010). Visualization of omics data for systems biology. Nat Methods 7, S56-S68.
Gehlenborg, N., et al., 2010. Visualization of omics data for systems biology. Nat Methods, 7(3s), p S56-S68.
N. Gehlenborg, et al., “Visualization of omics data for systems biology”, Nat Methods, vol. 7, 2010, pp. S56-S68.
Gehlenborg, N., O'Donoghue, S.I., Baliga, N.S., Goesmann, A., Hibbs, M.A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D., Gavin, A.-C.: Visualization of omics data for systems biology. Nat Methods. 7, S56-S68 (2010).
Gehlenborg, Nils, O'Donoghue, Sean I, Baliga, Nitin S, Goesmann, Alexander, Hibbs, Matthew A, Kitano, Hiroaki, Kohlbacher, Oliver, Neuweger, Heiko, Schneider, Reinhard, Tenenbaum, Dan, and Gavin, Anne-Claude. “Visualization of omics data for systems biology”. Nat Methods 7.3s (2010): S56-S68.

219 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

TOBMI: trans-omics block missing data imputation using a k-nearest neighbor weighted approach.
Dong X, Lin L, Zhang R, Zhao Y, Christiani DC, Wei Y, Chen F., Bioinformatics 35(8), 2019
PMID: 30202885
MKL1-actin pathway restricts chromatin accessibility and prevents mature pluripotency activation.
Hu X, Liu ZZ, Chen X, Schulz VP, Kumar A, Hartman AA, Weinstein J, Johnston JF, Rodriguez EC, Eastman AE, Cheng J, Min L, Zhong M, Carroll C, Gallagher PG, Lu J, Schwartz M, King MC, Krause DS, Guo S., Nat Commun 10(1), 2019
PMID: 30979898
SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines.
Lampa S, Dahlö M, Alvarsson J, Spjuth O., Gigascience 8(5), 2019
PMID: 31029061
Exploratory Gene Ontology Analysis with Interactive Visualization.
Zhu J, Zhao Q, Katsevich E, Sabatti C., Sci Rep 9(1), 2019
PMID: 31127124
A Single Visualization Technique for Displaying Multiple Metabolite-Phenotype Associations.
Henglin M, Niiranen T, Watrous JD, Lagerborg KA, Antonelli J, Claggett BL, Demosthenes EJ, von Jeinsen B, Demler O, Vasan RS, Larson MG, Jain M, Cheng S., Metabolites 9(7), 2019
PMID: 31269707
Decision Graph Embedding for High-Resolution Manometry Diagnosis.
Kreiser J, Hann A, Zizer E, Ropinski T., IEEE Trans Vis Comput Graph 24(1), 2018
PMID: 28866536
Use of Metabolomics in Improving Assessment of Dietary Intake.
Guasch-Ferré M, Bhupathiraju SN, Hu FB., Clin Chem 64(1), 2018
PMID: 29038146
Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions.
Rodrigues RR, Shulzhenko N, Morgun A., Methods Mol Biol 1849(), 2018
PMID: 30298258
Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data.
Marco-Ramell A, Palau-Rodriguez M, Alay A, Tulipani S, Urpi-Sarda M, Sanchez-Pla A, Andres-Lacueva C., BMC Bioinformatics 19(1), 2018
PMID: 29291722
Inflammatory Proteomic Network Analysis of Statin-treated and Lipopolysaccharide-activated Macrophages.
Kamal AHM, Chakrabarty JK, Udden SMN, Zaki MH, Chowdhury SM., Sci Rep 8(1), 2018
PMID: 29317699
Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation.
Touré V, Le Novère N, Waltemath D, Wolkenhauer O., PLoS Comput Biol 14(2), 2018
PMID: 29447151
Studying microbial functionality within the gut ecosystem by systems biology.
Hornung B, Martins Dos Santos VAP, Smidt H, Schaap PJ., Genes Nutr 13(), 2018
PMID: 29556373
Bipartite graphs in systems biology and medicine: a survey of methods and applications.
Pavlopoulos GA, Kontou PI, Pavlopoulou A, Bouyioukos C, Markou E, Bagos PG., Gigascience 7(4), 2018
PMID: 29648623
A Strategy for Discovery of Endocrine Interactions with Application to Whole-Body Metabolism.
Seldin MM, Koplev S, Rajbhandari P, Vergnes L, Rosenberg GM, Meng Y, Pan C, Phuong TMN, Gharakhanian R, Che N, Mäkinen S, Shih DM, Civelek M, Parks BW, Kim ED, Norheim F, Chella Krishnan K, Hasin-Brumshtein Y, Mehrabian M, Laakso M, Drevon CA, Koistinen HA, Tontonoz P, Reue K, Cantor RM, Björkegren JLM, Lusis AJ., Cell Metab 27(5), 2018
PMID: 29719227
Precision Medicine and Radiogenomics in Breast Cancer: New Approaches toward Diagnosis and Treatment.
Pinker K, Chin J, Melsaether AN, Morris EA, Moy L., Radiology 287(3), 2018
PMID: 29782246
AAVvector-mediated in vivo reprogramming into pluripotency.
Senís E, Mosteiro L, Wilkening S, Wiedtke E, Nowrouzi A, Afzal S, Fronza R, Landerer H, Abad M, Niopek D, Schmidt M, Serrano M, Grimm D., Nat Commun 9(1), 2018
PMID: 29985406
HiGlass: web-based visual exploration and analysis of genome interaction maps.
Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H, Luber JM, Ouellette SB, Azhir A, Kumar N, Hwang J, Lee S, Alver BH, Pfister H, Mirny LA, Park PJ, Gehlenborg N., Genome Biol 19(1), 2018
PMID: 30143029
Interrupted reprogramming of alveolar type II cells induces progenitor-like cells that ameliorate pulmonary fibrosis.
Guo L, Karoubi G, Duchesneau P, Aoki FG, Shutova MV, Rogers I, Nagy A, Waddell TK., NPJ Regen Med 3(), 2018
PMID: 30210809
Protein complex analysis: From raw protein lists to protein interaction networks.
Meysman P, Titeca K, Eyckerman S, Tavernier J, Goethals B, Martens L, Valkenborg D, Laukens K., Mass Spectrom Rev 36(5), 2017
PMID: 26709718
The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health.
Gomez A, Nelson KE., Microb Ecol 73(2), 2017
PMID: 27628595
PRECISION MEDICINE: DATA AND DISCOVERY FOR IMPROVED HEALTH AND THERAPY.
Morgan AA, Crawford DC, Denny JC, Mooney SD, Aronow BJ, Brenner SE., Pac Symp Biocomput 22(), 2017
PMID: 27896988
Translating genomic profiling to gastrointestinal cancer treatment.
Harada K, Mizrak Kaya D, Shimodaira Y, Song S, Baba H, Ajani JA., Future Oncol 13(10), 2017
PMID: 28067073
Epigenetic Landscape during Coronavirus Infection.
Schäfer A, Baric RS., Pathogens 6(1), 2017
PMID: 28212305
A taxonomy of visualization tasks for the analysis of biological pathway data.
Murray P, McGee F, Forbes AG., BMC Bioinformatics 18(suppl 2), 2017
PMID: 28251869
Transplant genetics and genomics.
Yang JY, Sarwal MM., Nat Rev Genet 18(5), 2017
PMID: 28286337
General guidelines for biomedical software development.
Silva LB, Jimenez RC, Blomberg N, Luis Oliveira J., F1000Res 6(), 2017
PMID: 28443186
The biological knowledge discovery by PCCF measure and PCA-F projection.
Jia X, Zhu G, Han Q, Lu Z., PLoS One 12(4), 2017
PMID: 28399180
Methods, Tools and Current Perspectives in Proteogenomics.
Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR., Mol Cell Proteomics 16(6), 2017
PMID: 28456751
Using visual analytics for presenting comparative information on new drugs.
Lamy JB, Berthelot H, Favre M, Ugon A, Duclos C, Venot A., J Biomed Inform 71(), 2017
PMID: 28549568
Integrating 3-omics data analyze rat lung tissue of COPD states and medical intervention by delineation of molecular and pathway alterations.
Li J, Zhao P, Yang L, Li Y, Tian Y, Li S, Bai Y., Biosci Rep 37(3), 2017
PMID: 28450497
NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.
Theodosiou T, Efstathiou G, Papanikolaou N, Kyrpides NC, Bagos PG, Iliopoulos I, Pavlopoulos GA., BMC Res Notes 10(1), 2017
PMID: 28705239
Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis.
Pavlopoulos GA, Paez-Espino D, Kyrpides NC, Iliopoulos I., Adv Bioinformatics 2017(), 2017
PMID: 28804499
Verification of Three-Phase Dependency Analysis Bayesian Network Learning Method for Maize Carotenoid Gene Mining.
Liu J, Tian Z., Biomed Res Int 2017(), 2017
PMID: 28828382
Lipidomes of lung cancer and tumour-free lung tissues reveal distinct molecular signatures for cancer differentiation, age, inflammation, and pulmonary emphysema.
Eggers LF, Müller J, Marella C, Scholz V, Watz H, Kugler C, Rabe KF, Goldmann T, Schwudke D., Sci Rep 7(1), 2017
PMID: 28894173
A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants.
Cirillo E, Parnell LD, Evelo CT., Front Genet 8(), 2017
PMID: 29163640
Multiple-cumulative probabilities used to cluster and visualize transcriptomes.
Jia X, Liu Y, Han Q, Lu Z., FEBS Open Bio 7(12), 2017
PMID: 29226087
The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria.
Zuck M, Austin LS, Danziger SA, Aitchison JD, Kaushansky A., Front Microbiol 8(), 2017
PMID: 29201016
Using Interactive Data Visualizations for Exploratory Analysis in Undergraduate Genomics Coursework: Field Study Findings and Guidelines.
Mirel B, Kumar A, Nong P, Su G, Meng F., J Sci Educ Technol 25(1), 2016
PMID: 26877625
Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective.
Davidsen PK, Turan N, Egginton S, Falciani F., J Appl Physiol (1985) 120(3), 2016
PMID: 26542523
MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics.
Cai W, Guner H, Gregorich ZR, Chen AJ, Ayaz-Guner S, Peng Y, Valeja SG, Liu X, Ge Y., Mol Cell Proteomics 15(2), 2016
PMID: 26598644
Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers.
Yugi K, Kubota H, Hatano A, Kuroda S., Trends Biotechnol 34(4), 2016
PMID: 26806111
Quantification of read species behavior within whole genome sequencing of cancer genomes for the stratification and visualization of genomic variation.
Hibsh D, Buetow KH, Yaari G, Efroni S., Nucleic Acids Res 44(9), 2016
PMID: 26809676
C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4.
Di Stefano B, Collombet S, Jakobsen JS, Wierer M, Sardina JL, Lackner A, Stadhouders R, Segura-Morales C, Francesconi M, Limone F, Mann M, Porse B, Thieffry D, Graf T., Nat Cell Biol 18(4), 2016
PMID: 26974661
Combining systems pharmacology, transcriptomics, proteomics, and metabolomics to dissect the therapeutic mechanism of Chinese herbal Bufei Jianpi formula for application to COPD.
Zhao P, Yang L, Li J, Li Y, Tian Y, Li S., Int J Chron Obstruct Pulmon Dis 11(), 2016
PMID: 27042044
MONGKIE: an integrated tool for network analysis and visualization for multi-omics data.
Jang Y, Yu N, Seo J, Kim S, Lee S., Biol Direct 11(1), 2016
PMID: 26987515
Omics Profiling in Precision Oncology.
Yu KH, Snyder M., Mol Cell Proteomics 15(8), 2016
PMID: 27099341
Genetic manipulation of putrescine biosynthesis reprograms the cellular transcriptome and the metabolome.
Page AF, Cseke LJ, Minocha R, Turlapati SA, Podila GK, Ulanov A, Li Z, Minocha SC., BMC Plant Biol 16(1), 2016
PMID: 27188293
Metabolomics studies in brain tissue: A review.
Gonzalez-Riano C, Garcia A, Barbas C., J Pharm Biomed Anal 130(), 2016
PMID: 27451335
Systems Medicine as an Emerging Tool for Cardiovascular Genetics.
Haase T, Börnigen D, Müller C, Zeller T., Front Cardiovasc Med 3(), 2016
PMID: 27626034
Eigenvector metabolite analysis reveals dietary effects on the association among metabolite correlation patterns, gene expression, and phenotypes.
Scott Chialvo CH, Che R, Reif D, Motsinger-Reif A, Reed LK., Metabolomics 12(11), 2016
PMID: 28845148
Dynamic Variations in Genetic Integrity Accompany Changes in Cell Fate.
Chen IC, Hernandez C, Xu X, Cooney A, Wang Y, McCarrey JR., Stem Cells Dev 25(22), 2016
PMID: 27627671
Precision medicine and molecular imaging: new targeted approaches toward cancer therapeutic and diagnosis.
Ghasemi M, Nabipour I, Omrani A, Alipour Z, Assadi M., Am J Nucl Med Mol Imaging 6(6), 2016
PMID: 28078184
Proteome profiling of human cutaneous leishmaniasis lesion.
da Silva Santos C, Attarha S, Saini RK, Boaventura V, Costa J, Khouri R, Barral-Netto M, Brodskyn CI, Souchelnytskyi S., J Invest Dermatol 135(2), 2015
PMID: 25207817
MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data.
Kaever A, Landesfeind M, Feussner K, Mosblech A, Heilmann I, Morgenstern B, Feussner I, Meinicke P., Metabolomics 11(3), 2015
PMID: 25972773
Empowering biologists with multi-omics data: colorectal cancer as a paradigm.
Zhu J, Shi Z, Wang J, Zhang B., Bioinformatics 31(9), 2015
PMID: 25527095
Viewing the proteome: how to visualize proteomics data?
Oveland E, Muth T, Rapp E, Martens L, Berven FS, Barsnes H., Proteomics 15(8), 2015
PMID: 25504833
xiNET: cross-link network maps with residue resolution.
Combe CW, Fischer L, Rappsilber J., Mol Cell Proteomics 14(4), 2015
PMID: 25648531
Open source libraries and frameworks for biological data visualisation: a guide for developers.
Wang R, Perez-Riverol Y, Hermjakob H, Vizcaíno JA., Proteomics 15(8), 2015
PMID: 25475079
Emerging proteomic technologies for elucidating context-dependent cellular signaling events: A big challenge of tiny proportions.
Parker SJ, Raedschelders K, Van Eyk JE., Proteomics 15(9), 2015
PMID: 25545106
Bioinformatics approaches for the functional interpretation of protein lists: from ontology term enrichment to network analysis.
Laukens K, Naulaerts S, Berghe WV., Proteomics 15(5-6), 2015
PMID: 25430566
The shortest path is not the one you know: application of biological network resources in precision oncology research.
Kuperstein I, Grieco L, Cohen DP, Thieffry D, Zinovyev A, Barillot E., Mutagenesis 30(2), 2015
PMID: 25688112
Streaming visualisation of quantitative mass spectrometry data based on a novel raw signal decomposition method.
Zhang Y, Bhamber R, Riba-Garcia I, Liao H, Unwin RD, Dowsey AW., Proteomics 15(8), 2015
PMID: 25663356
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology.
Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, Hermjakob H., Proteomics 15(8), 2015
PMID: 25648416
Bacterial rose garden for metagenomic SNP-based phylogeny visualization.
Alexeev D, Bibikova T, Kovarsky B, Melnikov D, Tyakht A, Govorun V., BioData Min 8(), 2015
PMID: 25815061
Unlocking proteomic heterogeneity in complex diseases through visual analytics.
Bhavnani SK, Dang B, Bellala G, Divekar R, Visweswaran S, Brasier AR, Kurosky A., Proteomics 15(8), 2015
PMID: 25684269
RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells.
Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X., Science 348(6233), 2015
PMID: 25858977
Recent progress in the use of 'omics technologies in brassicaceous vegetables.
Witzel K, Neugart S, Ruppel S, Schreiner M, Wiesner M, Baldermann S., Front Plant Sci 6(), 2015
PMID: 25926843
Neuroblastoma tyrosine kinase signaling networks involve FYN and LYN in endosomes and lipid rafts.
Palacios-Moreno J, Foltz L, Guo A, Stokes MP, Kuehn ED, George L, Comb M, Grimes ML., PLoS Comput Biol 11(4), 2015
PMID: 25884760
VISIONET: intuitive visualisation of overlapping transcription factor networks, with applications in cardiogenic gene discovery.
Nim HT, Furtado MB, Costa MW, Rosenthal NA, Kitano H, Boyd SE., BMC Bioinformatics 16(), 2015
PMID: 25929466
NaviCell Web Service for network-based data visualization.
Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DP, Barillot E, Zinovyev A., Nucleic Acids Res 43(w1), 2015
PMID: 25958393
Autophagy and mTORC1 regulate the stochastic phase of somatic cell reprogramming.
Wu Y, Li Y, Zhang H, Huang Y, Zhao P, Tang Y, Qiu X, Ying Y, Li W, Ni S, Zhang M, Liu L, Xu Y, Zhuang Q, Luo Z, Benda C, Song H, Liu B, Lai L, Liu X, Tse HF, Bao X, Chan WY, Esteban MA, Qin B, Pei D., Nat Cell Biol 17(6), 2015
PMID: 25985393
NetworkPainter: dynamic intracellular pathway animation in Cytobank.
Karr JR, Guturu H, Chen EY, Blair SL, Irish JM, Kotecha N, Covert MW., BMC Bioinformatics 16(), 2015
PMID: 26003204
FunRich: An open access standalone functional enrichment and interaction network analysis tool.
Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill AF, Stroud DA, Ryan MT, Agbinya JI, Mariadason JM, Burgess AW, Mathivanan S., Proteomics 15(15), 2015
PMID: 25921073
Metabolomics in chemical ecology.
Kuhlisch C, Pohnert G., Nat Prod Rep 32(7), 2015
PMID: 25926134
Rapid generation of secondary fibroblasts through teratoma formation.
Cho SM, Park JS, Min B, Kwon S, Kang YK., Biotechniques 59(1), 2015
PMID: 26156782
Choosing Cell Fate Through a Dynamic Cell Cycle.
Chen X, Hartman A, Guo S., Curr Stem Cell Rep 1(3), 2015
PMID: 28725536
Generation of Human Induced Pluripotent Stem Cells from Extraembryonic Tissues of Fetuses Affected by Monogenic Diseases.
Spitalieri P, Talarico RV, Botta A, Murdocca M, D'Apice MR, Orlandi A, Giardina E, Santoro M, Brancati F, Novelli G, Sangiuolo F., Cell Reprogram 17(4), 2015
PMID: 26474030
Genomewide effects of peroxisome proliferator-activated receptor gamma in macrophages and dendritic cells--revealing complexity through systems biology.
Cuaranta-Monroy I, Kiss M, Simandi Z, Nagy L., Eur J Clin Invest 45(9), 2015
PMID: 26251129
PathwayMatrix: visualizing binary relationships between proteins in biological pathways.
Dang TN, Murray P, Forbes AG., BMC Proc 9(suppl 6 proceedings of the 5th symposium on biological ), 2015
PMID: 26361499
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts.
Czerwinska U, Calzone L, Barillot E, Zinovyev A., BMC Syst Biol 9(), 2015
PMID: 26271256
Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.
Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I., Gigascience 4(), 2015
PMID: 26309733
Data integration in biological research: an overview.
Lapatas V, Stefanidakis M, Jimenez RC, Via A, Schneider MV., J Biol Res (Thessalon) 22(1), 2015
PMID: 26336651
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction.
Rouillard AD, Wang Z, Ma'ayan A., Comput Biol Chem 58(), 2015
PMID: 26101093
microRNAs as pharmacogenomic biomarkers for drug efficacy and drug safety assessment.
Koturbash I, Tolleson WH, Guo L, Yu D, Chen S, Hong H, Mattes W, Ning B., Biomark Med 9(11), 2015
PMID: 26501795
Facilitating the use of large-scale biological data and tools in the era of translational bioinformatics.
Kouskoumvekaki I, Shublaq N, Brunak S., Brief Bioinform 15(6), 2014
PMID: 23908249
Procedures for the biochemical enrichment and proteomic analysis of the cytoskeletome.
Choi S, Kelber J, Jiang X, Strnadel J, Fujimura K, Pasillas M, Coppinger J, Klemke R., Anal Biochem 446(), 2014
PMID: 24161902
Protter: interactive protein feature visualization and integration with experimental proteomic data.
Omasits U, Ahrens CH, Müller S, Wollscheid B., Bioinformatics 30(6), 2014
PMID: 24162465
C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells.
Di Stefano B, Sardina JL, van Oevelen C, Collombet S, Kallin EM, Vicent GP, Lu J, Thieffry D, Beato M, Graf T., Nature 506(7487), 2014
PMID: 24336202
Ondex Web: web-based visualization and exploration of heterogeneous biological networks.
Taubert J, Hassani-Pak K, Castells-Brooke N, Rawlings CJ., Bioinformatics 30(7), 2014
PMID: 24363379
Integration, visualization and analysis of human interactome.
Pastrello C, Pasini E, Kotlyar M, Otasek D, Wong S, Sangrar W, Rahmati S, Jurisica I., Biochem Biophys Res Commun 445(4), 2014
PMID: 24491561
BiNA: a visual analytics tool for biological network data.
Gerasch A, Faber D, Küntzer J, Niermann P, Kohlbacher O, Lenhof HP, Kaufmann M., PLoS One 9(2), 2014
PMID: 24551056
PPI layouts: BioJS components for the display of Protein-Protein Interactions.
Salazar GA, Meintjes A, Mulder N., F1000Res 3(), 2014
PMID: 25075288
Meta-analysis of pathway enrichment: combining independent and dependent omics data sets.
Kaever A, Landesfeind M, Feussner K, Morgenstern B, Feussner I, Meinicke P., PLoS One 9(2), 2014
PMID: 24586671
Predictive in silico off-target profiling in drug discovery.
Schmidt F, Matter H, Hessler G, Czich A., Future Med Chem 6(3), 2014
PMID: 24575966
Plant systems biology: insights, advances and challenges.
Sheth BP, Thaker VS., Planta 240(1), 2014
PMID: 24671625
Interactive Visualization for Patient-to-Patient Comparison.
Nguyen QV, Nelmes G, Huang ML, Simoff S, Catchpoole D., Genomics Inform 12(1), 2014
PMID: 24748858
New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes.
Islam MA, Waller AS, Hug LA, Provart NJ, Edwards EA, Mahadevan R., PLoS One 9(4), 2014
PMID: 24733489
Scientists' sense making when hypothesizing about disease mechanisms from expression data and their needs for visualization support.
Mirel B, Görg C., BMC Bioinformatics 15(), 2014
PMID: 24766796
A web-based protein interaction network visualizer.
Salazar GA, Meintjes A, Mazandu GK, Rapanoël HA, Akinola RO, Mulder NJ., BMC Bioinformatics 15(), 2014
PMID: 24885165
Proteogenomic convergence for understanding cancer pathways and networks.
Boja ES, Rodriguez H., Clin Proteomics 11(1), 2014
PMID: 24994965
How implementation of systems biology into clinical trials accelerates understanding of diseases.
Bielekova B, Vodovotz Y, An G, Hallenbeck J., Front Neurol 5(), 2014
PMID: 25018747
eXamine: exploring annotated modules in networks.
Dinkla K, El-Kebir M, Bucur CI, Siderius M, Smit MJ, Westenberg MA, Klau GW., BMC Bioinformatics 15(), 2014
PMID: 25002203
dendsort: modular leaf ordering methods for dendrogram representations in R.
Sakai R, Winand R, Verbeiren T, Moere AV, Aerts J., F1000Res 3(), 2014
PMID: 25232468
dendsort: modular leaf ordering methods for dendrogram representations in R
Sakai R, Winand R, Verbeiren T, Moere AV, Aerts J., 2014
PMID: PPR42727
Grouping annotations on the subcellular layered interactome demonstrates enhanced autophagy activity in a recurrent experimental autoimmune uveitis T cell line.
Jia X, Li J, Shi D, Zhao Y, Dong Y, Ju H, Yang J, Sun J, Li X, Ren H., PLoS One 9(8), 2014
PMID: 25116327
Integrated network analysis and effective tools in plant systems biology.
Fukushima A, Kanaya S, Nishida K., Front Plant Sci 5(), 2014
PMID: 25408696
Data mining in the Life Sciences with Random Forest: a walk in the park or lost in the jungle?
Touw WG, Bayjanov JR, Overmars L, Backus L, Boekhorst J, Wels M, van Hijum SA., Brief Bioinform 14(3), 2013
PMID: 22786785
Plasma microRNA profiles for bladder cancer detection.
Adam L, Wszolek MF, Liu CG, Jing W, Diao L, Zien A, Zhang JD, Jackson D, Dinney CP., Urol Oncol 31(8), 2013
PMID: 22863868
Analytical glycobiology at high sensitivity: current approaches and directions.
Novotny MV, Alley WR, Mann BF., Glycoconj J 30(2), 2013
PMID: 22945852
The Comparative Toxicogenomics Database: update 2013.
Davis AP, Murphy CG, Johnson R, Lay JM, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Rosenstein MC, Wiegers TC, Mattingly CJ., Nucleic Acids Res 41(database issue), 2013
PMID: 23093600
Toxicogenomic analysis of the particle dose- and size-response relationship of silica particles-induced toxicity in mice.
Lu X, Jin T, Jin Y, Wu L, Hu B, Tian Y, Fan X., Nanotechnology 24(1), 2013
PMID: 23221170
Proteomic and biochemical methods to study the cytoskeletome.
Klemke RL, Jiang X, Choi S, Kelber JA., Methods Mol Biol 1046(), 2013
PMID: 23868590
Wrangling phosphoproteomic data to elucidate cancer signaling pathways.
Grimes ML, Lee WJ, van der Maaten L, Shannon P., PLoS One 8(1), 2013
PMID: 23300999
Post-translational events and modifications regulating plant enzymes involved in isoprenoid precursor biosynthesis.
Hemmerlin A., Plant Sci 203-204(), 2013
PMID: 23415327
Visualizing multidimensional cancer genomics data.
Schroeder MP, Gonzalez-Perez A, Lopez-Bigas N., Genome Med 5(1), 2013
PMID: 23363777
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.
Csermely P, Korcsmáros T, Kiss HJ, London G, Nussinov R., Pharmacol Ther 138(3), 2013
PMID: 23384594
Integrated analysis of transcriptomics and metabonomics profiles in aflatoxin B1-induced hepatotoxicity in rat.
Lu X, Hu B, Shao L, Tian Y, Jin T, Jin Y, Ji S, Fan X., Food Chem Toxicol 55(), 2013
PMID: 23385219
Systems metabolic engineering in an industrial setting.
Sagt CM., Appl Microbiol Biotechnol 97(6), 2013
PMID: 23397485
Network analysis for gene discovery in plant-specialized metabolism.
Higashi Y, Saito K., Plant Cell Environ 36(9), 2013
PMID: 23336321
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.
Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A., BMC Syst Biol 7(), 2013
PMID: 23453054
Game on, science - how video game technology may help biologists tackle visualization challenges.
Lv Z, Tek A, Da Silva F, Empereur-mot C, Chavent M, Baaden M., PLoS One 8(3), 2013
PMID: 23483961
Label-free integrative pharmacology on-target of opioid ligands at the opioid receptor family.
Morse M, Sun H, Tran E, Levenson R, Fang Y., BMC Pharmacol Toxicol 14(), 2013
PMID: 23497702
Information engineering infrastructure for life sciences and its implementation in China.
Zhu W, Zhu Y, Yang X., Sci China Life Sci 56(3), 2013
PMID: 23526387
High-sensitivity analytical approaches for the structural characterization of glycoproteins.
Alley WR, Mann BF, Novotny MV., Chem Rev 113(4), 2013
PMID: 23531120
Pattern recognition in bioinformatics.
de Ridder D, de Ridder J, Reinders MJ., Brief Bioinform 14(5), 2013
PMID: 23559637
Systematic curation of protein and genetic interaction data for computable biology.
Dolinski K, Chatr-Aryamontri A, Tyers M., BMC Biol 11(), 2013
PMID: 23587305
Proteomic analysis reveals differentially expressed proteins in macrophages infected with Leishmania amazonensis or Leishmania major.
Menezes JP, Almeida TF, Petersen AL, Guedes CE, Mota MS, Lima JG, Palma LC, Buck GA, Krieger MA, Probst CM, Veras PS., Microbes Infect 15(8-9), 2013
PMID: 23628411
Information content and scalability in signal transduction network reconstruction formats.
Rother M, Münzner U, Thieme S, Krantz M., Mol Biosyst 9(8), 2013
PMID: 23636168
Automation of dimethylation after guanidination labeling chemistry and its compatibility with common buffers and surfactants for mass spectrometry-based shotgun quantitative proteome analysis.
Lo A, Tang Y, Chen L, Li L., Anal Chim Acta 788(), 2013
PMID: 23845485
NetGestalt: integrating multidimensional omics data over biological networks.
Shi Z, Wang J, Zhang B., Nat Methods 10(7), 2013
PMID: 23807191
RCytoscape: tools for exploratory network analysis.
Shannon PT, Grimes M, Kutlu B, Bot JJ, Galas DJ., BMC Bioinformatics 14(), 2013
PMID: 23837656
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data.
Kuo TC, Tian TF, Tseng YJ., BMC Syst Biol 7(), 2013
PMID: 23875761
The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases.
Moulos P, Klein J, Jupp S, Stevens R, Bascands JL, Schanstra JP., BMC Bioinformatics 14(), 2013
PMID: 23883183
Metabolomics, peptidomics and proteomics applications of capillary electrophoresis-mass spectrometry in Foodomics: a review.
Ibáñez C, Simó C, García-Cañas V, Cifuentes A, Castro-Puyana M., Anal Chim Acta 802(), 2013
PMID: 24176500
GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks.
Camilo E, Bovolenta LA, Acencio ML, Rybarczyk-Filho JL, Castro MA, Moreira JC, Lemke N., Bioinformatics 29(19), 2013
PMID: 23894138
Single-cell sequencing-based technologies will revolutionize whole-organism science.
Shapiro E, Biezuner T, Linnarsson S., Nat Rev Genet 14(9), 2013
PMID: 23897237
Unraveling DNA damage response-signaling networks through systems approaches.
von Stechow L, van de Water B, Danen EH., Arch Toxicol 87(9), 2013
PMID: 23943208
Use of single nucleotide polymorphism array technology to improve the identification of chromosomal lesions in leukemia.
Iacobucci I, Lonetti A, Papayannidis C, Martinelli G., Curr Cancer Drug Targets 13(7), 2013
PMID: 23941516
Reprogramming in vivo produces teratomas and iPS cells with totipotency features.
Abad M, Mosteiro L, Pantoja C, Cañamero M, Rayon T, Ors I, Graña O, Megías D, Domínguez O, Martínez D, Manzanares M, Ortega S, Serrano M., Nature 502(7471), 2013
PMID: 24025773
Transcriptional landscapes of emerging autoimmunity: transient aberrations in the targeted tissue's extracellular milieu precede immune responses in Sjögren's syndrome.
Delaleu N, Nguyen CQ, Tekle KM, Jonsson R, Peck AB., Arthritis Res Ther 15(5), 2013
PMID: 24286337
enRoute: dynamic path extraction from biological pathway maps for exploring heterogeneous experimental datasets.
Partl C, Lex A, Streit M, Kalkofen D, Kashofer K, Schmalstieg D., BMC Bioinformatics 14 Suppl 19(), 2013
PMID: 24564375
Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum).
Lee YP, Giorgi FM, Lohse M, Kvederaviciute K, Klages S, Usadel B, Meskiene I, Reinhardt R, Hincha DK., BMC Genomics 14(), 2013
PMID: 24228715
Entourage: visualizing relationships between biological pathways using contextual subsets.
Lex A, Partl C, Kalkofen D, Streit M, Gratzl S, Wassermann AM, Schmalstieg D, Pfister H., IEEE Trans Vis Comput Graph 19(12), 2013
PMID: 24051820
Toward an integrated software platform for systems pharmacology.
Ghosh S, Matsuoka Y, Asai Y, Hsin KY, Kitano H., Biopharm Drug Dispos 34(9), 2013
PMID: 24150748
POMO--Plotting Omics analysis results for Multiple Organisms.
Lin J, Kreisberg R, Kallio A, Dudley AM, Nykter M, Shmulevich I, May P, Autio R., BMC Genomics 14(), 2013
PMID: 24365393
Foodomics: MS-based strategies in modern food science and nutrition.
Herrero M, Simó C, García-Cañas V, Ibáñez E, Cifuentes A., Mass Spectrom Rev 31(1), 2012
PMID: 21374694
Pair-wise multicomparison and OPLS analyses of cold-acclimation phases in Siberian spruce.
Shiryaeva L, Antti H, Schröder WP, Strimbeck R, Shiriaev AS., Metabolomics 8(suppl 1), 2012
PMID: 22593724
Hive plots--rational approach to visualizing networks.
Krzywinski M, Birol I, Jones SJ, Marra MA., Brief Bioinform 13(5), 2012
PMID: 22155641
Mass spectrometry-based proteomics and network biology.
Bensimon A, Heck AJ, Aebersold R., Annu Rev Biochem 81(), 2012
PMID: 22439968
CHROMATRA: a Galaxy tool for visualizing genome-wide chromatin signatures.
Hentrich T, Schulze JM, Emberly E, Kobor MS., Bioinformatics 28(5), 2012
PMID: 22238257
To label or not to label: applications of quantitative proteomics in neuroscience research.
Filiou MD, Martins-de-Souza D, Guest PC, Bahn S, Turck CW., Proteomics 12(4-5), 2012
PMID: 22247077
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.
Lepoivre C, Bergon A, Lopez F, Perumal NB, Nguyen C, Imbert J, Puthier D., BMC Bioinformatics 13(), 2012
PMID: 22292669
Systems medicine and metabolic modelling.
Mardinoglu A, Nielsen J., J Intern Med 271(2), 2012
PMID: 22142312
Array-based cytogenetic approaches in acute myeloid leukemia: clinical impact and biological insights.
Bullinger L, Fröhling S., Semin Oncol 39(1), 2012
PMID: 22289490
Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation.
Junker A, Rohn H, Czauderna T, Klukas C, Hartmann A, Schreiber F., Nat Protoc 7(3), 2012
PMID: 22383037
Concordance of changes in metabolic pathways based on plasma metabolomics and skeletal muscle transcriptomics in type 1 diabetes.
Dutta T, Chai HS, Ward LE, Ghosh A, Persson XM, Ford GC, Kudva YC, Sun Z, Asmann YW, Kocher JP, Nair KS., Diabetes 61(5), 2012
PMID: 22415876
A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization.
Tuikkala J, Vähämaa H, Salmela P, Nevalainen OS, Aittokallio T., BioData Min 5(), 2012
PMID: 22448851
Visualization of the interactome: what are we looking at?
Fung DC, Li SS, Goel A, Hong SH, Wilkins MR., Proteomics 12(10), 2012
PMID: 22610544
An eQTL biological data visualization challenge and approaches from the visualization community.
Bartlett CW, Cheong SY, Hou L, Paquette J, Lum PY, Jäger G, Battke F, Vehlow C, Heinrich J, Nieselt K, Sakai R, Aerts J, Ray WC., BMC Bioinformatics 13 Suppl 8(), 2012
PMID: 22607587
Model-driven design for the visual analysis of heterogeneous data.
Streit M, Schulz HJ, Lex A, Schmalstieg D, Schumann H., IEEE Trans Vis Comput Graph 18(6), 2012
PMID: 21690642
Human amniotic epithelial cells are reprogrammed more efficiently by induced pluripotency than adult fibroblasts.
Easley CA, Miki T, Castro CA, Ozolek JA, Minervini CF, Ben-Yehudah A, Schatten GP., Cell Reprogram 14(3), 2012
PMID: 22686477
Application of approximate pattern matching in two dimensional spaces to grid layout for biochemical network maps.
Inoue K, Shimozono S, Yoshida H, Kurata H., PLoS One 7(6), 2012
PMID: 22679486
Postgenomic approaches to using corynebacteria as biocatalysts.
Vertès AA, Inui M, Yukawa H., Annu Rev Microbiol 66(), 2012
PMID: 22803796
High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization.
Xu M, Alber F., BMC Syst Biol 6 Suppl 1(), 2012
PMID: 23046491
atBioNet--an integrated network analysis tool for genomics and biomarker discovery.
Ding Y, Chen M, Liu Z, Ding D, Ye Y, Zhang M, Kelly R, Guo L, Su Z, Harris SC, Qian F, Ge W, Fang H, Xu X, Tong W., BMC Genomics 13(), 2012
PMID: 22817640
Dynamic mass redistribution assay decodes differentiation of a neural progenitor stem cell.
Pai S, Verrier F, Sun H, Hu H, Ferrie AM, Eshraghi A, Fang Y., J Biomol Screen 17(9), 2012
PMID: 22885730
Information visualization to enhance sensitivity and selectivity in biosensing.
Oliveira ON, Pavinatto FJ, Constantino CJ, Paulovich FV, de Oliveira MC., Biointerphases 7(1-4), 2012
PMID: 22911268
Bioinformatics for cancer immunology and immunotherapy.
Charoentong P, Angelova M, Efremova M, Gallasch R, Hackl H, Galon J, Trajanoski Z., Cancer Immunol Immunother 61(11), 2012
PMID: 22986455
More than meets the eye. Modern experimental techniques require increasingly sophisticated approaches to data visualization.
Rinaldi A., EMBO Rep 13(10), 2012
PMID: 22986549
Pathway-based visualization of cross-platform microarray datasets.
Wrzodek C, Eichner J, Zell A., Bioinformatics 28(23), 2012
PMID: 23047564
A global genome segmentation method for exploration of epigenetic patterns.
Steiner L, Hopp L, Wirth H, Galle J, Binder H, Prohaska SJ, Rohlf T., PLoS One 7(10), 2012
PMID: 23077526
Validation of a robust proteomic analysis carried out on formalin-fixed paraffin-embedded tissues of the pancreas obtained from mouse and human.
Kojima K, Bowersock GJ, Kojima C, Klug CA, Grizzle WE, Mobley JA., Proteomics 12(22), 2012
PMID: 22997103
VANTED v2: a framework for systems biology applications.
Rohn H, Junker A, Hartmann A, Grafahrend-Belau E, Treutler H, Klapperstück M, Czauderna T, Klukas C, Schreiber F., BMC Syst Biol 6(), 2012
PMID: 23140568
Visual analysis of transcriptome data in the context of anatomical structures and biological networks.
Junker A, Rohn H, Schreiber F., Front Plant Sci 3(), 2012
PMID: 23162564
Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era.
Praneenararat T, Takagi T, Iwasaki W., BMC Genomics 13 Suppl 7(), 2012
PMID: 23281970
Metabolomics of sepsis-induced acute lung injury: a new approach for biomarkers.
Lacy P., Am J Physiol Lung Cell Mol Physiol 300(1), 2011
PMID: 21056960
KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data.
Sakurai N, Ara T, Ogata Y, Sano R, Ohno T, Sugiyama K, Hiruta A, Yamazaki K, Yano K, Aoki K, Aharoni A, Hamada K, Yokoyama K, Kawamura S, Otsuka H, Tokimatsu T, Kanehisa M, Suzuki H, Saito K, Shibata D., Nucleic Acids Res 39(database issue), 2011
PMID: 21097783
The Protein Information and Property Explorer 2: gaggle-like exploration of biological proteomic data within one webpage.
Ramos H, Shannon P, Brusniak MY, Kusebauch U, Moritz RL, Aebersold R., Proteomics 11(1), 2011
PMID: 21182202
Gradient-based high precision alignment of cryo-electron subtomograms.
Xu M, Alber F., IEEE Int Conf Systems Biol (), 2011
PMID: 25068871
ePlant and the 3D data display initiative: integrative systems biology on the world wide web.
Fucile G, Di Biase D, Nahal H, La G, Khodabandeh S, Chen Y, Easley K, Christendat D, Kelley L, Provart NJ., PLoS One 6(1), 2011
PMID: 21249219
Evolution and applications of plant pathway resources and databases.
Sucaet Y, Deva T., Brief Bioinform 12(5), 2011
PMID: 21949268
Integration of lipidomics and transcriptomics data towards a systems biology model of sphingolipid metabolism.
Gupta S, Maurya MR, Merrill AH, Glass CK, Subramaniam S., BMC Syst Biol 5(), 2011
PMID: 21303545
Interactive, multiscale navigation of large and complicated biological networks.
Praneenararat T, Takagi T, Iwasaki W., Bioinformatics 27(8), 2011
PMID: 21349867
A systems biological view of intracellular pathogens.
Beiting DP, Roos DS., Immunol Rev 240(1), 2011
PMID: 21349090
A cognitive task analysis of a visual analytic workflow: Exploring molecular interaction networks in systems biology.
Mirel B, Eichinger F, Keller BJ, Kretzler M., J Biomed Discov Collab 6(), 2011
PMID: 21455901
Adaptive informatics for multifactorial and high-content biological data.
Millard BL, Niepel M, Menden MP, Muhlich JL, Sorger PK., Nat Methods 8(6), 2011
PMID: 21516115
Systems biology approaches to heart development and congenital heart disease.
Sperling SR., Cardiovasc Res 91(2), 2011
PMID: 21527437
Update in acute lung injury and critical care 2010.
Vadász I, Sznajder JI., Am J Respir Crit Care Med 183(9), 2011
PMID: 21531954
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans.
Korcsmáros T, Szalay MS, Rovó P, Palotai R, Fazekas D, Lenti K, Farkas IJ, Csermely P, Vellai T., PLoS One 6(5), 2011
PMID: 21559328
Creating views on integrated multidomain data.
Rohn H, Klukas C, Schreiber F., Bioinformatics 27(13), 2011
PMID: 21551150
Evolutionary forces shaping the Golgi glycosylation machinery: why cell surface glycans are universal to living cells.
Varki A., Cold Spring Harb Perspect Biol 3(6), 2011
PMID: 21525513
LinkinPath: from sequence to interconnected pathway.
Ingsriswang S, Yokwai S, Wichadakul D., Bioinformatics 27(14), 2011
PMID: 21636594
MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles.
Ferry-Dumazet H, Gil L, Deborde C, Moing A, Bernillon S, Rolin D, Nikolski M, de Daruvar A, Jacob D., BMC Plant Biol 11(), 2011
PMID: 21668943
Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation.
Echeverría PC, Forafonov F, Pandey DP, Mühlebach G, Picard D., BioData Min 4(1), 2011
PMID: 21672238
An intuitive graphical visualization technique for the interrogation of transcriptome data.
Bushati N, Smith J, Briscoe J, Watkins C., Nucleic Acids Res 39(17), 2011
PMID: 21690098
Intuitive visualization and analysis of multi-omics data and application to Escherichia coli carbon metabolism.
Enjalbert B, Jourdan F, Portais JC., PLoS One 6(6), 2011
PMID: 21731702
Visualizing meta-features in proteomic maps.
Giannopoulou EG, Lepouras G, Manolakos ES., BMC Bioinformatics 12(), 2011
PMID: 21798033
Integrating transcriptomics and metabonomics to unravel modes-of-action of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in HepG2 cells.
Jennen D, Ruiz-Aracama A, Magkoufopoulou C, Peijnenburg A, Lommen A, van Delft J, Kleinjans J., BMC Syst Biol 5(), 2011
PMID: 21880148
Bioinformatics and systems biology of the lipidome.
Subramaniam S, Fahy E, Gupta S, Sud M, Byrnes RW, Cotter D, Dinasarapu AR, Maurya MR., Chem Rev 111(10), 2011
PMID: 21939287
Omics and integrated omics for the promotion of food and nutrition science.
Kato H, Takahashi S, Saito K., J Tradit Complement Med 1(1), 2011
PMID: 24716102
MyBioNet: interactively visualize, edit and merge biological networks on the web.
Huang D, Huang Y, Bai Y, Chen D, Hofestädt R, Klukas C, Chen M., Bioinformatics 27(23), 2011
PMID: 21984760
Proteomics advances in the last decade: What is next?
Penque D, Simões T, Amado F., J Proteomics 75(1), 2011
PMID: 22061663
Interactive, graph-based visual analysis of high-dimensional, multi-parameter fluorescence microscopy data in toponomics.
Oeltze S, Freiler W, Hillert R, Doleisch H, Preim B, Schubert W., IEEE Trans Vis Comput Graph 17(12), 2011
PMID: 22034305
Comparative microbial modules resource: generation and visualization of multi-species biclusters.
Kacmarczyk T, Waltman P, Bate A, Eichenberger P, Bonneau R., PLoS Comput Biol 7(12), 2011
PMID: 22144874
Computational mass spectrometry-based proteomics.
Käll L, Vitek O., PLoS Comput Biol 7(12), 2011
PMID: 22144880
Advances in omics and bioinformatics tools for systems analyses of plant functions.
Mochida K, Shinozaki K., Plant Cell Physiol 52(12), 2011
PMID: 22156726
Visualizing biological data-now and in the future.
O'Donoghue SI, Gavin AC, Gehlenborg N, Goodsell DS, Hériché JK, Nielsen CB, North C, Olson AJ, Procter JB, Shattuck DW, Walter T, Wong B., Nat Methods 7(3 suppl), 2010
PMID: 20195254
Visualization of image data from cells to organisms.
Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Hériché JK., Nat Methods 7(3 suppl), 2010
PMID: 20195255
Visualization of macromolecular structures.
O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ., Nat Methods 7(3 suppl), 2010
PMID: 20195256
Genome-wide approaches to schizophrenia.
Duan J, Sanders AR, Gejman PV., Brain Res Bull 83(3-4), 2010
PMID: 20433910
Urinary proteomics evaluation in interstitial cystitis/painful bladder syndrome: a pilot study.
Goo YA, Tsai YS, Liu AY, Goodlett DR, Yang CC., Int Braz J Urol 36(4), 2010
PMID: 20815953
Systems biology of the gut: the interplay of food, microbiota and host at the mucosal interface.
Martins dos Santos V, Müller M, de Vos WM., Curr Opin Biotechnol 21(4), 2010
PMID: 20817507
Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: the existence of genome vehicles revealed.
Tsuchiya M, Piras V, Giuliani A, Tomita M, Selvarajoo K., PLoS One 5(8), 2010
PMID: 20725638
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets.
Kelder T, Conklin BR, Evelo CT, Pico AR., PLoS Biol 8(8), 2010
PMID: 20824171
Root hair systems biology.
Libault M, Brechenmacher L, Cheng J, Xu D, Stacey G., Trends Plant Sci 15(11), 2010
PMID: 20851035
Practical application of toxicogenomics for profiling toxicant-induced biological perturbations.
Kiyosawa N, Manabe S, Yamoto T, Sanbuissho A., Int J Mol Sci 11(9), 2010
PMID: 20957103
Metabolic networks, microbial ecology and 'omics' technologies: towards understanding in situ biodegradation processes.
Vilchez-Vargas R, Junca H, Pieper DH., Environ Microbiol 12(12), 2010
PMID: 20860734
MulteeSum: a tool for comparative spatial and temporal gene expression data.
Meyer M, Munzner T, DePace A, Pfister H., IEEE Trans Vis Comput Graph 16(6), 2010
PMID: 20975127
Current trends and new challenges of databases and web applications for systems driven biological research.
Sreenivasaiah PK, Kim DH., Front Physiol 1(), 2010
PMID: 21423387

138 References

Daten bereitgestellt von Europe PubMed Central.


AUTHOR UNKNOWN, 0
The role of protein kinase C in cell surface signal transduction and tumour promotion.
Nishizuka Y., Nature 308(5961), 1984
PMID: 6232463
Gene regulatory networks for development.
Levine M, Davidson EH., Proc. Natl. Acad. Sci. U.S.A. 102(14), 2005
PMID: 15788537
Pathguide: a pathway resource list.
Bader GD, Cary MP, Sander C., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381921

Saraiya, Inf. Vis. 4(), 2005
Tools for visually exploring biological networks.
Suderman M, Hallett M., Bioinformatics 23(20), 2007
PMID: 17720984
A survey of visualization tools for biological network analysis.
Pavlopoulos GA, Wegener AL, Schneider R., BioData Min 1(), 2008
PMID: 19040716
The social network of a cell: recent advances in interactome mapping.
Charbonnier S, Gallego O, Gavin AC., Biotechnol Annu Rev 14(), 2008
PMID: 18606358
High-quality binary protein interaction map of the yeast interactome network.
Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, Sahalie J, Hirozane-Kishikawa T, Gebreab F, Li N, Simonis N, Hao T, Rual JF, Dricot A, Vazquez A, Murray RR, Simon C, Tardivo L, Tam S, Svrzikapa N, Fan C, de Smet AS, Motyl A, Hudson ME, Park J, Xin X, Cusick ME, Moore T, Boone C, Snyder M, Roth FP, Barabasi AL, Tavernier J, Hill DE, Vidal M., Science 322(5898), 2008
PMID: 18719252
Proteome survey reveals modularity of the yeast cell machinery.
Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G., Nature 440(7084), 2006
PMID: 16429126
An evaluation of human protein-protein interaction data in the public domain.
Mathivanan S, Periaswamy B, Gandhi TK, Kandasamy K, Suresh S, Mohmood R, Ramachandra YL, Pandey A., BMC Bioinformatics 7 Suppl 5(), 2006
PMID: 17254303
Network integration and graph analysis in mammalian molecular systems biology.
Ma'ayan A., IET Syst Biol 2(5), 2008
PMID: 19045817
The Database of Interacting Proteins: 2004 update.
Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681454
Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology.
Prasad TS, Kandasamy K, Pandey A., Methods Mol. Biol. 577(), 2009
PMID: 19718509
The IntAct molecular interaction database in 2010.
Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19850723
Comparative assessment of large-scale data sets of protein-protein interactions.
von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P., Nature 417(6887), 2002
PMID: 12000970

Fruchterman, Software Pract. Exper. 21(), 1991
An automated method for finding molecular complexes in large protein interaction networks.
Bader GD, Hogue CW., BMC Bioinformatics 4(), 2003
PMID: 12525261
Proteome organization in a genome-reduced bacterium.
Kuhner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castano-Diez D, Chen WH, Devos D, Guell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Bottcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC., Science 326(5957), 2009
PMID: 19965468
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T., Genome Res. 13(11), 2003
PMID: 14597658
VANTED: a system for advanced data analysis and visualization in the context of biological networks.
Junker BH, Klukas C, Schreiber F., BMC Bioinformatics 7(), 2006
PMID: 16519817
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology.
Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, DeLisi C., Nucleic Acids Res. 37(Web Server issue), 2009
PMID: 19465394
Interaction techniques for selecting and manipulating subgraphs in network visualizations.
McGuffin MJ, Jurisica I., IEEE Trans Vis Comput Graph 15(6), 2009
PMID: 19834157
Control of yeast filamentous-form growth by modules in an integrated molecular network.
Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, Galitski T., Genome Res. 14(3), 2004
PMID: 14993204
Towards zoomable multidimensional maps of the cell.
Hu Z, Mellor J, Wu J, Kanehisa M, Stuart JM, DeLisi C., Nat. Biotechnol. 25(5), 2007
PMID: 17483841
Cerebral: visualizing multiple experimental conditions on a graph with biological context.
Barsky A, Munzner T, Gardy J, Kincaid R., IEEE Trans Vis Comput Graph 14(6), 2008
PMID: 18988971

Genc, Inf. Sci. 176(), 2006
Dynamic complex formation during the yeast cell cycle.
de Lichtenberg U, Jensen LJ, Brunak S, Bork P., Science 307(5710), 2005
PMID: 15692050
KEGG for linking genomes to life and the environment.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18077471
Reactome knowledgebase of human biological pathways and processes.
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P., Nucleic Acids Res. 37(Database issue), 2008
PMID: 18981052
STITCH 2: an interaction network database for small molecules and proteins.
Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, Bork P., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19897548
Computational analysis of microarray data.
Quackenbush J., Nat. Rev. Genet. 2(6), 2001
PMID: 11389458
RNA-Seq: a revolutionary tool for transcriptomics.
Wang Z, Gerstein M, Snyder M., Nat. Rev. Genet. 10(1), 2009
PMID: 19015660
Quantitative mass spectrometry in proteomics: a critical review.
Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B., Anal Bioanal Chem 389(4), 2007
PMID: 17668192
Applying mass spectrometry-based proteomics to genetics, genomics and network biology.
Gstaiger M, Aebersold R., Nat. Rev. Genet. 10(9), 2009
PMID: 19687803

Westenberg, Comput. Graph. Forum 27(), 2008

Freeman, PLOS Comput. Biol. 3(), 2007

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
GenMAPP 2: new features and resources for pathway analysis.
Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR., BMC Bioinformatics 8(), 2007
PMID: 17588266
Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example.
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Huser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A., BMC Syst Biol 3(), 2009
PMID: 19698148
VistaClara: an expression browser plug-in for Cytoscape.
Kincaid R, Kuchinsky A, Creech M., Bioinformatics 24(18), 2008
PMID: 18678589
Coexpression analysis of human genes across many microarray data sets.
Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P., Genome Res. 14(6), 2004
PMID: 15173114

Dunn, TrAC Trends Anal. Chem. 24(), 2005

AUTHOR UNKNOWN, 0
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M., Plant J. 37(6), 2004
PMID: 14996223
The Pathway Tools cellular overview diagram and Omics Viewer.
Paley SM, Karp PD., Nucleic Acids Res. 34(13), 2006
PMID: 16893960
KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps.
Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibata D., Plant Physiol. 138(3), 2005
PMID: 16010003
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways.
Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980551
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases.
Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, Walk TC, Zhang P, Karp PD., Nucleic Acids Res. 36(Database issue), 2007
PMID: 17965431

Funahashi, Proc. IEEE 96(), 2008
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration.
Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H., OMICS 7(4), 2003
PMID: 14683609
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.
Demir E, Babur O, Dogrusoz U, Gursoy A, Nisanci G, Cetin-Atalay R, Ozturk M., Bioinformatics 18(7), 2002
PMID: 12117798
A generic algorithm for layout of biological networks.
Schreiber F, Dwyer T, Marriott K, Wybrow M., BMC Bioinformatics 10(), 2009
PMID: 19909528

AUTHOR UNKNOWN, 0
An insight-based methodology for evaluating bioinformatics visualizations.
Saraiya P, North C, Duca K., IEEE Trans Vis Comput Graph 11(4), 2005
PMID: 16138554
IPSEP-COLA: an incremental procedure for separation constraint layout of graphs.
Dwyer T, Koren Y, Marriott K., IEEE Trans Vis Comput Graph 12(5), 2006
PMID: 17080805
Exploration of networks using overview+detail with constraint-based cooperative layout.
Dwyer T, Marriott K, Schreiber F, Stuckey P, Woodward M, Wybrow M., IEEE Trans Vis Comput Graph 14(6), 2008
PMID: 18988976

Viégas, IEEE Trans. Vis. Comput. Graph. 13(), 2007

AUTHOR UNKNOWN, 0

Heer, Inf. Vis. 7(), 2008
WikiPathways: pathway editing for the people.
Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C., PLoS Biol. 6(7), 2008
PMID: 18651794
Arena3D: visualization of biological networks in 3D.
Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R., BMC Syst Biol 2(), 2008
PMID: 19040715

Ball, Comput. Graph. 31(), 2007
Announcing the worldwide Protein Data Bank.
Berman H, Henrick K, Nakamura H., Nat. Struct. Biol. 10(12), 2003
PMID: 14634627
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.
Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R., Nat. Biotechnol. 22(2), 2004
PMID: 14755292
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum., Bioinformatics 19(4), 2003
PMID: 12611808
CellML: its future, present and past.
Lloyd CM, Halstead MD, Nielsen PF., Prog. Biophys. Mol. Biol. 85(2-3), 2004
PMID: 15142756
The Systems Biology Graphical Notation.
Le Novere N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villeger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H., Nat. Biotechnol. 27(8), 2009
PMID: 19668183
Visualization of image data from cells to organisms.
Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Heriche JK., Nat. Methods 7(3 Suppl), 2010
PMID: 20195255
Visualization of macromolecular structures.
O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ., Nat. Methods 7(3 Suppl), 2010
PMID: 20195256
Visualizing genomes: techniques and challenges.
Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T., Nat. Methods 7(3 Suppl), 2010
PMID: 20195257
Visualization of multiple alignments, phylogenies and gene family evolution.
Procter JB, Thompson J, Letunic I, Creevey C, Jossinet F, Barton GJ., Nat. Methods 7(3 Suppl), 2010
PMID: 20195253
Advanced computing for systems biology.
Burrage K, Hood L, Ragan MA., Brief. Bioinformatics 7(4), 2006
PMID: 17000735
Caryoscope: an Open Source Java application for viewing microarray data in a genomic context.
Awad IA, Rees CA, Hernandez-Boussard T, Ball CA, Sherlock G., BMC Bioinformatics 5(), 2004
PMID: 15488149
Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain.
Lau C, Ng L, Thompson C, Pathak S, Kuan L, Jones A, Hawrylycz M., BMC Bioinformatics 9(), 2008
PMID: 18366675
Visual exploration of three-dimensional gene expression using physical views and linked abstract views.
Weber GH, Rubel O, Huang MY, DePace AH, Fowlkes CC, Keranen SV, Luengo Hendriks CL, Hagen H, Knowles DW, Malik J, Biggin MD, Hamann B., IEEE/ACM Trans Comput Biol Bioinform 6(2), 2009
PMID: 19407353
Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.
Barsky A, Gardy JL, Hancock RE, Munzner T., Bioinformatics 23(8), 2007
PMID: 17309895
Modulation of the TLR-mediated inflammatory response by the endogenous human host defense peptide LL-37.
Mookherjee N, Brown KL, Bowdish DM, Doria S, Falsafi R, Hokamp K, Roche FM, Mu R, Doho GH, Pistolic J, Powers JP, Bryan J, Brinkman FS, Hancock RE., J. Immunol. 176(4), 2006
PMID: 16456005
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B., Mol. Biol. Cell 9(12), 1998
PMID: 9843569
BNDB - the Biochemical Network Database.
Kuntzer J, Backes C, Blum T, Gerasch A, Kaufmann M, Kohlbacher O, Lenhof HP., BMC Bioinformatics 8(), 2007
PMID: 17910766
BiologicalNetworks: visualization and analysis tool for systems biology.
Baitaluk M, Sedova M, Ray A, Gupta A., Nucleic Acids Res. 34(Web Server issue), 2006
PMID: 16845051
Integration of biological networks and gene expression data using Cytoscape.
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD., Nat Protoc 2(10), 2007
PMID: 17947979
Medusa: a simple tool for interaction graph analysis.
Hooper SD, Bork P., Bioinformatics 21(24), 2005
PMID: 16188923

Kao, Curr. Protoc. Bioinformatics 9(), 2008
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto.
Brown KR, Otasek D, Ali M, McGuffin MJ, Xie W, Devani B, Toch IL, Jurisica I., Bioinformatics 25(24), 2009
PMID: 19837718
Graph-based analysis and visualization of experimental results with ONDEX.
Kohler J, Baumbach J, Taubert J, Specht M, Skusa A, Ruegg A, Rawlings C, Verrier P, Philippi S., Bioinformatics 22(11), 2006
PMID: 16533819
Osprey: a network visualization system.
Breitkreutz BJ, Stark C, Tyers M., Genome Biol. 4(3), 2003
PMID: 12620107

Batagelj, Connections 21(), 1998
SpectralNET--an application for spectral graph analysis and visualization.
Forman JJ, Clemons PA, Schreiber SL, Haggarty SJ., BMC Bioinformatics 6(), 2005
PMID: 16236170

AUTHOR UNKNOWN, 0
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks.
Zinovyev A, Viara E, Calzone L, Barillot E., Bioinformatics 24(6), 2007
PMID: 18024474
Graphle: Interactive exploration of large, dense graphs.
Huttenhower C, Mehmood SO, Troyanskaya OG., BMC Bioinformatics 10(), 2009
PMID: 20003429
Visualization, documentation, analysis, and communication of large-scale gene regulatory networks.
Longabaugh WJ, Davidson EH, Bolouri H., Biochim. Biophys. Acta 1789(4), 2008
PMID: 18757046
Caleydo: connecting pathways and gene expression.
Streit M, Lex A, Kalkusch M, Zatloukal K, Schmalstieg D., Bioinformatics 25(20), 2009
PMID: 19620095
KEGG Atlas mapping for global analysis of metabolic pathways.
Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M., Nucleic Acids Res. 36(Web Server issue), 2008
PMID: 18477636
Presenting and exploring biological pathways with PathVisio.
van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, Conklin BR, Evelo C., BMC Bioinformatics 9(), 2008
PMID: 18817533
VitaPad: visualization tools for the analysis of pathway data.
Holford M, Li N, Nadkarni P, Zhao H., Bioinformatics 21(8), 2004
PMID: 15564306
ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics.
Chung HJ, Kim M, Park CH, Kim J, Kim JH., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215430
Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context.
Weniger M, Engelmann JC, Schultz J., BMC Bioinformatics 8(), 2007
PMID: 17543125
iPath: interactive exploration of biochemical pathways and networks.
Letunic I, Yamada T, Kanehisa M, Bork P., Trends Biochem. Sci. 33(3), 2008
PMID: 18276143
The Pathway Tools software.
Karp PD, Paley S, Romero P., Bioinformatics 18 Suppl 1(), 2002
PMID: 12169551
PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.
Dogrusoz U, Erson EZ, Giral E, Demir E, Babur O, Cetintas A, Colak R., Bioinformatics 22(3), 2005
PMID: 16287939
BicOverlapper: a tool for bicluster visualization.
Santamaria R, Theron R, Quintales L., Bioinformatics 24(9), 2008
PMID: 18321885
BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data.
Goncalves JP, Madeira SC, Oliveira AL., BMC Res Notes 2(), 2009
PMID: 19583847
EXPANDER--an integrative program suite for microarray data analysis.
Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R., BMC Bioinformatics 6(), 2005
PMID: 16176576
Genesis: cluster analysis of microarray data.
Sturn A, Quackenbush J, Trajanoski Z., Bioinformatics 18(1), 2002
PMID: 11836235
Visualization methods for statistical analysis of microarray clusters.
Hibbs MA, Dirksen NC, Li K, Troyanskaya OG., BMC Bioinformatics 6(), 2005
PMID: 15890080

Seo, Computer 35(), 2002
Java Treeview--extensible visualization of microarray data.
Saldanha AJ., Bioinformatics 20(17), 2004
PMID: 15180930
Mayday--a microarray data analysis workbench.
Dietzsch J, Gehlenborg N, Nieselt K., Bioinformatics 22(8), 2006
PMID: 16500939

Gehlenborg, Inf. Vis. 4(), 2005
TM4: a free, open-source system for microarray data management and analysis.
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J., BioTechniques 34(2), 2003
PMID: 12613259

Hochheiser, Proc. IEEE Multimedia and Expo Int. Conf. 3(), 2003
Expression Profiler: next generation--an online platform for analysis of microarray data.
Kapushesky M, Kemmeren P, Culhane AC, Durinck S, Ihmels J, Korner C, Kull M, Torrente A, Sarkans U, Vilo J, Brazma A., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215431
GenePattern 2.0.
Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP., Nat. Genet. 38(5), 2006
PMID: 16642009
Microarray data normalization and transformation.
Quackenbush J., Nat. Genet. 32 Suppl(), 2002
PMID: 12454644

Brettschneider, Technometrics 50(), 2008
arrayQualityMetrics--a bioconductor package for quality assessment of microarray data.
Kauffmann A, Gentleman R, Huber W., Bioinformatics 25(3), 2008
PMID: 19106121
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data.
Morgan M, Anders S, Lawrence M, Aboyoun P, Pages H, Gentleman R., Bioinformatics 25(19), 2009
PMID: 19654119
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Robinson MD, McCarthy DJ, Smyth GK., Bioinformatics 26(1), 2009
PMID: 19910308
Statistical issues in cDNA microarray data analysis.
Smyth GK, Yang YH, Speed T., Methods Mol. Biol. 224(), 2003
PMID: 12710670
Analysis and validation of proteomic data generated by tandem mass spectrometry.
Nesvizhskii AI, Vitek O, Aebersold R., Nat. Methods 4(10), 2007
PMID: 17901868
Probability-based protein identification by searching sequence databases using mass spectrometry data.
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS., Electrophoresis 20(18), 1999
PMID: 10612281
A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry.
Li XJ, Pedrioli PG, Eng J, Martin D, Yi EC, Lee H, Aebersold R., Anal. Chem. 76(13), 2004
PMID: 15228367
TOPPView: an open-source viewer for mass spectrometry data.
Sturm M, Kohlbacher O., J. Proteome Res. 8(7), 2009
PMID: 19425593
Current challenges and developments in GC-MS based metabolite profiling technology.
Kopka J., J. Biotechnol. 124(1), 2006
PMID: 16434119
Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism.
Broeckling CD, Huhman DV, Farag MA, Smith JT, May GD, Mendes P, Dixon RA, Sumner LW., J. Exp. Bot. 56(410), 2004
PMID: 15596476
Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts.
Beckonert O, Keun HC, Ebbels TM, Bundy J, Holmes E, Lindon JC, Nicholson JK., Nat Protoc 2(11), 2007
PMID: 18007604
Spectroscopic and statistical techniques for information recovery in metabonomics and metabolomics.
Lindon JC, Nicholson JK., Annu Rev Anal Chem (Palo Alto Calif) 1(), 2008
PMID: 20636074
MetaboMiner--semi-automated identification of metabolites from 2D NMR spectra of complex biofluids.
Xia J, Bjorndahl TC, Tang P, Wishart DS., BMC Bioinformatics 9(), 2008
PMID: 19040747

Hotelling, J. Educ. Psychol. 24(), 1933

Kruskal, Psychometrika 29(), 1964

Venna, Inf. Vis. 6(), 2007

Inselberg, Vis. Comput. 1(), 1985
Cluster analysis and display of genome-wide expression patterns.
Eisen MB, Spellman PT, Brown PO, Botstein D., Proc. Natl. Acad. Sci. U.S.A. 95(25), 1998
PMID: 9843981

Wilkinson, Am. Stat. 63(), 2009
Biochemistry. A postgenomic visual icon.
Weinstein JN., Science 319(5871), 2008
PMID: 18369130
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 20195258
PubMed | Europe PMC

Suchen in

Google Scholar