1
|
Han G, Yan D, Sun Z, Fang J, Chang X, Wilson L, Liu Y. Bayesian-frequentist hybrid inference framework for single cell RNA-seq analyses. Hum Genomics 2024; 18:69. [PMID: 38902839 DOI: 10.1186/s40246-024-00638-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Single cell RNA sequencing technology (scRNA-seq) has been proven useful in understanding cell-specific disease mechanisms. However, identifying genes of interest remains a key challenge. Pseudo-bulk methods that pool scRNA-seq counts in the same biological replicates have been commonly used to identify differentially expressed genes. However, such methods may lack power due to the limited sample size of scRNA-seq datasets, which can be prohibitively expensive. RESULTS Motivated by this, we proposed to use the Bayesian-frequentist hybrid (BFH) framework to increase the power and we showed in simulated scenario, the proposed BFH would be an optimal method when compared with other popular single cell differential expression methods if both FDR and power were considered. As an example, the method was applied to an idiopathic pulmonary fibrosis (IPF) case study. CONCLUSION In our IPF example, we demonstrated that with a proper informative prior, the BFH approach identified more genes of interest. Furthermore, these genes were reasonable based on the current knowledge of IPF. Thus, the BFH offers a unique and flexible framework for future scRNA-seq analyses.
Collapse
Affiliation(s)
- Gang Han
- Department of Epidemiology and Biostatistics, School of Public Health, Texas A&M University, College Station, TX, USA
| | - Dongyan Yan
- Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA
| | - Zhe Sun
- Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA
| | - Jiyuan Fang
- Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA
| | - Xinyue Chang
- Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA
| | - Lucas Wilson
- Department of Epidemiology and Biostatistics, School of Public Health, Texas A&M University, College Station, TX, USA
| | - Yushi Liu
- Eli Lilly and Company, Lilly Corporate Center, 893 Delaware St, Indianapolis, IN, 46225, USA.
| |
Collapse
|
2
|
Han G, Yan D, Sun Z, Fang J, chang X, Wilson L, Liu Y. Bayesian-frequentist hybrid inference framework for single cell RNA-seq analyses. RESEARCH SQUARE 2023:rs.3.rs-3384541. [PMID: 37886581 PMCID: PMC10602069 DOI: 10.21203/rs.3.rs-3384541/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Background Single cell RNA sequencing technology (scRNA-seq) has been proven useful in understanding cell-specific disease mechanisms. However, identifying genes of interest remains a key challenge. Pseudo-bulk methods that pool scRNA-seq counts in the same biological replicates have been commonly used to identify differentially expressed genes. However, such methods may lack power due to the limited sample size of scRNA-seq datasets, which can be prohibitively expensive. Results Motivated by this, we proposed to use the Bayesian-frequentist hybrid (BFH) framework to increase the power. Conclusion In our idiopathic pulmonary fibrosis (IPF) case study, we demonstrated that with a proper informative prior, the BFH approach identified more genes of interest. Furthermore, these genes were reasonable based on the current knowledge of IPF. Thus, the BFH offers a unique and flexible framework for future scRNA-seq analyses.
Collapse
Affiliation(s)
- Gang Han
- Epidemiology & Biostatistics, 212 Adriance Lab Rd, 1266 TAMU College Station, TX 77843
| | - Dongyan Yan
- Eli Lilly and Company Corporate Center, 893 Delaware St, Indianapolis, IN 46225
| | - Zhe Sun
- Eli Lilly and Company Corporate Center, 893 Delaware St, Indianapolis, IN 46225
| | - Jiyuan Fang
- Eli Lilly and Company Corporate Center, 893 Delaware St, Indianapolis, IN 46225
| | - Xinyue chang
- Eli Lilly and Company Corporate Center, 893 Delaware St, Indianapolis, IN 46225
| | - Lucas Wilson
- Epidemiology & Biostatistics, 212 Adriance Lab Rd, 1266 TAMU College Station, TX 77843
| | - Yushi Liu
- Eli Lilly and Company Corporate Center, 893 Delaware St, Indianapolis, IN 46225
| |
Collapse
|
3
|
The LCNetWork: An electronic representation of the mRNA-lncRNA-miRNA regulatory network underlying mechanisms of non-small cell lung cancer in humans, and its explorative analysis. Comput Biol Chem 2022; 101:107781. [DOI: 10.1016/j.compbiolchem.2022.107781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022]
|
4
|
Xu X, Ramanujam M, Visvanathan S, Assassi S, Liu Z, Li L. Transcriptional insights into pathogenesis of cutaneous systemic sclerosis using pathway driven meta-analysis assisted by machine learning methods. PLoS One 2020; 15:e0242863. [PMID: 33253326 PMCID: PMC7703909 DOI: 10.1371/journal.pone.0242863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/10/2020] [Indexed: 11/19/2022] Open
Abstract
Pathophysiology of systemic sclerosis (SSc, Scleroderma), an autoimmune rheumatic disease, comprises of mechanisms that drive vasculopathy, inflammation and fibrosis. Understanding of the disease and associated clinical heterogeneity has advanced considerably in the past decade, highlighting the necessity of more specific targeted therapy. While many of the recent trials in SSc failed to meet the primary end points that predominantly relied on changes in modified Rodnan skin scores (MRSS), sub-group analysis, especially those focused on the basal skin transcriptomic data have provided insights into patient subsets that respond to therapies. These findings suggest that deeper understanding of the molecular changes in pathways is very important to define disease drivers in various patient subgroups. In view of these challenges, we performed meta-analysis on 9 public available SSc microarray studies using a novel pathway pivoted approach combining consensus clustering and machine learning assisted feature selection. Selected pathway modules were further explored through cluster specific topological network analysis in search of novel therapeutic concepts. In addition, we went beyond previously described SSc class divisions of 3 clusters (e.g. inflammation, fibro-proliferative, normal-like) and expanded into a much finer stratification in order to profile SSc patients more accurately. Our analysis unveiled an important 80 pathway signatures that differentiated SSc patients into 8 unique subtypes. The 5 pathway modules derived from such signature successfully defined the 8 SSc subsets and were validated by in-silico cellular deconvolution analysis. Myeloid cells and fibroblasts involvement in different clusters were confirmed and linked to corresponding pathway activities. Collectively, our findings revealed more complex disease subtypes in SSc; Key gene mediators such as IL6, FGFR1, TLR7, PLCG2, IRK2 identified by network analysis underscored the scientific rationale for exploring additional targets in treatment of SSc.
Collapse
Affiliation(s)
- Xiao Xu
- Computational Biology, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States of America
| | - Meera Ramanujam
- Immunology and Respiratory Diseases Research, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States of America
| | - Sudha Visvanathan
- Translational Medicine and Clinical Pharmacology, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States of America
| | - Shervin Assassi
- Division of Rheumatology, University of Texas Health Science Center at Houston, Houston, TX, United States of America
| | - Zheng Liu
- Computational Biology, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States of America
| | - Li Li
- Computational Biology, Boehringer-Ingelheim Pharmaceuticals Inc, Ridgefield, CT, United States of America
- * E-mail:
| |
Collapse
|
5
|
CHEMGENIE: integration of chemogenomics data for applications in chemical biology. Drug Discov Today 2017; 23:151-160. [PMID: 28917822 DOI: 10.1016/j.drudis.2017.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/25/2017] [Accepted: 09/08/2017] [Indexed: 12/16/2022]
Abstract
Increasing amounts of biological data are accumulating in the pharmaceutical industry and academic institutions. However, data does not equal actionable information, and guidelines for appropriate data capture, harmonization, integration, mining, and visualization need to be established to fully harness its potential. Here, we describe ongoing efforts at Merck & Co. to structure data in the area of chemogenomics. We are integrating complementary data from both internal and external data sources into one chemogenomics database (Chemical Genetic Interaction Enterprise; CHEMGENIE). Here, we demonstrate how this well-curated database facilitates compound set design, tool compound selection, target deconvolution in phenotypic screening, and predictive model building.
Collapse
|
6
|
Kandoi G, Acencio ML, Lemke N. Prediction of Druggable Proteins Using Machine Learning and Systems Biology: A Mini-Review. Front Physiol 2015; 6:366. [PMID: 26696900 PMCID: PMC4672042 DOI: 10.3389/fphys.2015.00366] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/17/2015] [Indexed: 12/11/2022] Open
Abstract
The emergence of -omics technologies has allowed the collection of vast amounts of data on biological systems. Although, the pace of such collection has been exponential, the impact of these data remains small on many critical biomedical applications such as drug development. Limited resources, high costs, and low hit-to-lead ratio have led researchers to search for more cost effective methodologies. A possible alternative is to incorporate computational methods of potential drug target prediction early during drug discovery workflow. Computational methods based on systems approaches have the advantage of taking into account the global properties of a molecule not limited to its sequence, structure or function. Machine learning techniques are powerful tools that can extract relevant information from massive and noisy data sets. In recent years the scientific community has explored the combined power of these fields to propose increasingly accurate and low cost methods to propose interesting drug targets. In this mini-review, we describe promising approaches based on the simultaneous use of systems biology and machine learning to access gene and protein druggability. Moreover, we discuss the state-of-the-art of this emerging and interdisciplinary field, discussing data sources, algorithms and the performance of the different methodologies. Finally, we indicate interesting avenues of research and some remaining open challenges.
Collapse
Affiliation(s)
- Gaurav Kandoi
- Department of Electrical and Computer Engineering, Iowa State University Ames, IA, USA
| | - Marcio L Acencio
- Department of Physics and Biophysics, Institute of Biosciences of Botucatu, UNESP - São Paulo State University Botucatu, Brazil
| | - Ney Lemke
- Department of Physics and Biophysics, Institute of Biosciences of Botucatu, UNESP - São Paulo State University Botucatu, Brazil
| |
Collapse
|
7
|
Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms. PLoS One 2014; 9:e102909. [PMID: 25170892 PMCID: PMC4149353 DOI: 10.1371/journal.pone.0102909] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 06/25/2014] [Indexed: 12/20/2022] Open
Abstract
Detailed analysis of disease-affected tissue provides insight into molecular mechanisms contributing to pathogenesis. Substantia nigra, striatum, and cortex are functionally connected with increasing degrees of alpha-synuclein pathology in Parkinson's disease. We undertook functional and causal pathway analysis of gene expression and proteomic alterations in these three regions, and the data revealed pathways that correlated with disease progression. In addition, microarray and RNAseq experiments revealed previously unidentified causal changes related to oligodendrocyte function and synaptic vesicle release, and these and other changes were reflected across all brain regions. Importantly, subsets of these changes were replicated in Parkinson's disease blood; suggesting peripheral tissue may provide important avenues for understanding and measuring disease status and progression. Proteomic assessment revealed alterations in mitochondria and vesicular transport proteins that preceded gene expression changes indicating defects in translation and/or protein turnover. Our combined approach of proteomics, RNAseq and microarray analyses provides a comprehensive view of the molecular changes that accompany functional loss and alpha-synuclein pathology in Parkinson's disease, and may be instrumental to understand, diagnose and follow Parkinson's disease progression.
Collapse
|
8
|
Bornot A, Blackett C, Engkvist O, Murray C, Bendtsen C. The Role of Historical Bioactivity Data in the Deconvolution of Phenotypic Screens. ACTA ACUST UNITED AC 2014; 19:696-706. [PMID: 24441646 DOI: 10.1177/1087057113518966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/07/2013] [Indexed: 12/20/2022]
Abstract
A substantial challenge in phenotypic drug discovery is the identification of the molecular targets that govern a phenotypic response of interest. Several experimental strategies are available for this, the so-called target deconvolution process. Most of these approaches exploit the affinity between a small-molecule compound and its putative targets or use large-scale genetic manipulations and profiling. Each of these methods has strengths but also limitations such as bias toward high-affinity interactions or risks from genetic compensation. The use of computational methods for target and mechanism of action identification is a complementary approach that can influence each step of a phenotypic screening campaign. Here, we describe how cheminformatics and bioinformatics are embedded in the process from initial selection of a focused compound library from a large set of historical small-molecule screens through the analysis of screening results. We present a deconvolution method based on enrichment analysis and using known bioactivity data of screened compounds to infer putative targets, pathways, and biological processes that are consistent with the observed phenotypic response. As an example, the approach is applied to a cellular screen aiming at identifying inhibitors of tumor necrosis factor-α production in lipopolysaccharide-stimulated THP-1 cells. In summary, we find that the approach can contribute to solving the often very complex target deconvolution task.
Collapse
Affiliation(s)
- Aurelie Bornot
- AstraZeneca R&D, Discovery Sciences, Computational Biology, Macclesfield, Cheshire, UK
| | - Carolyn Blackett
- AstraZeneca R&D, Discovery Sciences, HTS, Macclesfield, Cheshire, UK
| | - Ola Engkvist
- AstraZeneca R&D, Discovery Sciences, Chemistry Innovation Centre, Mölndal, Sweden
| | - Clare Murray
- AstraZeneca R&D, New Opportunities, Macclesfield, Cheshire, UK
| | - Claus Bendtsen
- AstraZeneca R&D, Discovery Sciences, Computational Biology, Macclesfield, Cheshire, UK
| |
Collapse
|
9
|
Emig D, Ivliev A, Pustovalova O, Lancashire L, Bureeva S, Nikolsky Y, Bessarabova M. Drug target prediction and repositioning using an integrated network-based approach. PLoS One 2013; 8:e60618. [PMID: 23593264 PMCID: PMC3617101 DOI: 10.1371/journal.pone.0060618] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 02/28/2013] [Indexed: 11/18/2022] Open
Abstract
The discovery of novel drug targets is a significant challenge in drug development. Although the human genome comprises approximately 30,000 genes, proteins encoded by fewer than 400 are used as drug targets in the treatment of diseases. Therefore, novel drug targets are extremely valuable as the source for first in class drugs. On the other hand, many of the currently known drug targets are functionally pleiotropic and involved in multiple pathologies. Several of them are exploited for treating multiple diseases, which highlights the need for methods to reliably reposition drug targets to new indications. Network-based methods have been successfully applied to prioritize novel disease-associated genes. In recent years, several such algorithms have been developed, some focusing on local network properties only, and others taking the complete network topology into account. Common to all approaches is the understanding that novel disease-associated candidates are in close overall proximity to known disease genes. However, the relevance of these methods to the prediction of novel drug targets has not yet been assessed. Here, we present a network-based approach for the prediction of drug targets for a given disease. The method allows both repositioning drug targets known for other diseases to the given disease and the prediction of unexploited drug targets which are not used for treatment of any disease. Our approach takes as input a disease gene expression signature and a high-quality interaction network and outputs a prioritized list of drug targets. We demonstrate the high performance of our method and highlight the usefulness of the predictions in three case studies. We present novel drug targets for scleroderma and different types of cancer with their underlying biological processes. Furthermore, we demonstrate the ability of our method to identify non-suspected repositioning candidates using diabetes type 1 as an example.
Collapse
Affiliation(s)
- Dorothea Emig
- IP & Science, Thomson Reuters, Carlsbad, California, United States of America
| | - Alexander Ivliev
- IP & Science, Thomson Reuters, Carlsbad, California, United States of America
| | - Olga Pustovalova
- IP & Science, Thomson Reuters, Carlsbad, California, United States of America
| | - Lee Lancashire
- IP & Science, Thomson Reuters, Carlsbad, California, United States of America
| | - Svetlana Bureeva
- IP & Science, Thomson Reuters, Carlsbad, California, United States of America
| | - Yuri Nikolsky
- IP & Science, Thomson Reuters, Carlsbad, California, United States of America
| | - Marina Bessarabova
- IP & Science, Thomson Reuters, Carlsbad, California, United States of America
- * E-mail:
| |
Collapse
|
10
|
Bornot A, Bauer U, Brown A, Firth M, Hellawell C, Engkvist O. Systematic Exploration of Dual-Acting Modulators from a Combined Medicinal Chemistry and Biology Perspective. J Med Chem 2013; 56:1197-210. [DOI: 10.1021/jm301653f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aurelie Bornot
- Discovery Sciences, Computational Biology, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Udo Bauer
- iMED CV/GI, Medicinal Chemistry, AstraZeneca R&D, Pepparedsleden 1, Mölndal, SE-431 83, Sweden
| | - Alastair Brown
- iMED CV/GI, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Mike Firth
- Discovery Sciences, Computational Biology, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Caroline Hellawell
- Discovery Sciences, Computational Biology, AstraZeneca R&D, Alderley Park, Macclesfield, Cheshire, SK10 4TG, U.K
| | - Ola Engkvist
- Discovery Sciences, Computational Chemistry, AstraZeneca R&D, Pepparedsleden 1, Mölndal, SE-431 83, Sweden
| |
Collapse
|
11
|
James K, Wipat A, Hallinan J. Is newer better?--evaluating the effects of data curation on integrated analyses in Saccharomyces cerevisiae. Integr Biol (Camb) 2012; 4:715-27. [PMID: 22526920 DOI: 10.1039/c2ib00123c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recent high-throughput experiments have produced a wealth of heterogeneous datasets, each of which provides information about different aspects of the cell. Consequently, integration of diverse data types is essential in order to address many biological questions. The quality of any integrated analysis system is dependent upon the quality of its component data, and upon the Gold Standard data used to evaluate it. It is commonly assumed that the quality of data improves as databases grow and change, particularly for manually curated databases. However, the validity of this assumption can be questioned, given the constant changes in the data coupled with the high level of noise associated with high-throughput experimental techniques. One of the most powerful approaches to data integration is the use of Probabilistic Functional Integrated Networks (PFINs). Here, we systematically analyse the changes in four highly-curated and widely-used online databases and evaluate the extent to which these changes affect the protein function prediction performance of PFINs in the yeast Saccharomyces cerevisiae. We find that the global trend in network performance improves over time. Where individual areas of biology are concerned, however, the most recent files do not always produce the best results. Individual datasets have unique biases towards different biological processes and by selecting and integrating relevant datasets performance can be improved. When using any type of integrated system to answer a specific biological question careful selection of raw data and Gold Standard is vital, since the most recent data may not be the most appropriate.
Collapse
Affiliation(s)
- Katherine James
- School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | | | | |
Collapse
|
12
|
Bureeva S, Nikolsky Y. Quantitative knowledge-based analysis in compound safety assessment. Expert Opin Drug Metab Toxicol 2011; 7:287-98. [DOI: 10.1517/17425255.2011.553191] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
13
|
Som A, Harder C, Greber B, Siatkowski M, Paudel Y, Warsow G, Cap C, Schöler H, Fuellen G. The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PLoS One 2010; 5:e15165. [PMID: 21179244 PMCID: PMC3003487 DOI: 10.1371/journal.pone.0015165] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/27/2010] [Indexed: 12/20/2022] Open
Abstract
Background Analysis of the mechanisms underlying pluripotency and reprogramming would benefit substantially from easy access to an electronic network of genes, proteins and mechanisms. Moreover, interpreting gene expression data needs to move beyond just the identification of the up-/downregulation of key genes and of overrepresented processes and pathways, towards clarifying the essential effects of the experiment in molecular terms. Methodology/Principal Findings We have assembled a network of 574 molecular interactions, stimulations and inhibitions, based on a collection of research data from 177 publications until June 2010, involving 274 mouse genes/proteins, all in a standard electronic format, enabling analyses by readily available software such as Cytoscape and its plugins. The network includes the core circuit of Oct4 (Pou5f1), Sox2 and Nanog, its periphery (such as Stat3, Klf4, Esrrb, and c-Myc), connections to upstream signaling pathways (such as Activin, WNT, FGF, BMP, Insulin, Notch and LIF), and epigenetic regulators as well as some other relevant genes/proteins, such as proteins involved in nuclear import/export. We describe the general properties of the network, as well as a Gene Ontology analysis of the genes included. We use several expression data sets to condense the network to a set of network links that are affected in the course of an experiment, yielding hypotheses about the underlying mechanisms. Conclusions/Significance We have initiated an electronic data repository that will be useful to understand pluripotency and to facilitate the interpretation of high-throughput data. To keep up with the growth of knowledge on the fundamental processes of pluripotency and reprogramming, we suggest to combine Wiki and social networking software towards a community curation system that is easy to use and flexible, and tailored to provide a benefit for the scientist, and to improve communication and exchange of research results. A PluriNetWork tutorial is available at http://www.ibima.med.uni-rostock.de/IBIMA/PluriNetWork/.
Collapse
Affiliation(s)
- Anup Som
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany
| | - Clemens Harder
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany
| | - Boris Greber
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Marcin Siatkowski
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany
- DZNE, German Center for Neurodegenerative Diseases, Rostock, Germany
| | - Yogesh Paudel
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany
| | - Gregor Warsow
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany
- Institute for Anatomy and Cell Biology, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
- Department of Mathematics and Informatics, Ernst Moritz Arndt University Greifswald, Greifswald, Germany
| | - Clemens Cap
- Department of Computer Science, University of Rostock, Rostock, Germany
| | - Hans Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany
- * E-mail:
| |
Collapse
|