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Emerging paradigms in applied bioinformatics

Sergey E. Ilyin, Albert Pinhasov, Anil H. Vaidya, Frank A. Amato, Jack Kauffman, Hong Xin, Patricia Andrade-Gordon, Carlos R. Plata-Salamán, Douglas E. Brenneman
To meet growing needs for target functional characterization and biomarker discovery, we combined two different technologies from traditionally separate areas of drug discovery (HTS and bioinformatics)  ...  As a crucially important process for identifying new targets for drug discovery, several strategies can be used for this purpose.  ... 
doi:10.1016/s1478-5382(03)02315-1 fatcat:i5ldkn4frrgzrhau5cwesvd3ye

NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology

Paolo Romano, Francesca Cordero
2016 BMC Bioinformatics  
The topics of the workshop were centred around bioinformatics methods, tools, applications, and perspectives for models, standards and management of high-throughput biological data, structural bioinformatics  ...  The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from structural bioinformatics, to proteomics and to integrative systems biology.  ...  The paper "Geena 2, improved automated analysis of MALDI/TOF mass spectra" [11] by Romano P et al. presents a web application for the automation of a pipeline concerning MALDI/TOF mass spectra data preprocessing  ... 
doi:10.1186/s12859-016-0907-y pmid:26960985 pmcid:PMC4896255 fatcat:az2a4fbdsvembc4aiywhxxb3me

XML in Motion from Genome to Drug

C. Gopi Mohan, C. Gopi Mohan
2007 Nature Precedings  
drug discovery.  ...  As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics  ...  Fig. 1 : 1 Schematic outline of the application of SB and its integration with XML in drug discovery process. experiments (Crystallography, NMR, Kinetic analysis etc.  ... 
doi:10.1038/npre.2007.287.1 fatcat:3c5nn4v4fbbqrgkgz5eculwylm

XML in Motion from Genome to Drug

C. Gopi Mohan, C. Gopi Mohan
2007 Nature Precedings  
drug discovery.  ...  As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics  ...  Fig. 1 : 1 Schematic outline of the application of SB and its integration with XML in drug discovery process. experiments (Crystallography, NMR, Kinetic analysis etc.  ... 
doi:10.1038/npre.2007.287 fatcat:x2uxyxnleva7ra53jgjecojolm

The breakdown on bioinformatics

Brendan Horton
1997 Nature  
organizations seeking to use bioinformatics to discover new drug targets.  ...  Reader Enquiry No. 102 GeneWorld 2.1 Pangea Systems A bioinformatics database application for automated sequence annotation and analysis This product should find use in informationbased pharmaceutical  ... 
doi:10.1038/41600 fatcat:kiq2skdgtnb5pndwx5nonhi3ia

From Molecules to Patients: The Clinical Applications of Translational Bioinformatics

K. Regan, P. R.O. Payne
2015 IMIA Yearbook of Medical Informatics  
In this review, we aim to evaluate the expanding field of TBI towards clinical applications, and define common themes and current gaps in order to motivate future research.  ...  Objective: In order to realize the promise of personalized medicine, Translational Bioinformatics (TBI) research will need to continue to address implementation issues across the clinical spectrum.  ...  data sets), hypothesis generation (e.g., the automated and/or semi-automated creation of rationale questions to be explored in terms of genotype-to-phenotype relationships in targeted data sets), and  ... 
doi:10.15265/iy-2015-005 pmid:26293863 pmcid:PMC4587059 fatcat:b5kt4idr4nagbiug5xkex2qbzm

Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform

Markus List
2017 Journal of Integrative Bioinformatics  
We demonstrate the power of this approach by example of a Docker compose setup for a drug target screening platform consisting of five integrated web applications and shared infrastructure, deployable  ...  AbstractDocker virtualization allows for software tools to be executed in an isolated and controlled environment referred to as a container.  ...  Acknowledgements Thanks to all former and present members of the NanoCAN Center for Excellence in Nanomedicine at the University of Southern Denmark for their thorough feedback on usability.  ... 
doi:10.1515/jib-2017-0016 pmid:28600904 fatcat:el64crsprfe7vnytk3tttbgkpa

Proteomics: delivering new routes to drug discovery – Part 2

Kewal K Jain
2001 Drug Discovery Today  
broad coverage of the application of innovative proteomic technologies for drug discovery.  ...  Integration of genomic, proteomic, transcript-level and biological data is achieved using bioinformatics.  ...  Marc Wilkins (Proteome Systems, Sydney, Australia) described a bioinformatic platform for the integration and analysis of proteomic data to derive meaningful results.  ... 
doi:10.1016/s1359-6446(01)01912-2 pmid:11495754 fatcat:ewzk6q7umjfj7fy4ocss52twxu

Cloud Based Big Data Infrastructure: Architectural Components And Automated Provisioning

Yuri Demchenko, Fatih Turkmen, Christophe Blanchet, Charles Loomis, Caees de Laat
2016 Zenodo  
The paper provides example of requirements analysis and implementation of two bioinformatics use cases on cloud and using SlipStream based cloud applications deployment and management automation platform  ...  SlipStream cloud automation platform that allows multi-cloud applications deployment and management  ...  The authors are thankful to the partners of the CYCLONE project and to the colleagues who collaborated on deploying selected bioinformatics applications in the CYCLONE testbed: Christian Baudet (Centre  ... 
doi:10.5281/zenodo.59159 fatcat:yxvau4m65vgkffgwwmy7nwrdmy

New developments and emerging trends in high-throughput screening methods for lead compound identification

James Noah
2010 International Journal of High Throughput Screening  
High-throughput screening (HTS) campaigns have become a starting point for many drug discovery programs and are being conducted not only by large pharmaceutical companies but increasingly by smaller biotechnology  ...  The underlying theme of any HTS campaign is the inventive application of brute force, and the pace and variety of invention strategies that have increased as HTS has evolved from a specialty capability  ...  The concept was not new, but since commercial automation was still sparsely available and expensive, early automation was often customized for the particular testing design and therefore not directly applicable  ... 
doi:10.2147/ijhts.s8683 fatcat:ojryzbuvozcvzcpqax6iek5s2u

Evidence evaluation in biomedical knowledge graphs for pharmaceutical discovery

Jeremy Yang
2022 Zenodo  
Jeremy Yang -Dissertation Defense -March 7, 2022 A simple web application for drug discovery scientist-friendly drug target hypothesis exploration and prioritization, druggable genome illumination use  ...  evidence for pharmaceutical discovery 43 TIN-X: Target Importance and Novelty Explorer, D.C.  ...  KGAP PD illuminated gene case study: SYNGR3 Publications indexed by TIN-X presenting experimental and theoretical evidence for connection between statin drugs, therapeutic effectiveness for PD, and the  ... 
doi:10.5281/zenodo.6600185 fatcat:vylweaemmfef3nitg7wmxwf6yq

Bioinformatics Resources for MicroRNA Discovery

Alyssa C. Moore, Jonathan S. Winkjer, Tsai-Tien Tseng
2015 Biomarker Insights  
With the advent of nextgeneration sequencing, the amount of data on miRNA has increased tremendously in the last decade, requiring new bioinformatics approaches for processing and storing new information  ...  This review focuses on several curated databases of miRNAs and their targets from both predicted and validated sources.  ...  Acknowledgment We thank Ashley Pedicini for her assistance in the prepara tion of this article. Author contributions Wrote the first draft of the manuscript: ACM, JSW, TTT.  ... 
doi:10.4137/bmi.s29513 pmid:26819547 pmcid:PMC4718083 fatcat:jczczhxxubayrgi4l27s6tzxbe

Current methodologies for translational bioinformatics

Yves A. Lussier, Atul J. Butte, Lawrence Hunter
2010 Journal of Biomedical Informatics  
Haiquan Li for his critical review of the editorial.  ...  With the accelerated discovery of biomarkers and gene expression signatures, the automations are of prime importance for quality control as the complexity of clinical trials is increasing with greater  ...  The following two manuscripts propose methods that enable integrative translational bioinformatics research.  ... 
doi:10.1016/j.jbi.2010.05.002 pmid:20470899 pmcid:PMC2894568 fatcat:7r2kuprwjrh3nb6qhy2sowfdly

D1.8 Tools Interoperability And Service Registry

Magnus Palmblad, Anna-Lena Lamprecht, Veit Schwämmle, Jon Ison
2018 Zenodo  
Instead, we took a much more targeted approach, focussing - as an exemplar - upon the systematic curation of tools for proteomics data analysis, and subsequent exploitation of the annotations for automated  ...  Automated workflow composition in mass spectrometry based proteomics Accepted for publication in Bioinformatics The first article (Tsiamis et†al†.) describes a systematic approach towards the comprehensive  ...  Objective Yes No 1 Deliver a discovery portal built upon a federated curation of a wide range of key resources for bioinformatics resources world-wide. x Service monitoring, resource integration, interoperability  ... 
doi:10.5281/zenodo.1456766 fatcat:hply4krokvfsroveizv3c7pdwi


Nutan Prakash, Dinta A. Gareja
2010 Journal of Proteomics & Bioinformatics  
Cheminformatics can also be applied to data analysis for various industries like paper and pulp, dyes and such applied industries. automated approach will make drug discovery a highly knowledge specific  ...  This has resulted in both targeted drug discovery and reduced drug development cycle time.  ...  Integration of Cheminformatics and bioinformatics methods will be key to this.  ... 
doi:10.4172/jpb.1000147 fatcat:4sydfwpdlzhhrajtxtjipf2rmm
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