Journal of integrative bioinformatics

Welcome to JIB.tools!

The official bioinformatics tool list for the Journal of Integrative Bioinformatics (JIB).


All bioinformatics tools published in JIB are automatically added to JIB.tools with first authors having the ability to edit their entries and directly import the tools information to bio.tools.


2020


Predicting and Designing Epitope Ensemble Vaccines against HTLV-1.

Alam S, Hasan MK, Manjur OHB, Khan AM, Sharmin Z, Pavel MA, Hossain MF. Predicting and Designing Epitope Ensemble Vaccines against HTLV-1.. J Integr Bioinform. 2020;16(4).
2020-01-08 | DOI 10.1515/jib-2018-0051 | PubMed 31913852

JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools.

Friedrichs M, Shoshi A, Chmura PJ, Ison J, Schwämmle V, Schreiber F, Hofestädt R, Sommer B. JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools.. J Integr Bioinform. 2020;16(4).
2020-01-08 | DOI 10.1515/jib-2019-0059 | PubMed 31913853

Programmatic Access to FAIRified Digital Plant Genetic Resources.

Ghaffar M, Schüler D, König P, Arend D, Junker A, Scholz U, Lange M. Programmatic Access to FAIRified Digital Plant Genetic Resources.. J Integr Bioinform. 2020;16(4).
2020-01-08 | DOI 10.1515/jib-2019-0060 | PubMed 31913851

2019


Ancestral Reconstruction and Investigations of Genomic Recombination on some Pentapetalae Chloroplasts.

Guyeux C, Salomon M, Al-Nuaimi B, AlKindy B, Couchot JF. Ancestral Reconstruction and Investigations of Genomic Recombination on some Pentapetalae Chloroplasts.. J Integr Bioinform. 2019;16(4).
2019-12-20 | DOI 10.1515/jib-2018-0057 | PubMed 31860470

The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development.

Sommer B. The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development.. J Integr Bioinform. 2019;.
2019-09-27 | DOI 10.1515/jib-2019-0057 | PubMed 31560649

Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions.

Li Y, Aguilar-Martinez E, Sharrocks AD. Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions.. J Integr Bioinform. 2019;.
2019-07-13 | DOI 10.1515/jib-2018-0090 | PubMed 31301672

Mental-Map Preserving Visualisation of Partitioned Networks in Vanted.

Garkov D, Klein K, Klukas C, Schreiber F. Mental-Map Preserving Visualisation of Partitioned Networks in Vanted.. J Integr Bioinform. 2019;.
2019-06-14 | DOI 10.1515/jib-2019-0026 | PubMed 31199771

2018


GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks.

Shoshi A, Hofestädt R, Zolotareva O, Friedrichs M, Maier A, Ivanisenko VA, Dosenko VE, Bragina EY. GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks.. J Integr Bioinform. 2018;15(4).
2018-12-25 | DOI 10.1515/jib-2018-0049 | PubMed 30864352

Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA.

Brinkrolf C, Henke NA, Ochel L, Pucker B, Kruse O, Lutter P. Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA.. J Integr Bioinform. 2018;15(3).
2018-09-15 | DOI 10.1515/jib-2018-0018 | PubMed 30218605

BioModelKit - An Integrative Framework for Multi-Scale Biomodel-Engineering.

Blätke MA. BioModelKit - An Integrative Framework for Multi-Scale Biomodel-Engineering.. J Integr Bioinform. 2018;15(3).
2018-09-06 | DOI 10.1515/jib-2018-0021 | PubMed 30205646

Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach.

Brandizi M, Singh A, Rawlings C, Hassani-Pak K. Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach.. J Integr Bioinform. 2018;15(3).
2018-08-07 | DOI 10.1515/jib-2018-0023 | PubMed 30085931

Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell.

Biere N, Ghaffar M, Doebbe A, Jäger D, Rothe N, Friedrich BM, Hofestädt R, Schreiber F, Kruse O, Sommer B. Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell.. J Integr Bioinform. 2018;15(2).
2018-07-11 | DOI 10.1515/jib-2018-0003 | PubMed 30001212

Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data.

Trellet M, Férey N, Flotyński J, Baaden M, Bourdot P. Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data.. J Integr Bioinform. 2018;15(2).
2018-07-09 | DOI 10.1515/jib-2018-0004 | PubMed 29982236

MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.

Maes A, Martinez X, Druart K, Laurent B, Guégan S, Marchand CH, Lemaire SD, Baaden M. MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.. J Integr Bioinform. 2018;15(2).
2018-06-21 | DOI 10.1515/jib-2018-0006 | PubMed 29927748

BioSankey: Visualization of Microbial Communities Over Time.

Platzer A, Polzin J, Rembart K, Han PP, Rauer D, Nussbaumer T. BioSankey: Visualization of Microbial Communities Over Time.. J Integr Bioinform. 2018;15(4).
2018-06-13 | DOI 10.1515/jib-2017-0063 | PubMed 29897884

MIRATE: MIps RATional dEsign Science Gateway.

Busato M, Distefano R, Bates F, Karim K, Bossi AM, López Vilariño JM, Piletsky S, Bombieri N, Giorgetti A. MIRATE: MIps RATional dEsign Science Gateway.. J Integr Bioinform. 2018;15(4).
2018-06-13 | DOI 10.1515/jib-2017-0075 | PubMed 29897885

BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform.

Chowdhury S, Sinha N, Ganguli P, Bhowmick R, Singh V, Nandi S, Sarkar RR. BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform.. J Integr Bioinform. 2018;15(3).
2018-03-16 | DOI 10.1515/jib-2017-0072 | PubMed 29547394

2017


A Novel Method to Detect Bias in Short Read NGS Data.

Alnasir J, Shanahan HP. A Novel Method to Detect Bias in Short Read NGS Data. J Integr Bioinform. 2017;14(3).
2017-09-23 | DOI 10.1515/jib-2017-0025 | PubMed 28941355

MUSTv2: An Improved De Novo Detection Program for Recently Active Miniature Inverted Repeat Transposable Elements (MITEs).

Ge R, Mai G, Zhang R, Wu X, Wu Q, Zhou F. MUSTv2: An Improved De Novo Detection Program for Recently Active Miniature Inverted Repeat Transposable Elements (MITEs). J Integr Bioinform. 2017;14(3).
2017-08-10 | DOI 10.1515/jib-2017-0029 | PubMed 28796642

CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape.

Larsen SJ, Baumbach J. CytoMCS: A Multiple Maximum Common Subgraph Detection Tool for Cytoscape. J Integr Bioinform. 2017;14(2).
2017-07-21 | DOI 10.1515/jib-2017-0014 | PubMed 28731857

LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis.

Barbosa E, Röttger R, Hauschild A-C, et al. LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. J Integr Bioinform. 2017;14(2).
2017-07-05 | DOI 10.1515/jib-2017-0010 | PubMed 28678736

Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA.

Hamzeiy H, Suluyayla R, Brinkrolf C, Janowski SJ, Hofestaedt R, Allmer J. Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA.. J Integr Bioinform. 2017;14(1).
2017-06-13 | DOI 10.1515/jib-2016-0004 | PubMed 28609293

clubber: removing the bioinformatics bottleneck in big data analyses.

Miller M, Zhu C, Bromberg Y. clubber: removing the bioinformatics bottleneck in big data analyses. J Integr Bioinform. 2017;14(2).
2017-06-13 | DOI 10.1515/jib-2017-0020 | PubMed 28609295

2016


A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes.

Saçar demirci MD, Toprak M, Allmer J. A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes. J Integr Bioinform. 2016;13(5):303.
2016-12-22 | DOI 10.2390/biecoll-jib-2016-303 | PubMed 28187417

Current progress of high-throughput microRNA differential expression analysis and random forest gene selection for model and non-model systems: an R implementation.

Zhang J, Hadj-Moussa H, Storey KB. Current Progress of High-Throughput MicroRNA Differential Expression Analysis and Random Forest Gene Selection for Model and Non-Model Systems: an R Implementation. J Integr Bioinform. 2016;13(5).
2016-12-22 | DOI 10.2390/biecoll-jib-2016-306 | PubMed 28187420

miRquant 2.0: an Expanded Tool for Accurate Annotation and Quantification of MicroRNAs and their isomiRs from Small RNA-Sequencing Data.

Kanke M, Baran-Gale J, Villanueva J, Sethupathy P. miRquant 2.0: an Expanded Tool for Accurate Annotation and Quantification of MicroRNAs and their isomiRs from Small RNA-Sequencing Data. J Integr Bioinform. 2016;13(5).
2016-12-22 | DOI 10.2390/biecoll-jib-2016-307 | PubMed 28187421

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios.

Kovanci G, Ghaffar M, Sommer B. Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios. J Integr Bioinform. 2016;13(4):47–58.
2016-12-21 | DOI 10.2390/biecoll-jib-2016-298 | PubMed 28187414

PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes.

Has C, Lashin SA, Kochetov A, Allmer J. PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes. J Integr Bioinform. 2016;13(4):16–23.
2016-12-18 | DOI 10.2390/biecoll-jib-2016-293 | PubMed 28187409

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing.

Almeida D, Skov I, Lund J, et al. Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing. J Integr Bioinform. 2016;13(4):294.
2016-12-18 | DOI 10.2390/biecoll-jib-2016-294 | PubMed 28187410

Omics Fusion - A Platform for Integrative Analysis of Omics Data.

Brink BG, Seidel A, Kleinbölting N, Nattkemper TW, Albaum SP. Omics Fusion - A Platform for Integrative Analysis of Omics Data. J Integr Bioinform. 2016;13(4):296.
2016-12-18 | DOI 10.2390/biecoll-jib-2016-296 | PubMed 28187412

DaTo: an atlas of biological databases and tools.

Li Q, Zhou Y, Jiao Y, et al. DaTo: an atlas of biological databases and tools. J Integr Bioinform. 2016;13(4):297.
2016-12-18 | DOI 10.2390/biecoll-jib-2016-297 | PubMed 28187413

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

Damkliang K, Tandayya P, Sangket U, Pasomsub E. Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services. J Integr Bioinform. 2016;13(1):287.
2016-11-28 | DOI 10.2390/biecoll-jib-2016-287 | PubMed 28187423

Estimation of biomass composition from genomic and transcriptomic information.

Santos S, Rocha I. Estimation of biomass composition from genomic and transcriptomic information. J Integr Bioinform. 2016;13(2):285.
2016-11-27 | DOI 10.2390/biecoll-jib-2016-285 | PubMed 28187415

PetriScape - A plugin for discrete Petri net simulations in Cytoscape.

Almeida D, Azevedo V, Silva A, Baumbach J. PetriScape - A plugin for discrete Petri net simulations in Cytoscape. J Integr Bioinform. 2016;13(1):284.
2016-06-04 | DOI 10.2390/biecoll-jib-2016-284 | PubMed 27402693

2015


Extracting kinetic information from literature with KineticRE.

Alão Freitas A, Costa H, Rocha I. Extracting kinetic information from literature with KineticRE. J Integr Bioinform. 2015;12(4).
2015-11-03 | DOI 10.2390/biecoll-jib-2015-282 | PubMed 26673933

OpenLabNotes--An Electronic Laboratory Notebook Extension for OpenLabFramework.

List M, Franz M, Tan Q, Mollenhauer J, Baumbach J. OpenLabNotes--An Electronic Laboratory Notebook Extension for OpenLabFramework. J Integr Bioinform. 2015;12(3):274.
2015-10-06 | DOI 10.2390/biecoll-jib-2015-274 | PubMed 26673790

RetroMine, or how to provide in-depth retrospective studies from Medline in a glance: the hepcidin use-case.

Ameline de cadeville B, Loréal O, Moussouni-marzolf F. RetroMine, or how to provide in-depth retrospective studies from Medline in a glance: the hepcidin use-case. J Integr Bioinform. 2015;12(3):275.
2015-10-06 | DOI 10.2390/biecoll-jib-2015-275 | PubMed 26673791

Managing and Documenting Legacy Scientific Workflows.

Acuña R, Chomilier J, Lacroix Z. Managing and Documenting Legacy Scientific Workflows. J Integr Bioinform. 2015;12(3).
2015-10-06 | DOI 10.2390/biecoll-jib-2015-277 | PubMed 26673793

Web application for automatic prediction of gene translation elongation efficiency.

Sokolov V, Zuraev B, Lashin S, Matushkin Y. Web application for automatic prediction of gene translation elongation efficiency.. J Integr Bioinform. 2015;12(1).
2015-09-03 | DOI 10.2390/biecoll-jib-2015-256 | PubMed 26527190

Shared bioinformatics databases within the Unipro UGENE platform.

Protsyuk IV, Grekhov GA, Tiunov AV, Fursov MY. Shared bioinformatics databases within the Unipro UGENE platform. J Integr Bioinform. 2015;12(1):257.
2015-09-03 | DOI 10.2390/biecoll-jib-2015-257 | PubMed 26527191

GITIRBio: A Semantic and Distributed Service Oriented-Architecture for Bioinformatics Pipeline.

Castillo LF, López-Gartner G, Isaza GA, et al. GITIRBio: A Semantic and Distributed Service Oriented- Architecture for Bioinformatics Pipeline. J Integr Bioinform. 2015;12(1):1–15.
2015-05-20 | DOI 10.2390/biecoll-jib-2015-255 | PubMed 26527189

Online High-throughput Mutagenesis Designer Using Scoring Matrix of Sequence-specific Endonucleases.

Guo D, Li X, Zhu P, Feng Y, Yang J, Zheng Z, Yang W, Zhang E, Zhou S, Wang H. Online High-throughput Mutagenesis Designer Using Scoring Matrix of Sequence-specific Endonucleases.. J Integr Bioinform. 2015;12(1).
2015-03-01 | DOI 10.1515/jib-2015-283 | PubMed 29220955

2014


Identifying interactions between chemical entities in biomedical text.

Lamurias A, Ferreira JD, Couto FM. Identifying interactions between chemical entities in biomedical text. J Integr Bioinform. 2014;11(3):247.
2014-10-23 | DOI 10.2390/biecoll-jib-2014-247 | PubMed 25339081

Profiling of genetic switches using boolean implications in expression data.

Çakır MV, Binder H, Wirth H. Profiling of Genetic Switches using Boolean Implications in Expression Data. J Integr Bioinform. 2014;11(1).
2014-10-15 | DOI 10.2390/biecoll-jib-2014-246 | PubMed 25318120

LmTDRM database: a comprehensive database on thiol metabolic gene/gene products in Listeria monocytogenes EGDe.

Srinivas V, Gopal S. LmTDRM Database: A Comprehensive Database on Thiol Metabolic Gene/Gene Products in Listeria monocytogenes EGDe. J Integr Bioinform. 2014;11(1).
2014-09-17 | DOI 10.2390/biecoll-jib-2014-245 | PubMed 25228549

BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species.

Misirli G, Hallinan J, Röttger R, Baumbach J, Wipat A. BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species. J Integr Bioinform. 2014;11(2).
2014-07-08 | DOI 10.2390/biecoll-jib-2014-244 | PubMed 25001169

BioNetLink - an architecture for working with network data.

Klapperstück M, Schreiber F. BioNetLink - An Architecture for Working with Network Data. J Integr Bioinform. 2014;11(2).
2014-06-30 | DOI 10.2390/biecoll-jib-2014-241 | PubMed 24980619

VANESA - a software application for the visualization and analysis of networks in system biology applications.

Brinkrolf C, Janowski SJ, Kormeier B, et al. VANESA - a software application for the visualization and analysis of networks in system biology applications. J Integr Bioinform. 2014;11(2):239.
2014-06-23 | DOI 10.2390/biecoll-jib-2014-239 | PubMed 24953454

A query suggestion workflow for life science IR-systems.

Esch M, Chen J, Weise S, Hassani-Pak K, Scholz U, Lange M. A query suggestion workflow for life science IR-systems. J Integr Bioinform. 2014;11(2):237.
2014-06-13 | DOI 10.2390/biecoll-jib-2014-237 | PubMed 24953306

Integrated visualization of a multi-omics study of starvation in mouse intestine.

Van iersel MP, Sokolović M, Lenaerts K, et al. Integrated visualization of a multi-omics study of starvation in mouse intestine. J Integr Bioinform. 2014;11(1):235.
2014-03-28 | DOI 10.2390/biecoll-jib-2014-235 | PubMed 24675236

2013


An evolutionary and visual framework for clustering of DNA microarray data.

Castellanos-garzón JA, Díaz F. An evolutionary and visual framework for clustering of DNA microarray data. J Integr Bioinform. 2013;10(3):232.
2013-11-15 | DOI 10.2390/biecoll-jib-2013-232 | PubMed 24231146

Re-annotation of the genome sequence of Helicobacter pylori 26695.

Resende T, Correia DM, Rocha M, Rocha I. Re-annotation of the genome sequence of Helicobacter pylori 26695. J Integr Bioinform. 2013;10(3):233.
2013-11-15 | DOI 10.2390/biecoll-jib-2013-233 | PubMed 24231147

Discovery of miR-mRNA interactions via simultaneous Bayesian inference of gene networks and clusters using sequence-based predictions and expression data.

Godsey B. Discovery of miR-mRNA interactions via simultaneous Bayesian inference of gene networks and clusters using sequence-based predictions and expression data. J Integr Bioinform. 2013;10(1).
2013-07-10 | DOI 10.2390/biecoll-jib-2013-227 | PubMed 23846182

BacillOndex: an integrated data resource for systems and synthetic biology.

Misirli G, Wipat A, Mullen J, et al. BacillOndex: an integrated data resource for systems and synthetic biology. J Integr Bioinform. 2013;10(2):224.
2013-04-10 | DOI 10.2390/biecoll-jib-2013-224 | PubMed 23571273

An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice.

Liu L, Mei Q, Yu Z, Sun T, Zhang Z, Chen M. An integrative bioinformatics framework for genome-scale multiple level network reconstruction of rice. J Integr Bioinform. 2013;10(2):223.
2013-04-05 | DOI 10.2390/biecoll-jib-2013-223 | PubMed 23563093

An integrative clinical database and diagnostics platform for biomarker identification and analysis in ion mobility spectra of human exhaled air.

Schneider T, Hauschild A-C, Baumbach JI, Baumbach J. An Integrative Clinical Database and Diagnostics Platform for Biomarker Identification and Analysis in Ion Mobility Spectra of Human Exhaled Air. J Integr Bioinform. 2013;10(2).
2013-04-02 | DOI 10.2390/biecoll-jib-2013-218 | PubMed 23545212

2012


Microbase2.0: a generic framework for computationally intensive bioinformatics workflows in the cloud.

Flanagan K, Nakjang S, Hallinan J, et al. Microbase2.0: A Generic Framework for Computationally Intensive Bioinformatics Workflows in the Cloud. J Integr Bioinform. 2012;9(2).
2012-09-24 | DOI 10.2390/biecoll-jib-2012-212 | PubMed 23001322

ADOPS--Automatic Detection Of Positively Selected Sites.

Reboiro-jato D, Reboiro-jato M, Fdez-riverola F, Vieira CP, Fonseca NA, Vieira J. ADOPS--Automatic Detection Of Positively Selected Sites. J Integr Bioinform. 2012;9(3):200.
2012-07-24 | DOI 10.2390/biecoll-jib-2012-200 | PubMed 22829571

Computational approaches to standard-compliant biofilm data for reliable analysis and integration.

Sousa AM, Ferreira A, Azevedo NF, Pereira MO, Lourenço A. Computational approaches to standard-compliant biofilm data for reliable analysis and integration. J Integr Bioinform. 2012;9(3).
2012-07-24 | DOI 10.2390/biecoll-jib-2012-203 | PubMed 22829574

A rational framework for production decision making in blood establishments.

Ramoa A, Maia S, Lourenço A. A rational framework for production decision making in blood establishments. J Integr Bioinform. 2012;9(3):204.
2012-07-24 | DOI 10.2390/biecoll-jib-2012-204 | PubMed 22829575

Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing.

González R, Zato C, Benito R, et al. Automatic knowledge extraction in sequencing analysis with multiagent system and grid computing. J Integr Bioinform. 2012;9(3):206.
2012-07-24 | DOI 10.2390/biecoll-jib-2012-206 | PubMed 22829577

Nutrilyzer: a tool for deciphering atomic stoichiometry of differentially expressed paralogous proteins.

Lotz K, Schreiber F, Wünschiers R. Nutrilyzer: A Tool for Deciphering Atomic Stoichiometry of Differentially Expressed Paralogous Proteins. J Integr Bioinform. 2012;9(2).
2012-07-16 | DOI 10.2390/biecoll-jib-2012-196 | PubMed 22796635

UBioLab: a web-laboratory for ubiquitous in-silico experiments.

Bartocci E, Cacciagrano D, Di berardini MR, Merelli E, Vito L. UBioLab: a web-laboratory for ubiquitous in-silico experiments. J Integr Bioinform. 2012;9(1):192.
2012-07-09 | DOI 10.2390/biecoll-jib-2012-192 | PubMed 22773116

Oncology in vivo data integration for hypothesis generation.

Wei J, Chen M. Oncology In Vivo Data Integration for Hypothesis Generation. J Integr Bioinform. 2012;9(2).
2012-07-09 | DOI 10.2390/biecoll-jib-2012-193 | PubMed 22773158

Analysis of high-throughput plant image data with the information system IAP.

Klukas C, Pape JM, Entzian A. Analysis of high-throughput plant image data with the information system IAP. J Integr Bioinform. 2012;9(2):191.
2012-06-29 | DOI 10.2390/biecoll-jib-2012-191 | PubMed 22745177

IDPredictor: predict database links in biomedical database.

Mehlhorn H, Lange M, Scholz U, Schreiber F. IDPredictor: predict database links in biomedical database. J Integr Bioinform. 2012;9(2):1–15.
2012-06-26 | DOI 10.2390/biecoll-jib-2012-190 | PubMed 22736059

2011


METU-SNP: an integrated software system for SNP-complex disease association analysis.

Üstünkar G, Son YA. METU-SNP: An Integrated Software System for SNPComplex Disease Association Analysis. J Integr Bioinform. 2011;8(2).
2011-12-12 | DOI 10.2390/biecoll-jib-2011-187 | PubMed 22156365

The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks.

Swainston N, Smallbone K, Mendes P, Kell DB, Paton NW. The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. J Integr Bioinform. 2011;8(2).
2011-11-18 | DOI 10.2390/biecoll-jib-2011-186 | PubMed 22095399

A relational learning approach to Structure-Activity Relationships in drug design toxicity studies.

Camacho R, Pereira M, Costa VS, et al. A relational learning approach to Structure-Activity Relationships in drug design toxicity studies. J Integr Bioinform. 2011;8(3):182.
2011-09-16 | DOI 10.2390/biecoll-jib-2011-182 | PubMed 21926445

Rapid development of Proteomic applications with the AIBench framework.

López-Fernández H, Reboiro-Jato M, Glez-Peña D, et al. Rapid development of Proteomic applications with the AIBench framework. J Integr Bioinform. 2011;8(3):171.
2011-09-15 | DOI 10.2390/biecoll-jib-2011-171 | PubMed 21926434

Parallel Niche Pareto AlineaGA--an evolutionary multiobjective approach on multiple sequence alignment.

Silva FJM da, Pérez JMS, Pulido JAG, Rodríguez MAV. Parallel Niche Pareto AlineaGA – an Evolutionary Multiobjective approach on Multiple Sequence Alignment. J Integr Bioinform. 2011;8(3).
2011-09-15 | DOI 10.2390/biecoll-jib-2011-174 | PubMed 21926437

Prognostic prediction through biclustering-based classification of clinical gene expression time series.

Carreiro AV, Anunciação O, Carriço JA, Madeira SC. Prognostic Prediction through Biclustering-Based Classification of Clinical Gene Expression Time Series. J Integr Bioinform. 2011;8(3).
2011-09-15 | DOI 10.2390/biecoll-jib-2011-175 | PubMed 21926438

Protein analysis tools and services at IBIVU.

Brandt BW, Heringa J. Protein analysis tools and services at IBIVU. J Integr Bioinform. 2011;8(2).
2011-09-08 | DOI 10.2390/biecoll-jib-2011-168 | PubMed 21900709

GMB: an efficient query processor for biological data.

Taha K, Elmasri R. GMB: an efficient query processor for biological data. J Integr Bioinform. 2011;8(2):165.
2011-08-31 | DOI 10.2390/biecoll-jib-2011-165 | PubMed 21881166

DBE2 - management of experimental data for the VANTED system.

Mehlhorn H, Schreiber F. DBE2 - management of experimental data for the VANTED system. J Integr Bioinform. 2011;8(2):162.
2011-07-26 | DOI 10.2390/biecoll-jib-2011-162 | PubMed 21788680

MADMAX - Management and analysis database for multiple ~omics experiments.

Lin K, Kools H, De groot PJ, et al. MADMAX - Management and analysis database for multiple ~omics experiments. J Integr Bioinform. 2011;8(2):160.
2011-07-21 | DOI 10.2390/biecoll-jib-2011-160 | PubMed 21778530

Integrative visualization of temporally varying medical image patterns.

Soh J, Xiao M, Do T, Meruvia-Pastor O, Sensen CW. Integrative visualization of temporally varying medical image patterns. J Integr Bioinform. 2011;8(2):161.
2011-07-21 | DOI 10.2390/biecoll-jib-2011-161 | PubMed 21778531

Life sciences data and application integration with B-fabric.

Türker C, Akal F, Schlapbach R. Life Sciences Data and Application Integration with B-Fabric. J Integr Bioinform. 2011;8(2).
2011-07-20 | DOI 10.2390/biecoll-jib-2011-159 | PubMed 21772064

Web2.0 paves new ways for collaborative and exploratory analysis of chemical compounds in spectrometry data.

Loyek C, Bunkowski A, Vautz W, Nattkemper TW. Web2.0 paves new ways for collaborative and exploratory analysis of chemical compounds in spectrometry data. J Integr Bioinform. 2011;8(2):158.
2011-07-18 | DOI 10.2390/biecoll-jib-2011-158 | PubMed 21768655

Database supported candidate search for metabolite identification.

Hildebrandt C, Wolf S, Neumann S. Database supported candidate search for metabolite identification. J Integr Bioinform. 2011;8(2):157.
2011-07-07 | DOI 10.2390/biecoll-jib-2011-157 | PubMed 21734330

WIBL: Workbench for Integrative Biological Learning.

Lesk V, Taubert J, Rawlings C, Dunbar S, Muggleton S. WIBL: Workbench for Integrative Biological Learning. J Integr Bioinform. 2011;8(2).
2011-06-27 | DOI 10.2390/biecoll-jib-2011-156 | PubMed 21705808

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data.

Alawi M, Kurtz S, Beckstette M. CASSys: an integrated software-system for the interactive analysis of ChIP-seq data. J Integr Bioinform. 2011;8(2):155.
2011-06-21 | DOI 10.2390/biecoll-jib-2011-155 | PubMed 21690655

Key2Ann: a tool to process sequence sets by replacing database identifiers with a human-readable annotation.

Pürzer A, Grassmann F, Birzer D, Merkl R. Key2Ann: a tool to process sequence sets by replacing database identifiers with a human-readable annotation. J Integr Bioinform. 2011;8(1).
2011-03-04 | DOI 10.2390/biecoll-jib-2011-153 | PubMed 21372341

2010


From binary to multivalued to continuous models: the lac operon as a case study.

Franke R, Theis FJ, Klamt S. From Binary to Multivalued to Continuous Models: The lac Operon as a Case Study. J Integr Bioinform. 2010;7(1).
2010-12-14 | DOI 10.2390/biecoll-jib-2010-151 | PubMed 21200084

Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient.

Lecca P, Ihekwaba AEC, Dematté L, Priami C. Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient. J Integr Bioinform. 2010;7(1).
2010-11-23 | DOI 10.2390/biecoll-jib-2010-150 | PubMed 21098882

Visualization and analysis of a cardio vascular disease- and MUPP1-related biological network combining text mining and data warehouse approaches.

Sommer B, Tiys ES, Kormeier B, et al. Visualization and Analysis of a Cardio Vascular Diseaseand MUPP1-related Biological Network combining Text Mining and Data Warehouse Approaches. J Integr Bioinform. 2010;7(1).
2010-11-11 | DOI 10.2390/biecoll-jib-2010-148 | PubMed 21068463

PathJam: a new service for integrating biological pathway information.

Glez-Peña D, Reboiro-Jato M, Domínguez R, Gómez-López G, Pisano DG, Fdez-Riverola F. PathJam: a new service for integrating biological pathway information. J Integr Bioinform. 2010;7(1).
2010-10-28 | DOI 10.2390/biecoll-jib-2010-147 | PubMed 20980714

Reconstruction of biological networks based on life science data integration.

Kormeier B, Hippe K, Arrigo P, Töpel T, Janowski S, Hofestädt R. Reconstruction of biological networks based on life science data integration. J Integr Bioinform. 2010;7(2).
2010-10-27 | DOI 10.2390/biecoll-jib-2010-146 | PubMed 20978286

miReg: a resource for microRNA regulation.

Barh D, Bhat D, Viero C. miReg: a resource for microRNA regulation. J Integr Bioinform. 2010;7(1).
2010-08-06 | DOI 10.2390/biecoll-jib-2010-144 | PubMed 20693604

Kernel based machine learning algorithm for the efficient prediction of type III polyketide synthase family of proteins.

Mallika V, Sivakumar KC, Jaichand S, Soniya EV. Kernel based machine learning algorithm for the efficient prediction of type III polyketide synthase family of proteins. J Integr Bioinform. 2010;7(1).
2010-07-13 | DOI 10.2390/biecoll-jib-2010-143 | PubMed 20625199

CardioVINEdb: a data warehouse approach for integration of life science data in cardiovascular diseases.

Kormeier B, Hippe K, Töpel T, Hofestädt R. CardioVINEdb: a data warehouse approach for integration of life science data in cardiovascular diseases. J Integr Bioinform. 2010;7(1):142.
2010-06-28 | DOI 10.2390/biecoll-jib-2010-142 | PubMed 20585146

Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction.

Thiele H, Glandorf J, Hufnagel P. Bioinformatics strategies in life sciences: from data processing and data warehousing to biological knowledge extraction. J Integr Bioinform. 2010;7(1):141.
2010-05-27 | DOI 10.2390/biecoll-jib-2010-141 | PubMed 20508300

Integrative systems biology visualization with MAYDAY.

Symonsy S, Zipplies C, Battke F, Nieselt K. Integrative Systems Biology Visualization with MAYDAY. J Integr Bioinform. 2010;7(3):1–14.
2010-03-25 | DOI 10.2390/biecoll-jib-2010-115 | PubMed 20375461

Efficient online transcription factor binding site adjustment by integrating transitive graph projection with MoRAine 2.0.

Wittkop T, Rahmann S, Baumbach J. Efficient online transcription factor binding site adjustment by integrating transitive graph projection with MoRAine 2.0. J Integr Bioinform. 2010;7(3).
2010-03-25 | DOI 10.2390/biecoll-jib-2010-117 | PubMed 20375458

The LAILAPS search engine: a feature model for relevance ranking in life science databases.

Lange M, Spies K, Colmsee C, Flemming S, Klapperstück M, Scholz U. The LAILAPS Search Engine: A Feature Model for Relevance Ranking in Life Science Databases. J Integr Bioinform. 2010;7(3).
2010-03-25 | DOI 10.2390/biecoll-jib-2010-118 | PubMed 20375444

Enhancing data integration with text analysis to find proteins implicated in plant stress response.

Hassani-Pak K, Legaie R, Canevet C, van den Berg HA, Moore JD, Rawlings CJ. Enhancing data integration with text analysis to find proteins implicated in plant stress response. J Integr Bioinform. 2010;7(3).
2010-03-25 | DOI 10.2390/biecoll-jib-2010-121 | PubMed 20375451

MEMOPS: data modelling and automatic code generation.

Fogh RH, Boucher W, Ionides JMC, Vranken WF, Stevens TJ, Laue ED. MEMOPS: Data modelling and automatic code generation. J Integr Bioinform. 2010;7(3).
2010-03-25 | DOI 10.2390/biecoll-jib-2010-123 | PubMed 20375445

Novel developments of the MetaCrop information system for facilitating systems biological approaches.

Hippe K, Colmsee C, Czauderna T, et al. Novel Developments of the MetaCrop Information System for Facilitating Systems Biological Approaches. J Integr Bioinform. 2010;7(3).
2010-03-25 | DOI 10.2390/biecoll-jib-2010-125 | PubMed 20375443

Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues.

Lee HM, Dietz KJ, Hofestädt R. Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues. J Integr Bioinform. 2010;7(3).
2010-03-25 | DOI 10.2390/biecoll-jib-2010-130 | PubMed 20375441

SNPRanker: a tool for identification and scoring of SNPs associated to target genes.

Calabria A, Mosca E, Viti F, Merelli I, Milanesi L. SNPRanker: a tool for identification and scoring of SNPs associated to target genes. J Integr Bioinform. 2010;7(3).
2010-03-25 | DOI 10.2390/biecoll-jib-2010-138 | PubMed 20375450

The LAILAPS search engine: relevance ranking in life science databases.

Lange M, Spies K, Bargsten J, et al. The LAILAPS Search Engine: Relevance Ranking in Life Science Databases. J Integr Bioinform. 2010;7(2):1–11.
2010-01-15 | DOI 10.2390/biecoll-jib-2010-110 | PubMed 20134080

2009


Goober: a fully integrated and user-friendly microarray data management and analysis solution for core labs and bench biologists.

Luo W, Gudipati M, Jung K, Chen M, Marschke KB. Goober: a fully integrated and user-friendly microarray data management and analysis solution for core labs and bench biologists. J Integr Bioinform. 2009;6(1):108.
2009-08-23 | DOI 10.2390/biecoll-jib-2009-108 | PubMed 20134074

2008


WebStruct and VisualStruct: Web interfaces and visualization for Structure software implemented in a cluster environment.

Jayashree B, Rajgopal S, Hoisington D, Prasanth VP, Chandra S. WebStruct and VisualStruct: Web interfaces and visualization for Structure software implemented in a cluster environment. J Integr Bioinform. 2008;5(1).
2008-09-24 | DOI 10.2390/biecoll-jib-2008-89 | PubMed 20134055

MoRAine--a web server for fast computational transcription factor binding motif re-annotation.

Baumbach J, Wittkop T, Weile J, Kohl T, Rahmann S. MoRAine--a web server for fast computational transcription factor binding motif re-annotation. J Integr Bioinform. 2008;5(2).
2008-08-25 | DOI 10.2390/biecoll-jib-2008-91 | PubMed 20134062

Data integration for spatio-temporal patterns of gene expression of zebrafish development: the GEMS database.

Belmamoune M, Verbeek FJ. Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database. J Integr Bioinform. 2008;5(2).
2008-08-25 | DOI 10.2390/biecoll-jib-2008-92 | PubMed 20134060

BioDWH: a data warehouse kit for life science data integration.

Töpel T, Kormeier B, Klassen A, Hofestädt R. BioDWH: A Data Warehouse Kit for Life Science Data Integration. J Integr Bioinform. 2008;5(2).
2008-08-25 | DOI 10.2390/biecoll-jib-2008-93 | PubMed 20134070

Graph-based sequence annotation using a data integration approach.

Pesch R, Lysenko A, Hindle M, et al. Graph-based sequence annotation using a data integration approach. J Integr Bioinform. 2008;5(2).
2008-08-25 | DOI 10.2390/biecoll-jib-2008-94 | PubMed 20134069

Visual comparison of multiple gene expression datasets in a genomic context.

Borowski K, Soh J, Sensen CW. Visual Comparison of Multiple Gene Expression Datasets in a Genomic Context. J Integr Bioinform. 2008;5(2).
2008-08-25 | DOI 10.2390/biecoll-jib-2008-97 | PubMed 20134066

Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks.

Emig D, Cline MS, Klein K, et al. Integrative visual analysis of the effects of alternative splicing on protein domain interaction networks. J Integr Bioinform. 2008;5(2).
2008-08-25 | DOI 10.2390/biecoll-jib-2008-101 | PubMed 20134061

ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis.

Pitkänen E, Åkerlund A, Rantanen A, Jouhten P, Ukkonen E. ReMatch: a web-based tool to construct, store and share stoichiometric metabolic models with carbon maps for metabolic flux analysis. J Integr Bioinform. 2008;5(2).
2008-08-25 | DOI 10.2390/biecoll-jib-2008-102 | PubMed 20134058

GOblet: annotation of anonymous sequence data with gene ontology and pathway terms.

Groth D, Hartmann S, Panopoulou G, Poustka AJ, Hennig S. GOblet: annotation of anonymous sequence data with gene ontology and pathway terms. J Integr Bioinform. 2008;5(2).
2008-08-25 | DOI 10.2390/biecoll-jib-2008-104 | PubMed 20134064