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.


2024


Transformers meets neoantigen detection: a systematic literature review.

Machaca V, Goyzueta V, Cruz MG, Sejje E, Pilco LM, López J, Túpac Y. Transformers meets neoantigen detection: a systematic literature review.. J Integr Bioinform. 2024;.
2024-07-04 | DOI 10.1515/jib-2023-0043 | PubMed 38960869

MakeSBML: a tool for converting between Antimony and SBML.

Jardine BE, Smith LP, Sauro HM. MakeSBML: a tool for converting between Antimony and SBML.. J Integr Bioinform. 2024;.
2024-06-11 | DOI 10.1515/jib-2024-0002 | PubMed 38860571

SBMLToolkit.jl: a Julia package for importing SBML into the SciML ecosystem.

Lang PF, Jain A, Rackauckas C. SBMLToolkit.jl: a Julia package for importing SBML into the SciML ecosystem.. J Integr Bioinform. 2024;.
2024-05-28 | DOI 10.1515/jib-2024-0003 | PubMed 38801698

Unlocking the power of AI models: exploring protein folding prediction through comparative analysis.

Tejera-Nevado P, Serrano E, González-Herrero A, Bermejo R, Rodríguez-González A. Unlocking the power of AI models: exploring protein folding prediction through comparative analysis.. J Integr Bioinform. 2024;.
2024-05-27 | DOI 10.1515/jib-2023-0041 | PubMed 38797876

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5.

Smith LP, Bergmann FT, Garny A, Helikar T, Karr J, Nickerson D, Sauro H, Waltemath D, König M. The simulation experiment description markup language (SED-ML): language specification for level 1 version 5.. J Integr Bioinform. 2024;.
2024-04-15 | DOI 10.1515/jib-2024-0008 | PubMed 38613325

Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites.

López-Fernández H, Pinto M, Vieira CP, Duque P, Reboiro-Jato M, Vieira J. Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites.. J Integr Bioinform. 2024;.
2024-03-27 | DOI 10.1515/jib-2023-0046 | PubMed 38529929

MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps.

Aghakhani S, Niarakis A, Soliman S. MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps.. J Integr Bioinform. 2024;.
2024-02-06 | DOI 10.1515/jib-2023-0048 | PubMed 38314776

2023


TidyGEO: preparing analysis-ready datasets from Gene Expression Omnibus.

Mecham A, Stephenson A, Quinteros BI, Brown GS, Piccolo SR. TidyGEO: preparing analysis-ready datasets from Gene Expression Omnibus.. J Integr Bioinform. 2023;.
2023-12-05 | DOI 10.1515/jib-2023-0021 | PubMed 38047898

An overview of machine learning and deep learning techniques for predicting epileptic seizures.

Zurdo-Tabernero M, Canal-Alonso Á, de la Prieta F, Rodríguez S, Prieto J, Corchado JM. An overview of machine learning and deep learning techniques for predicting epileptic seizures.. J Integr Bioinform. 2023;20(4).
2023-12-01 | DOI 10.1515/jib-2023-0002 | PubMed 38099461

SAMNA: accurate alignment of multiple biological networks based on simulated annealing.

Chen J, Wang Z, Huang J. SAMNA: accurate alignment of multiple biological networks based on simulated annealing.. J Integr Bioinform. 2023;20(4).
2023-12-01 | DOI 10.1515/jib-2023-0006 | PubMed 38097366

Gene-network based analysis of human placental trophoblast subtypes identifies critical genes as potential targets of therapeutic drugs.

Lackner AI, Pollheimer J, Latos P, Knöfler M, Haider S. Gene-network based analysis of human placental trophoblast subtypes identifies critical genes as potential targets of therapeutic drugs.. J Integr Bioinform. 2023;20(4).
2023-12-01 | DOI 10.1515/jib-2023-0011 | PubMed 38127662

PharmoCo: a graph-based visualization of pharmacogenomic plausibility check reports for clinical decision support systems.

Raupach L, Königs C. PharmoCo: a graph-based visualization of pharmacogenomic plausibility check reports for clinical decision support systems.. J Integr Bioinform. 2023;20(4).
2023-12-01 | DOI 10.1515/jib-2023-0026 | PubMed 38150373

Data literacy in genome research.

Wolff K, Friedhoff R, Schwarzer F, Pucker B. Data literacy in genome research.. J Integr Bioinform. 2023;20(4).
2023-12-01 | DOI 10.1515/jib-2023-0033 | PubMed 38047760

STARGATE-X: a Python package for statistical analysis on the REACTOME network.

Marino A, Sinaimeri B, Tronci E, Calamoneri T. STARGATE-X: a Python package for statistical analysis on the REACTOME network.. J Integr Bioinform. 2023;.
2023-09-21 | DOI 10.1515/jib-2022-0029 | PubMed 37732505

Reconstruction of the regulatory hypermethylation network controlling hepatocellular carcinoma development during hepatitis C viral infection.

Antropova EA, Khlebodarova TM, Demenkov PS, Volianskaia AR, Venzel AS, Ivanisenko NV, Gavrilenko AD, Ivanisenko TV, Adamovskaya AV, Revva PM, Kolchanov NA, Lavrik IN, Ivanisenko VA. Reconstruction of the regulatory hypermethylation network controlling hepatocellular carcinoma development during hepatitis C viral infection.. J Integr Bioinform. 2023;20(3).
2023-09-01 | DOI 10.1515/jib-2023-0013 | PubMed 37978846

Application of Artificial Intelligence or machine learning in risk sharing agreements for pharmacotherapy risk management.

Oborotov GA, Koshechkin KA, Orlov YL. Application of Artificial Intelligence or machine learning in risk sharing agreements for pharmacotherapy risk management.. J Integr Bioinform. 2023;20(3).
2023-09-01 | DOI 10.1515/jib-2023-0014 | PubMed 38073025

Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder.

Uvarova YE, Demenkov PS, Kuzmicheva IN, Venzel AS, Mischenko EL, Ivanisenko TV, Efimov VM, Bannikova SV, Vasilieva AR, Ivanisenko VA, Peltek SE. Accurate noise-robust classification of Bacillus species from MALDI-TOF MS spectra using a denoising autoencoder.. J Integr Bioinform. 2023;20(3).
2023-09-01 | DOI 10.1515/jib-2023-0017 | PubMed 37978847

RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions.

Anders J, Stadler PF. RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions.. J Integr Bioinform. 2023;.
2023-08-25 | DOI 10.1515/jib-2022-0046 | PubMed 37615674

SnakeLines: integrated set of computational pipelines for sequencing reads.

Budiš J, Krampl W, Kucharík M, Hekel R, Goga A, Sitarčík J, Lichvár M, Smol'ak D, Böhmer M, Baláž A, Ďuriš F, Gazdarica J, Šoltys K, Turňa J, Radvánszky J, Szemes T. SnakeLines: integrated set of computational pipelines for sequencing reads.. J Integr Bioinform. 2023;.
2023-08-21 | DOI 10.1515/jib-2022-0059 | PubMed 37602733

Application of machine learning approach in emergency department to support clinical decision making for SARS-CoV-2 infected patients.

Casano N, Santini SJ, Vittorini P, Sinatti G, Carducci P, Mastroianni CM, Ciardi MR, Pasculli P, Petrucci E, Marinangeli F, Balsano C. Application of machine learning approach in emergency department to support clinical decision making for SARS-CoV-2 infected patients.. J Integr Bioinform. 2023;20(2).
2023-06-01 | DOI 10.1515/jib-2022-0047 | PubMed 36877860

Discovering NDM-1 inhibitors using molecular substructure embeddings representations.

Papastergiou T, Azé J, Bringay S, Louet M, Poncelet P, Rosales-Hurtado M, Vo-Hoang Y, Licznar-Fajardo P, Docquier JD, Gavara L. Discovering NDM-1 inhibitors using molecular substructure embeddings representations.. J Integr Bioinform. 2023;20(2).
2023-06-01 | DOI 10.1515/jib-2022-0050 | PubMed 37498676

Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks.

Ghazikhani H, Butler G. Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks.. J Integr Bioinform. 2023;20(2).
2023-06-01 | DOI 10.1515/jib-2022-0055 | PubMed 37497772

On the identification of potential novel therapeutic targets for spinocerebellar ataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3.

Sousa A, Rocha S, Vieira J, Reboiro-Jato M, López-Fernández H, Vieira CP. On the identification of potential novel therapeutic targets for spinocerebellar ataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3.. J Integr Bioinform. 2023;20(2).
2023-06-01 | DOI 10.1515/jib-2022-0056 | PubMed 36848492

Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots.

Konagaya A, Gutmann G, Zhang Y. Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots.. J Integr Bioinform. 2023;20(1).
2023-03-01 | DOI 10.1515/jib-2022-0017 | PubMed 36194394

2022


GraphML-SBGN bidirectional converter for metabolic networks.

Balaur I, Roy L, Touré V, Mazein A, Auffray C. GraphML-SBGN bidirectional converter for metabolic networks.. J Integr Bioinform. 2022;19(4).
2022-12-01 | DOI 10.1515/jib-2022-0030 | PubMed 36563404

Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality.

Aichem M, Klein K, Czauderna T, Garkov D, Zhao J, Li J, Schreiber F. Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality.. J Integr Bioinform. 2022;19(4).
2022-12-01 | DOI 10.1515/jib-2022-0034 | PubMed 36215728

Bridging data management platforms and visualization tools to enable ad-hoc and smart analytics in life sciences.

Panse C, Trachsel C, Türker C. Bridging data management platforms and visualization tools to enable ad-hoc and smart analytics in life sciences.. J Integr Bioinform. 2022;.
2022-09-08 | DOI 10.1515/jib-2022-0031 | PubMed 36073980

Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool.

Oliveira A, Cunha E, Cruz F, Capela J, Sequeira JC, Sampaio M, Sampaio C, Dias O. Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool.. J Integr Bioinform. 2022;.
2022-09-05 | DOI 10.1515/jib-2022-0014 | PubMed 36054839

Federated machine learning for a facilitated implementation of Artificial Intelligence in healthcare - a proof of concept study for the prediction of coronary artery calcification scores.

Wolff J, Matschinske J, Baumgart D, Pytlik A, Keck A, Natarajan A, von Schacky CE, Pauling JK, Baumbach J. Federated machine learning for a facilitated implementation of Artificial Intelligence in healthcare - a proof of concept study for the prediction of coronary artery calcification scores.. J Integr Bioinform. 2022;.
2022-09-05 | DOI 10.1515/jib-2022-0032 | PubMed 36054833

On the way to plant data commons - a genotyping use case.

Feser M, König P, Fiebig A, Arend D, Lange M, Scholz U. On the way to plant data commons - a genotyping use case.. J Integr Bioinform. 2022;.
2022-09-05 | DOI 10.1515/jib-2022-0033 | PubMed 36065132

A device and an app for the diagnosis and self-management of tinnitus.

Vittorini P, Chamoso P, De la Prieta F. A device and an app for the diagnosis and self-management of tinnitus.. J Integr Bioinform. 2022;.
2022-08-30 | DOI 10.1515/jib-2022-0004 | PubMed 36039680

Evaluating molecular representations in machine learning models for drug response prediction and interpretability.

Baptista D, Correia J, Pereira B, Rocha M. Evaluating molecular representations in machine learning models for drug response prediction and interpretability.. J Integr Bioinform. 2022;.
2022-08-26 | DOI 10.1515/jib-2022-0006 | PubMed 36017668

KaIDA: a modular tool for assisting image annotation in deep learning.

Schilling MP, Schmelzer S, Klinger L, Reischl M. KaIDA: a modular tool for assisting image annotation in deep learning.. J Integr Bioinform. 2022;.
2022-08-26 | DOI 10.1515/jib-2022-0018 | PubMed 36017752

A hybrid of Bees algorithm and regulatory on/off minimization for optimizing lactate and succinate production.

Yong MI, Mohamad MS, Choon YW, Chan WH, Adli HK, Syazwan Wsw KN, Yusoff N, Remli MA. A hybrid of Bees algorithm and regulatory on/off minimization for optimizing lactate and succinate production.. J Integr Bioinform. 2022;.
2022-07-19 | DOI 10.1515/jib-2022-0003 | PubMed 35852123

Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning.

Orozco-Arias S, Candamil-Cortes MS, Jaimes PA, Valencia-Castrillon E, Tabares-Soto R, Isaza G, Guyot R. Automatic curation of LTR retrotransposon libraries from plant genomes through machine learning.. J Integr Bioinform. 2022;.
2022-07-12 | DOI 10.1515/jib-2021-0036 | PubMed 35822734

Colors in the representation of biological structures.

Zoppè M. Colors in the representation of biological structures.. J Integr Bioinform. 2022;19(2).
2022-07-04 | DOI 10.1515/jib-2022-0021 | PubMed 35786236

Design considerations for representing systems biology information with the Systems Biology Graphical Notation.

Schreiber F, Czauderna T. Design considerations for representing systems biology information with the Systems Biology Graphical Notation.. J Integr Bioinform. 2022;19(2).
2022-07-04 | DOI 10.1515/jib-2022-0024 | PubMed 35786424

Design - a new way to look at old molecules.

Spalvieri D, Mauviel AM, Lambert M, Férey N, Sacquin-Mora S, Chavent M, Baaden M. Design - a new way to look at old molecules.. J Integr Bioinform. 2022;19(2).
2022-07-01 | DOI 10.1515/jib-2022-0020 | PubMed 35776840

Integrative illustration of a JCVI-syn3A minimal cell.

Goodsell DS. Integrative illustration of a JCVI-syn3A minimal cell.. J Integr Bioinform. 2022;19(2).
2022-06-27 | DOI 10.1515/jib-2022-0013 | PubMed 35749071

Considering best practices in color palettes for molecular visualizations.

Garrison L, Bruckner S. Considering best practices in color palettes for molecular visualizations.. J Integr Bioinform. 2022;19(2).
2022-06-22 | DOI 10.1515/jib-2022-0016 | PubMed 35731632

Integrative analysis of chemical properties and functions of drugs for adverse drug reaction prediction based on multi-label deep neural network.

Das P, Yogita , Pal V. Integrative analysis of chemical properties and functions of drugs for adverse drug reaction prediction based on multi-label deep neural network.. J Integr Bioinform. 2022;.
2022-05-19 | DOI 10.1515/jib-2022-0007 | PubMed 35585715

Genome-wide expression reveals potential biomarkers in breast cancer bone metastasis.

Singh Y, Subbarao N, Jaimini A, Hathaway QA, Kunovac A, Erickson B, Swarup V, Singh HN. Genome-wide expression reveals potential biomarkers in breast cancer bone metastasis.. J Integr Bioinform. 2022;.
2022-04-08 | DOI 10.1515/jib-2021-0041 | PubMed 35388653

A review on methods for predicting miRNA-mRNA regulatory modules.

Madhumita M, Paul S. A review on methods for predicting miRNA-mRNA regulatory modules.. J Integr Bioinform. 2022;.
2022-04-01 | DOI 10.1515/jib-2020-0048 | PubMed 35357793

ExceS-A: an exon-centric split aligner.

Reinhardt F, Stadler PF. ExceS-A: an exon-centric split aligner.. J Integr Bioinform. 2022;19(1).
2022-03-07 | DOI 10.1515/jib-2021-0040 | PubMed 35254744

A systematic study of motif pairs that may facilitate enhancer-promoter interactions.

Wang S, Hu H, Li X. A systematic study of motif pairs that may facilitate enhancer-promoter interactions.. J Integr Bioinform. 2022;19(1).
2022-02-07 | DOI 10.1515/jib-2021-0038 | PubMed 35130376

SCARF: a biomedical association rule finding webserver.

Szalkai B, Grolmusz V. SCARF: a biomedical association rule finding webserver.. J Integr Bioinform. 2022;19(1).
2022-02-04 | DOI 10.1515/jib-2021-0035 | PubMed 35119233

2021


Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data.

Dergilev AI, Orlova NG, Dobrovolskaya OB, Orlov YL. Statistical estimates of multiple transcription factors binding in the model plant genomes based on ChIP-seq data.. J Integr Bioinform. 2021;.
2021-12-21 | DOI 10.1515/jib-2020-0036 | PubMed 34953471

Predicting the possible effect of miR-203a-3p and miR-29a-3p on and genes expression.

Ali A, Mahla SB, Reza V, Alireza F. Predicting the possible effect of miR-203a-3p and miR-29a-3p on and genes expression.. J Integr Bioinform. 2021;.
2021-12-16 | DOI 10.1515/jib-2021-0016 | PubMed 34914337

Modular network inference between miRNA-mRNA expression profiles using weighted co-expression network analysis.

Wani N, Barh D, Raza K. Modular network inference between miRNA-mRNA expression profiles using weighted co-expression network analysis.. J Integr Bioinform. 2021;18(4).
2021-11-22 | DOI 10.1515/jib-2021-0029 | PubMed 34800012

Disparity-filtered differential correlation network analysis: a case study on CRC metabolomics.

Sabatini S, Gastaldelli A. Disparity-filtered differential correlation network analysis: a case study on CRC metabolomics.. J Integr Bioinform. 2021;18(4).
2021-11-19 | DOI 10.1515/jib-2021-0030 | PubMed 34792303

approach to understand epigenetics of POTEE in ovarian cancer.

Qazi S, Raza K. approach to understand epigenetics of POTEE in ovarian cancer.. J Integr Bioinform. 2021;18(4).
2021-11-18 | DOI 10.1515/jib-2021-0028 | PubMed 34788504

Fast alignment of reads to a variation graph with application to SNP detection.

Monsu M, Comin M. Fast alignment of reads to a variation graph with application to SNP detection.. J Integr Bioinform. 2021;18(4).
2021-11-16 | DOI 10.1515/jib-2021-0032 | PubMed 34783230

An evaluation study of biclusters visualization techniques of gene expression data.

Aouabed H, Elloumi M, Santamaría R. An evaluation study of biclusters visualization techniques of gene expression data.. J Integr Bioinform. 2021;18(4).
2021-10-27 | DOI 10.1515/jib-2021-0019 | PubMed 34699698

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.

Smith LP, Bergmann FT, Garny A, Helikar T, Karr J, Nickerson D, Sauro H, Waltemath D, König M. The simulation experiment description markup language (SED-ML): language specification for level 1 version 4.. J Integr Bioinform. 2021;18(3).
2021-10-05 | DOI 10.1515/jib-2021-0021 | PubMed 35330701

Big data in the healthcare system: a synergy with artificial intelligence and blockchain technology.

Pablo RJ, Roberto DP, Victor SU, Isabel GR, Paul C, Elizabeth OR. Big data in the healthcare system: a synergy with artificial intelligence and blockchain technology.. J Integr Bioinform. 2021;.
2021-08-18 | DOI 10.1515/jib-2020-0035 | PubMed 34412176

gene knockout prediction using a hybrid of Bat algorithm and minimization of metabolic adjustment.

Man MY, Mohamad MS, Choon YW, Ismail MA. gene knockout prediction using a hybrid of Bat algorithm and minimization of metabolic adjustment.. J Integr Bioinform. 2021;.
2021-08-03 | DOI 10.1515/jib-2020-0037 | PubMed 34348418

On the border of the amyloidogenic sequences: prefix analysis of the parallel beta sheets in the PDB_Amyloid collection.

Takács K, Grolmusz V. On the border of the amyloidogenic sequences: prefix analysis of the parallel beta sheets in the PDB_Amyloid collection.. J Integr Bioinform. 2021;.
2021-07-26 | DOI 10.1515/jib-2020-0043 | PubMed 34303324

Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions.

Quadrini M. Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions.. J Integr Bioinform. 2021;18(2).
2021-05-31 | DOI 10.1515/jib-2020-0039 | PubMed 34051708

Cross-evaluation of social mining for classification of depressed online personas.

Trifan A, Oliveira JL. Cross-evaluation of social mining for classification of depressed online personas.. J Integr Bioinform. 2021;18(2).
2021-05-20 | DOI 10.1515/jib-2020-0051 | PubMed 34013675

Cardiac well-being indexes: a decision support tool to monitor cardiovascular health.

Duarte A, Belo O. Cardiac well-being indexes: a decision support tool to monitor cardiovascular health.. J Integr Bioinform. 2021;.
2021-03-26 | DOI 10.1515/jib-2020-0040 | PubMed 33770831

OverCOVID: an integrative web portal for SARS-CoV-2 bioinformatics resources.

Ahsan MA, Liu Y, Feng C, Hofestädt R, Chen M. OverCOVID: an integrative web portal for SARS-CoV-2 bioinformatics resources.. J Integr Bioinform. 2021;18(1).
2021-03-19 | DOI 10.1515/jib-2020-0046 | PubMed 33735949

Novel perspectives for SARS-CoV-2 genome browsing.

Gültekin V, Allmer J. Novel perspectives for SARS-CoV-2 genome browsing.. J Integr Bioinform. 2021;18(1).
2021-03-16 | DOI 10.1515/jib-2021-0001 | PubMed 33721918

BioDWH2: an automated graph-based data warehouse and mapping tool.

Friedrichs M. BioDWH2: an automated graph-based data warehouse and mapping tool.. J Integr Bioinform. 2021;.
2021-02-22 | DOI 10.1515/jib-2020-0033 | PubMed 33618440

2020


A computational model for GPCR-ligand interaction prediction.

Karimi S, Ahmadi M, Goudarzi F, Ferdousi R. A computational model for GPCR-ligand interaction prediction.. J Integr Bioinform. 2020;18(2).
2020-12-29 | DOI 10.1515/jib-2019-0084 | PubMed 34171942

A novel gene expression test method of minimizing breast cancer risk in reduced cost and time by improving SVM-RFE gene selection method combined with LASSO.

Gupta M, Gupta B. A novel gene expression test method of minimizing breast cancer risk in reduced cost and time by improving SVM-RFE gene selection method combined with LASSO.. J Integr Bioinform. 2020;18(2).
2020-12-29 | DOI 10.1515/jib-2019-0110 | PubMed 34171941

HPREP: a comprehensive database for human proteome repeats.

Mary Rajathei D, Parthasarathy S, Selvaraj S. HPREP: a comprehensive database for human proteome repeats.. J Integr Bioinform. 2020;.
2020-11-03 | DOI 10.1515/jib-2020-0024 | PubMed 33136065

Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).

Martorelli I, Helwerda LS, Kerkvliet J, Gomes SIF, Nuytinck J, van der Werff CRA, Ramackers GJ, Gultyaev AP, Merckx VSFT, Verbeek FJ. Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).. J Integr Bioinform. 2020;.
2020-05-28 | DOI 10.1515/jib-2019-0046 | PubMed 32463383

A Lock Free Approach To Parallelize The Cellular Potts Model: Application To Ductal Carcinoma In Situ.

Tomeu AJ, Salguero AG. A Lock Free Approach To Parallelize The Cellular Potts Model: Application To Ductal Carcinoma In Situ.. J Integr Bioinform. 2020;.
2020-04-07 | DOI 10.1515/jib-2019-0070 | PubMed 32267247

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


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

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

Dynamics of miRNA biogenesis and nuclear transport.

Kotipalli A, Gutti R, Mitra CK. Dynamics of miRNA biogenesis and nuclear transport.. J Integr Bioinform. 2017;13(5).
2017-04-20 | DOI 10.1515/jib-2016-305 | PubMed 34348448

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