Journal of integrative bioinformatics

Keyphrases

Publications

2024

Hugo López-Fernández, Miguel Pinto, Cristina P Vieira, Pedro Duque, Miguel Reboiro-Jato, Jorge Vieira
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. Journal of integrative bioinformatics (2024)
Xiangyu Li, Xiumin Shi, Yuxuan Li, Lu Wang
MCMVDRP: a multi-channel multi-view deep learning framework for cancer drug response prediction. Journal of integrative bioinformatics (2024)
Bartholomew E Jardine, Lucian P Smith, Herbert M Sauro
MakeSBML: a tool for converting between Antimony and SBML. Journal of integrative bioinformatics (2024)
Michal J Okoniewski, Anna Wiegand, Diana Coman Schmid, Christian Bolliger, Cristian Bovino, Mattia Belluco, Thomas Wüst, Olivier Byrde, Sergio Maffioletti, Bernd Rinn
Leonhard Med , a trusted research environment for processing sensitive research data. Journal of integrative bioinformatics (2024)
Ihsanul Arief, Gagus Ketut Sunnardianto, Syahrul Khairi, Wahyu Dita Saputri
The potential of Mitragyna speciosa leaves as a natural source of antioxidants for disease prevention. Journal of integrative bioinformatics (2024)
Sahar Aghakhani, Anna Niarakis, Sylvain Soliman
MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps. Journal of integrative bioinformatics (2024)
Bartholomew E Jardine, Lucian P Smith, Herbert M Sauro
MakeSBML: a tool for converting between Antimony and SBML. Journal of integrative bioinformatics (2024)
Valentin Wesp, Lukas Scholz, Janine M Ziermann-Canabarro, Stefan Schuster, Heiko Stark
Constructing networks for comparison of collagen types. Journal of integrative bioinformatics (2024)
Daniel Glez-Peña, Hugo López-Fernández, Pedro Duque, Cristina P Vieira, Jorge Vieira
Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information. Journal of integrative bioinformatics (2024)
Paul F Lang, Anand Jain, Christopher Rackauckas
SBMLToolkit.jl: a Julia package for importing SBML into the SciML ecosystem. Journal of integrative bioinformatics (2024)
Stefan Paul Feyer, Bruno Pinaud, Karsten Klein, Etienne Lein, Falk Schreiber
Exploring animal behaviour multilayer networks in immersive environments - a conceptual framework. Journal of integrative bioinformatics (2024)
Daniel Martins, Maryam Abbasi, Conceição Egas, Joel P Arrais
Detecting outliers in case-control cohorts for improving deep learning networks on Schizophrenia prediction. Journal of integrative bioinformatics (2024)
Martin Golebiewski, Gary D Baider, Padraig Gleeson, Thomas E Gorochowski, Sarah M Keating, Matthias König, Chris J Myers, David P Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. Journal of integrative bioinformatics (2024)
Sahar Aghakhani, Anna Niarakis, Sylvain Soliman
MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps. Journal of integrative bioinformatics (2024)
Lucian P Smith, Frank T Bergmann, Alan Garny, Tomas Helikar, Jonathan R Karr, David P Nickerson, Herbert M Sauro, Dagmar Waltemath, Matthias König
The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. Journal of integrative bioinformatics (2024)
Niklas Gröne, Benjamin Grüneisen, Karsten Klein, Bernard de Bono, Tobias Czauderna, Falk Schreiber
Layout of anatomical structures and blood vessels based on the foundational model of anatomy. Journal of integrative bioinformatics (2024)
Paloma Tejera-Nevado, Emilio Serrano, Ana González-Herrero, Rodrigo Bermejo, Alejandro Rodríguez-González
Unlocking the power of AI models: exploring protein folding prediction through comparative analysis. Journal of integrative bioinformatics (2024)
Vicente Machaca, Valeria Goyzueta, María Graciel Cruz, Erika Sejje, Luz Marina Pilco, Julio López, Yván Túpac
Transformers meets neoantigen detection: a systematic literature review. Journal of integrative bioinformatics (2024)

volume 21, number 1, 2024

Paul F Lang, Anand Jain, Christopher Rackauckas
SBMLToolkit.jl: a Julia package for importing SBML into the SciML ecosystem. Journal of integrative bioinformatics 21 (1) (2024)
Bartholomew E Jardine, Lucian P Smith, Herbert M Sauro
MakeSBML: a tool for converting between Antimony and SBML. Journal of integrative bioinformatics 21 (1) (2024)
Martin Golebiewski, Gary D Baider, Padraig Gleeson, Thomas E Gorochowski, Sarah M Keating, Matthias König, Chris J Myers, David P Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. Journal of integrative bioinformatics 21 (1) (2024)
Sahar Aghakhani, Anna Niarakis, Sylvain Soliman
MetaLo: metabolic analysis of Logical models extracted from molecular interaction maps. Journal of integrative bioinformatics 21 (1) (2024)
Bartholomew E Jardine, Lucian P Smith, Herbert M Sauro
MakeSBML: a tool for converting between Antimony and SBML. Journal of integrative bioinformatics 21 (1) (2024)
Lucian P Smith, Frank T Bergmann, Alan Garny, Tomas Helikar, Jonathan R Karr, David P Nickerson, Herbert M Sauro, Dagmar Waltemath, Matthias König
The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. Journal of integrative bioinformatics 21 (1) (2024)
Bartholomew E Jardine, Lucian P Smith, Herbert M Sauro
MakeSBML: a tool for converting between Antimony and SBML. Journal of integrative bioinformatics 21 (1) (2024)

2023

Hamed Ghazikhani, Gregory Butler
Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks. Journal of integrative bioinformatics (2023)
Avery Mecham, Ashlie Stephenson, Badi I Quinteros, Grace S Brown, Stephen R Piccolo
TidyGEO: preparing analysis-ready datasets from Gene Expression Omnibus. Journal of integrative bioinformatics (2023)
Carlos A C Bastos, Vera Afreixo, João Manuel Rodrigues, Armando J Pinho
Concentration of inverted repeats along human DNA. Journal of integrative bioinformatics (2023)
Grigory A Oborotov, Konstantin A Koshechkin, Yuriy L Orlov
Application of Artificial Intelligence or machine learning in risk sharing agreements for pharmacotherapy risk management. Journal of integrative bioinformatics (2023)
Jing Chen, Zixiang Wang, Jia Huang
SAMNA: accurate alignment of multiple biological networks based on simulated annealing. Journal of integrative bioinformatics (2023)
Haoyu Chao, Shilong Zhang, Yueming Hu, Qingyang Ni, Saige Xin, Liang Zhao, Vladimir A Ivanisenko, Yuriy L Orlov, Ming Chen
Integrating omics databases for enhanced crop breeding. Journal of integrative bioinformatics (2023)
Sara Duarte-Pereira, Sérgio Matos, José Luís Oliveira, Raquel M Silva
Study of NAD-interacting proteins highlights the extent of NAD regulatory roles in the cell and its potential as a therapeutic target. Journal of integrative bioinformatics (2023)
Abdulrahman A Alsewari, AbdulRahman A Alsewari, Shadi S Basurra, Jagdev Bhogal, Mohammed A H Ali
Diabetes disease prediction system using HNB classifier based on discretization method. Journal of integrative bioinformatics (2023)
André Sousa, Sara Rocha, Jorge Vieira, Miguel Reboiro-Jato, Hugo López-Fernández, Cristina P Vieira
On the identification of potential novel therapeutic targets for spinocerebellar ataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3. Journal of integrative bioinformatics (2023)

volume 20, number 1, 2023

Matthias König, Padraig Gleeson, Martin Golebiewski, Thomas E Gorochowski, Michael Hucka, Sarah M Keating, Chris J Myers, David P Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber
Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. Journal of integrative bioinformatics 20 (1) (2023)
Matthias König, Padraig Gleeson, Martin Golebiewski, Thomas E Gorochowski, Michael Hucka, Sarah M Keating, Chris J Myers, David P Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber
Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. Journal of integrative bioinformatics 20 (1) (2023)
Matthias König, Padraig Gleeson, Martin Golebiewski, Thomas E Gorochowski, Michael Hucka, Sarah M Keating, Chris J Myers, David P Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber
Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. Journal of integrative bioinformatics 20 (1) (2023)

volume 20, number 4, 2023

Lena Raupach, Cassandra Königs
PharmoCo: a graph-based visualization of pharmacogenomic plausibility check reports for clinical decision support systems. Journal of integrative bioinformatics 20 (4) (2023)
Lena Raupach, Cassandra Königs
PharmoCo: a graph-based visualization of pharmacogenomic plausibility check reports for clinical decision support systems. Journal of integrative bioinformatics 20 (4) (2023)
Marco Zurdo-Tabernero, Ángel Canal-Alonso, Fernando de la Prieta, Sara Rodríguez-González, Javier Prieto Tejedor, Juan Manuel Corchado Rodríguez
An overview of machine learning and deep learning techniques for predicting epileptic seizures. Journal of integrative bioinformatics 20 (4) (2023)
Marco Zurdo-Tabernero, Ángel Canal-Alonso, Fernando de la Prieta, Sara Rodríguez-González, Javier Prieto Tejedor, Juan Manuel Corchado Rodríguez
An overview of machine learning and deep learning techniques for predicting epileptic seizures. Journal of integrative bioinformatics 20 (4) (2023)
Andreas Ian Lackner, Jürgen Pollheimer, Paulina Latos, Martin Knöfler, Sandra Haider
Gene-network based analysis of human placental trophoblast subtypes identifies critical genes as potential targets of therapeutic drugs. Journal of integrative bioinformatics 20 (4) (2023)
Andreas Ian Lackner, Jürgen Pollheimer, Paulina Latos, Martin Knöfler, Sandra Haider
Gene-network based analysis of human placental trophoblast subtypes identifies critical genes as potential targets of therapeutic drugs. Journal of integrative bioinformatics 20 (4) (2023)
Jing Chen, Zixiang Wang, Jia Huang
SAMNA: accurate alignment of multiple biological networks based on simulated annealing. Journal of integrative bioinformatics 20 (4) (2023)
Lena Raupach, Cassandra Königs
PharmoCo: a graph-based visualization of pharmacogenomic plausibility check reports for clinical decision support systems. Journal of integrative bioinformatics 20 (4) (2023)
Jing Chen, Zixiang Wang, Jia Huang
SAMNA: accurate alignment of multiple biological networks based on simulated annealing. Journal of integrative bioinformatics 20 (4) (2023)
Andreas Ian Lackner, Jürgen Pollheimer, Paulina Latos, Martin Knöfler, Sandra Haider
Gene-network based analysis of human placental trophoblast subtypes identifies critical genes as potential targets of therapeutic drugs. Journal of integrative bioinformatics 20 (4) (2023)
Jing Chen, Zixiang Wang, Jia Huang
SAMNA: accurate alignment of multiple biological networks based on simulated annealing. Journal of integrative bioinformatics 20 (4) (2023)
Marco Zurdo-Tabernero, Ángel Canal-Alonso, Fernando de la Prieta, Sara Rodríguez-González, Javier Prieto Tejedor, Juan Manuel Corchado Rodríguez
An overview of machine learning and deep learning techniques for predicting epileptic seizures. Journal of integrative bioinformatics 20 (4) (2023)
Lena Raupach, Cassandra Königs
PharmoCo: a graph-based visualization of pharmacogenomic plausibility check reports for clinical decision support systems. Journal of integrative bioinformatics 20 (4) (2023)