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Discovering NDM-1 inhibitors using molecular substructure embeddings representations
In this study, we deliver a new, curated NDM-1 bioactivities database, along with a set of unifying rules for managing different activity properties and inconsistencies. We define the activity classification problem in terms of Multiple Instance Learning, employing embeddings corresponding to molecular substructures and present an ensemble ranking and classification framework, relaying on a k-fold Cross Validation method employing a per fold hyper-parameter optimization procedure, showing promising generalization ability. The MIL paradigm displayed an improvement up to 45.7 %, in terms of Balanced Accuracy, in comparison t...
Source: Journal of integrative bioinformatics - July 27, 2023 Category: Bioinformatics Authors: Thomas Papastergiou J érôme Azé Sandra Bringay Maxime Louet Pascal Poncelet Miyanou Rosales-Hurtado Yen Vo-Hoang Patricia Licznar-Fajardo Jean-Denis Docquier Laurent Gavara Source Type: research

Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks
In this study, we expand upon this approach by utilizing representations from ProtBERT, ProtBERT-BFD, and MembraneBERT in combination with classical classifiers. Additionally, we introduce TooT-BERT-CNN-T, a novel method that fine-tunes ProtBERT-BFD and discriminates transporters using a Convolutional Neural Network (CNN). Our experimental results reveal that CNN surpasses traditional classifiers in discriminating transporters from non-transporters, achieving an MCC of 0.89 and an accuracy of 95.1 % on the independent test set. This represents an improvement of 0.03 and 1.11 percentage points compared to TooT-BERT-T, respe...
Source: Journal of integrative bioinformatics - July 27, 2023 Category: Bioinformatics Authors: Hamed Ghazikhani Gregory Butler Source Type: research

Discovering NDM-1 inhibitors using molecular substructure embeddings representations
In this study, we deliver a new, curated NDM-1 bioactivities database, along with a set of unifying rules for managing different activity properties and inconsistencies. We define the activity classification problem in terms of Multiple Instance Learning, employing embeddings corresponding to molecular substructures and present an ensemble ranking and classification framework, relaying on a k-fold Cross Validation method employing a per fold hyper-parameter optimization procedure, showing promising generalization ability. The MIL paradigm displayed an improvement up to 45.7 %, in terms of Balanced Accuracy, in comparison t...
Source: Journal of integrative bioinformatics - July 27, 2023 Category: Bioinformatics Authors: Thomas Papastergiou J érôme Azé Sandra Bringay Maxime Louet Pascal Poncelet Miyanou Rosales-Hurtado Yen Vo-Hoang Patricia Licznar-Fajardo Jean-Denis Docquier Laurent Gavara Source Type: research

Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks
In this study, we expand upon this approach by utilizing representations from ProtBERT, ProtBERT-BFD, and MembraneBERT in combination with classical classifiers. Additionally, we introduce TooT-BERT-CNN-T, a novel method that fine-tunes ProtBERT-BFD and discriminates transporters using a Convolutional Neural Network (CNN). Our experimental results reveal that CNN surpasses traditional classifiers in discriminating transporters from non-transporters, achieving an MCC of 0.89 and an accuracy of 95.1 % on the independent test set. This represents an improvement of 0.03 and 1.11 percentage points compared to TooT-BERT-T, respe...
Source: Journal of integrative bioinformatics - July 27, 2023 Category: Bioinformatics Authors: Hamed Ghazikhani Gregory Butler Source Type: research

Discovering NDM-1 inhibitors using molecular substructure embeddings representations
In this study, we deliver a new, curated NDM-1 bioactivities database, along with a set of unifying rules for managing different activity properties and inconsistencies. We define the activity classification problem in terms of Multiple Instance Learning, employing embeddings corresponding to molecular substructures and present an ensemble ranking and classification framework, relaying on a k-fold Cross Validation method employing a per fold hyper-parameter optimization procedure, showing promising generalization ability. The MIL paradigm displayed an improvement up to 45.7 %, in terms of Balanced Accuracy, in comparison t...
Source: Journal of integrative bioinformatics - July 27, 2023 Category: Bioinformatics Authors: Thomas Papastergiou J érôme Azé Sandra Bringay Maxime Louet Pascal Poncelet Miyanou Rosales-Hurtado Yen Vo-Hoang Patricia Licznar-Fajardo Jean-Denis Docquier Laurent Gavara Source Type: research

Enhanced identification of membrane transport proteins: a hybrid approach combining ProtBERT-BFD and convolutional neural networks
In this study, we expand upon this approach by utilizing representations from ProtBERT, ProtBERT-BFD, and MembraneBERT in combination with classical classifiers. Additionally, we introduce TooT-BERT-CNN-T, a novel method that fine-tunes ProtBERT-BFD and discriminates transporters using a Convolutional Neural Network (CNN). Our experimental results reveal that CNN surpasses traditional classifiers in discriminating transporters from non-transporters, achieving an MCC of 0.89 and an accuracy of 95.1 % on the independent test set. This represents an improvement of 0.03 and 1.11 percentage points compared to TooT-BERT-T, respe...
Source: Journal of integrative bioinformatics - July 27, 2023 Category: Bioinformatics Authors: Hamed Ghazikhani Gregory Butler Source Type: research

Discovering NDM-1 inhibitors using molecular substructure embeddings representations
In this study, we deliver a new, curated NDM-1 bioactivities database, along with a set of unifying rules for managing different activity properties and inconsistencies. We define the activity classification problem in terms of Multiple Instance Learning, employing embeddings corresponding to molecular substructures and present an ensemble ranking and classification framework, relaying on a k-fold Cross Validation method employing a per fold hyper-parameter optimization procedure, showing promising generalization ability. The MIL paradigm displayed an improvement up to 45.7 %, in terms of Balanced Accuracy, in comparison t...
Source: Journal of integrative bioinformatics - July 27, 2023 Category: Bioinformatics Authors: Thomas Papastergiou J érôme Azé Sandra Bringay Maxime Louet Pascal Poncelet Miyanou Rosales-Hurtado Yen Vo-Hoang Patricia Licznar-Fajardo Jean-Denis Docquier Laurent Gavara Source Type: research

Integrating omics databases for enhanced crop breeding
J Integr Bioinform. 2023 Jul 25. doi: 10.1515/jib-2023-0012. Online ahead of print.ABSTRACTCrop plant breeding involves selecting and developing new plant varieties with desirable traits such as increased yield, improved disease resistance, and enhanced nutritional value. With the development of high-throughput technologies, such as genomics, transcriptomics, and metabolomics, crop breeding has entered a new era. However, to effectively use these technologies, integration of multi-omics data from different databases is required. Integration of omics data provides a comprehensive understanding of the biological processes un...
Source: Journal of integrative bioinformatics - July 24, 2023 Category: Bioinformatics Authors: Haoyu Chao Shilong Zhang Yueming Hu Qingyang Ni Saige Xin Liang Zhao Vladimir A Ivanisenko Yuriy L Orlov Ming Chen Source Type: research

Concentration of inverted repeats along human DNA
J Integr Bioinform. 2023 Jul 25. doi: 10.1515/jib-2022-0052. Online ahead of print.ABSTRACTThis work aims to describe the observed enrichment of inverted repeats in the human genome; and to identify and describe, with detailed length profiles, the regions with significant and relevant enriched occurrence of inverted repeats. The enrichment is assessed and tested with a recently proposed measure (z-scores based measure). We simulate a genome using an order 7 Markov model trained with the data from the real genome. The simulated genome is used to establish the critical values which are used as decision thresholds to identify...
Source: Journal of integrative bioinformatics - July 24, 2023 Category: Bioinformatics Authors: Carlos A C Bastos Vera Afreixo Jo ão M O S Rodrigues Armando J Pinho Source Type: research

Integrating omics databases for enhanced crop breeding
J Integr Bioinform. 2023 Jul 25. doi: 10.1515/jib-2023-0012. Online ahead of print.ABSTRACTCrop plant breeding involves selecting and developing new plant varieties with desirable traits such as increased yield, improved disease resistance, and enhanced nutritional value. With the development of high-throughput technologies, such as genomics, transcriptomics, and metabolomics, crop breeding has entered a new era. However, to effectively use these technologies, integration of multi-omics data from different databases is required. Integration of omics data provides a comprehensive understanding of the biological processes un...
Source: Journal of integrative bioinformatics - July 24, 2023 Category: Bioinformatics Authors: Haoyu Chao Shilong Zhang Yueming Hu Qingyang Ni Saige Xin Liang Zhao Vladimir A Ivanisenko Yuriy L Orlov Ming Chen Source Type: research

Concentration of inverted repeats along human DNA
J Integr Bioinform. 2023 Jul 25. doi: 10.1515/jib-2022-0052. Online ahead of print.ABSTRACTThis work aims to describe the observed enrichment of inverted repeats in the human genome; and to identify and describe, with detailed length profiles, the regions with significant and relevant enriched occurrence of inverted repeats. The enrichment is assessed and tested with a recently proposed measure (z-scores based measure). We simulate a genome using an order 7 Markov model trained with the data from the real genome. The simulated genome is used to establish the critical values which are used as decision thresholds to identify...
Source: Journal of integrative bioinformatics - July 24, 2023 Category: Bioinformatics Authors: Carlos A C Bastos Vera Afreixo Jo ão M O S Rodrigues Armando J Pinho Source Type: research

Integrating omics databases for enhanced crop breeding
J Integr Bioinform. 2023 Jul 25. doi: 10.1515/jib-2023-0012. Online ahead of print.ABSTRACTCrop plant breeding involves selecting and developing new plant varieties with desirable traits such as increased yield, improved disease resistance, and enhanced nutritional value. With the development of high-throughput technologies, such as genomics, transcriptomics, and metabolomics, crop breeding has entered a new era. However, to effectively use these technologies, integration of multi-omics data from different databases is required. Integration of omics data provides a comprehensive understanding of the biological processes un...
Source: Journal of integrative bioinformatics - July 24, 2023 Category: Bioinformatics Authors: Haoyu Chao Shilong Zhang Yueming Hu Qingyang Ni Saige Xin Liang Zhao Vladimir A Ivanisenko Yuriy L Orlov Ming Chen Source Type: research

Concentration of inverted repeats along human DNA
J Integr Bioinform. 2023 Jul 25. doi: 10.1515/jib-2022-0052. Online ahead of print.ABSTRACTThis work aims to describe the observed enrichment of inverted repeats in the human genome; and to identify and describe, with detailed length profiles, the regions with significant and relevant enriched occurrence of inverted repeats. The enrichment is assessed and tested with a recently proposed measure (z-scores based measure). We simulate a genome using an order 7 Markov model trained with the data from the real genome. The simulated genome is used to establish the critical values which are used as decision thresholds to identify...
Source: Journal of integrative bioinformatics - July 24, 2023 Category: Bioinformatics Authors: Carlos A C Bastos Vera Afreixo Jo ão M O S Rodrigues Armando J Pinho Source Type: research

Artificial Bee Colony algorithm in estimating kinetic parameters for yeast fermentation pathway
J Integr Bioinform. 2023 Jun 22. doi: 10.1515/jib-2022-0051. Online ahead of print.ABSTRACTAnalyzing metabolic pathways in systems biology requires accurate kinetic parameters that represent the simulated in vivo processes. Simulation of the fermentation pathway in the Saccharomyces cerevisiae kinetic model help saves much time in the optimization process. Fitting the simulated model into the experimental data is categorized under the parameter estimation problem. Parameter estimation is conducted to obtain the optimal values for parameters related to the fermentation process. This step is essential because insufficient id...
Source: Journal of integrative bioinformatics - June 21, 2023 Category: Bioinformatics Authors: Ahmad Muhaimin Ismail Muhammad Akmal Remli Yee Wen Choon Nurul Athirah Nasarudin Nor-Syahidatul N Ismail Mohd Arfian Ismail Mohd Saberi Mohamad Source Type: research