Volume 25, issue 1, December 2024
195 articles in this issue
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HMMF: a hybrid multi-modal fusion framework for predicting drug side effect frequencies
Authors (first, second and last of 6)
- Wuyong Liu
- Jingyu Zhang
- Yang Li
- Content type: Research
- Open Access
- Published: 20 May 2024
- Article: 196
This is part of 2 collections: -
Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads
Authors (first, second and last of 7)
- Ananthan Nambiar
- Chao Pan
- Olgica Milenkovic
- Content type: Research
- Open Access
- Published: 17 May 2024
- Article: 195
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Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation
Authors
- Zachary Stephens
- Jean-Pierre Kocher
- Content type: Research
- Open Access
- Published: 17 May 2024
- Article: 194
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AMRViz enables seamless genomics analysis and visualization of antimicrobial resistance
Authors (first, second and last of 9)
- Duc Quang Le
- Son Hoang Nguyen
- Minh Duc Cao
- Content type: Software
- Open Access
- Published: 16 May 2024
- Article: 193
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MR-GGI: accurate inference of gene–gene interactions using Mendelian randomization
Authors
- Wonseok Oh
- Junghyun Jung
- Jong Wha J. Joo
- Content type: Research
- Open Access
- Published: 15 May 2024
- Article: 192
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Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches
Authors
- Ryan Kuster
- Margaret Staton
- Content type: Software
- Open Access
- Published: 15 May 2024
- Article: 191
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Correction: NanoBERTa-ASP: predicting nanobody paratope based on a pretrained RoBERTa model
Authors (first, second and last of 5)
- Shangru Li
- Xiangpeng Meng
- Xin Wang
- Content type: Correction
- Open Access
- Published: 14 May 2024
- Article: 190
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PrimerEvalPy: a tool for in-silico evaluation of primers for targeting the microbiome
Authors (first, second and last of 6)
- Lara Vázquez-González
- Alba Regueira-Iglesias
- MarÃa J. Carreira
- Content type: Software
- Open Access
- Published: 14 May 2024
- Article: 189
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Multi-class boosting for the analysis of multiple incomplete views on microbiome data
Authors (first, second and last of 6)
- Andrea Simeon
- Miloš Radovanović
- Gianvito Pio
- Content type: Research
- Open Access
- Published: 14 May 2024
- Article: 188
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Neighborhood based computational approaches for the prediction of lncRNA-disease associations
Authors
- Mariella Bonomo
- Simona E. Rombo
- Content type: Research
- Open Access
- Published: 13 May 2024
- Article: 187
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CAREx: context-aware read extension of paired-end sequencing data
Authors
- Felix Kallenborn
- Bertil Schmidt
- Content type: Software
- Open Access
- Published: 10 May 2024
- Article: 186
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Machine learning based DNA melt curve profiling enables automated novel genotype detection
Authors (first, second and last of 10)
- Aaron Boussina
- Lennart Langouche
- Stephanie I. Fraley
- Content type: Research
- Open Access
- Published: 10 May 2024
- Article: 185
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OMD Curation Toolkit: a workflow for in-house curation of public omics datasets
Authors (first, second and last of 4)
- Samuel Piquer-Esteban
- Vicente Arnau
- Andrés Moya
- Content type: Software
- Open Access
- Published: 09 May 2024
- Article: 184
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Biclustering analysis on tree-shaped time-series single cell gene expression data of Caenorhabditis elegans
Authors (first, second and last of 5)
- Qi Guan
- Xianzhong Yan
- Jie Hu
- Content type: Research
- Open Access
- Published: 09 May 2024
- Article: 183
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Prediction of anticancer drug sensitivity using an interpretable model guided by deep learning
Authors
- Weixiong Pang
- Ming Chen
- Yufang Qin
- Content type: Research
- Open Access
- Published: 09 May 2024
- Article: 182
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A comparison of RNA-Seq data preprocessing pipelines for transcriptomic predictions across independent studies
Authors (first, second and last of 7)
- Richard Van
- Daniel Alvarez
- Mira V. Han
- Content type: Research
- Open Access
- Published: 08 May 2024
- Article: 181
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Integrated approach to generate artificial samples with low tumor fraction for somatic variant calling benchmarking
Authors (first, second and last of 4)
- Aldo Sergi
- Luca Beltrame
- Marco Masseroli
- Content type: Software
- Open Access
- Published: 08 May 2024
- Article: 180
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Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization
Authors (first, second and last of 6)
- Samuel Rosean
- Eric A. Sosa
- John M. Greally
- Content type: Software
- Open Access
- Published: 07 May 2024
- Article: 179
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Computer vision digitization of smartphone images of anesthesia paper health records from low-middle income countries
Authors (first, second and last of 4)
- Ryan D. Folks
- Bhiken I. Naik
- Marcel E. Durieux
- Content type: Research
- Open Access
- Published: 07 May 2024
- Article: 178
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ViroISDC: a method for calling integration sites of hepatitis B virus based on feature encoding
Authors (first, second and last of 7)
- Lei Qiao
- Chang Li
- Jingyang Gao
- Content type: Research
- Open Access
- Published: 04 May 2024
- Article: 177
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Freeprotmap: waiting-free prediction method for protein distance map
Authors (first, second and last of 6)
- Jiajian Huang
- Jinpeng Li
- Jin Tang
- Content type: Research
- Open Access
- Published: 04 May 2024
- Article: 176
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A transformer model for cause-specific hazard prediction
Authors (first, second and last of 5)
- Matthieu Oliver
- Nicolas Allou
- Cyril Ferdynus
- Content type: Research
- Open Access
- Published: 03 May 2024
- Article: 175
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Protein function prediction through multi-view multi-label latent tensor reconstruction
Authors
- Robert Ebo Armah-Sekum
- Sandor Szedmak
- Juho Rousu
- Content type: Research
- Open Access
- Published: 02 May 2024
- Article: 174
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VCF2PCACluster: a simple, fast and memory-efficient tool for principal component analysis of tens of millions of SNPs
Authors (first, second and last of 8)
- Weiming He
- Lian Xu
- Xiaodong Fang
- Content type: Software
- Open Access
- Published: 01 May 2024
- Article: 173
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Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein–protein interfaces
Authors
- Sagara N. S. Gurusinghe
- Julia M. Shifman
- Content type: Software
- Open Access
- Published: 30 April 2024
- Article: 172
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The effect of data transformation on low-dimensional integration of single-cell RNA-seq
Authors
- Youngjun Park
- Anne-Christin Hauschild
- Content type: Research
- Open Access
- Published: 30 April 2024
- Article: 171
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Assessing the reliability of point mutation as data augmentation for deep learning with genomic data
Authors (first, second and last of 6)
- Hyunjung Lee
- Utku Ozbulak
- Joris Vankerschaver
- Content type: Research
- Open Access
- Published: 30 April 2024
- Article: 170
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Cauchy hyper-graph Laplacian nonnegative matrix factorization for single-cell RNA-sequencing data analysis
Authors
- Gao-Fei Wang
- Longying Shen
- Content type: Research
- Open Access
- Published: 29 April 2024
- Article: 169
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Optimizing spatio-temporal correlation structures for modeling food security in Africa: a simulation-based investigation
Authors
- Adusei Bofa
- Temesgen Zewotir
- Content type: Research
- Open Access
- Published: 27 April 2024
- Article: 168
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Exploring combinations of dimensionality reduction, transfer learning, and regularization methods for predicting binary phenotypes with transcriptomic data
Authors (first, second and last of 4)
- S. R. Oshternian
- S. Loipfinger
- R. S. N. Fehrmann
- Content type: Research
- Open Access
- Published: 26 April 2024
- Article: 167
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Biology System Description Language (BiSDL): a modeling language for the design of multicellular synthetic biological systems
Authors (first, second and last of 4)
- Leonardo Giannantoni
- Roberta Bardini
- Stefano Di Carlo
- Content type: Research
- Open Access
- Published: 25 April 2024
- Article: 166
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Improvements in viral gene annotation using large language models and soft alignments
Authors (first, second and last of 6)
- William L. Harrigan
- Barbra D. Ferrell
- Mahdi Belcaid
- Content type: Research
- Open Access
- Published: 25 April 2024
- Article: 165
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Orthogonal multimodality integration and clustering in single-cell data
Authors (first, second and last of 6)
- Yufang Liu
- Yongkai Chen
- Ping Ma
- Content type: Research
- Open Access
- Published: 25 April 2024
- Article: 164
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OrthoRefine: automated enhancement of prior ortholog identification via synteny
Authors
- J. Ludwig
- J. Mrázek
- Content type: Software
- Open Access
- Published: 25 April 2024
- Article: 163
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OmicNavigator: open-source software for the exploration, visualization, and archival of omic studies
Authors (first, second and last of 10)
- Terrence R. Ernst
- John D. Blischak
- Brett Warren Engelmann
- Content type: Software
- Open Access
- Published: 24 April 2024
- Article: 162
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Mora: abundance aware metagenomic read re-assignment for disentangling similar strains
Authors
- Andrew Zheng
- Jim Shaw
- Yun William Yu
- Content type: Research
- Open Access
- Published: 23 April 2024
- Article: 161
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SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses
Authors (first, second and last of 7)
- Luan Pinto Rabelo
- Davidson Sodré
- Marcelo Vallinoto
- Content type: Software
- Open Access
- Published: 22 April 2024
- Article: 160
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TEC-miTarget: enhancing microRNA target prediction based on deep learning of ribonucleic acid sequences
Authors
- Tingpeng Yang
- Yu Wang
- Yonghong He
- Content type: Research
- Open Access
- Published: 20 April 2024
- Article: 159
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MMGAT: a graph attention network framework for ATAC-seq motifs finding
Authors (first, second and last of 8)
- Xiaotian Wu
- Wenju Hou
- Yan Wang
- Content type: Research
- Open Access
- Published: 20 April 2024
- Article: 158
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A protein network refinement method based on module discovery and biological information
Authors (first, second and last of 4)
- Li Pan
- Haoyue Wang
- Wenbin Li
- Content type: Research
- Open Access
- Published: 20 April 2024
- Article: 157
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Drug-Online: an online platform for drug-target interaction, affinity, and binding sites identification using deep learning
Authors (first, second and last of 6)
- Xin Zeng
- Guang-Peng Su
- Yi Li
- Content type: Software
- Open Access
- Published: 20 April 2024
- Article: 156
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Noisecut: a python package for noise-tolerant classification of binary data using prior knowledge integration and max-cut solutions
Authors (first, second and last of 4)
- Moein E. Samadi
- Hedieh Mirzaieazar
- Andreas Schuppert
- Content type: Software
- Open Access
- Published: 20 April 2024
- Article: 155
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TrieDedup: a fast trie-based deduplication algorithm to handle ambiguous bases in high-throughput sequencing
Authors (first, second and last of 4)
- Jianqiao Hu
- Sai Luo
- Adam Yongxin Ye
- Content type: Software
- Open Access
- Published: 18 April 2024
- Article: 154
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Biomedical semantic text summarizer
Authors (first, second and last of 8)
- Mahira Kirmani
- Gagandeep Kour
- Abid Hussain Wani
- Content type: Research
- Open Access
- Published: 16 April 2024
- Article: 152
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Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed)
Authors (first, second and last of 8)
- Claus Vogl
- Mariia Karapetiants
- Lynette Caitlin Mikula
- Content type: Research
- Open Access
- Published: 16 April 2024
- Article: 151
This is part of 2 collections: -
Designing and delivering bioinformatics project-based learning in East Africa
Authors (first, second and last of 8)
- Caleb K. Kibet
- Jean-Baka Domelevo Entfellner
- Daniel Masiga
- Content type: Research
- Open Access
- Published: 14 April 2024
- Article: 150
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Biomarker discovery with quantum neural networks: a case-study in CTLA4-activation pathways
Authors
- Phuong-Nam Nguyen
- Content type: Research
- Open Access
- Published: 12 April 2024
- Article: 149
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MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach
Authors (first, second and last of 6)
- Jorge F. Beltrán
- Lisandra Herrera-Belén
- Stefania Short
- Content type: Software
- Open Access
- Published: 12 April 2024
- Article: 148
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Control of false discoveries in grouped hypothesis testing for eQTL data
Authors (first, second and last of 4)
- Pratyaydipta Rudra
- Yi-Hui Zhou
- Fred A. Wright
- Content type: Research
- Open Access
- Published: 11 April 2024
- Article: 147