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ORCIDFrontiers in Bioinformatics, Volume 5
Volume 5, 2025
- Maofei Zhu, Yueming Chu, Qiang Yuan, Junfeng Li, Silin Chen, Lin Li:
Integrated bioinformatics analysis to explore potential therapeutic targets and drugs for small cell carcinoma of the esophagus. - Samina Malik, Mirza Jawad ul Hasnain
, Gul Zaib, Haleema Saadia, Arif Malik, Ayesha Zahid:
Comprehensive structural and functional analyses of RAD50 nsSNPs: from prediction to impact assessment. - Phillip E. Davis, Joseph A. Russell:
ORF1ab codon frequency model predicts host-pathogen relationship in orthocoronavirinae. - Niklas Binder, Ashkan Khavaran, Roman Sankowski:
Primer on machine learning applications in brain immunology. - Julienne Lehmann, Ali M. Yazbeck, Jörg Hackermüller, Sebastian Canzler:
An extended miRNA repertoire in Rattus norvegicus. - Philomina Princiya Mascarenhas, M. S. Sannidhan, Ancilla J. Pinto, Dabis Camero, Jason Elroy Martis:
Improving acne severity detection: a GAN framework with contour accentuation for image deblurring. - Tasshitra Subramaniam, Siti Aisyah Mualif, Weng Howe Chan, Khairul Bariyyah Abd Halim:
Unlocking the potential of in silico approach in designing antibodies against SARS-CoV-2. - Nicolina Sciaraffa, Daniele Santoni, Andrea Li Greci, Swonild Ilenia Genovese, Claudia Coronnello, Walter Arancio:
Transcripts derived from AmnSINE1 repetitive sequences are depleted in the cortex of autism spectrum disorder patients. - Dawei Jiang, Zixi Chen, Hongli Du:
Cyclic peptide membrane permeability prediction using deep learning model based on molecular attention transformer. - Sonsiray Álvarez-Narváez, Telvin L. Harrell, Islam Nour, Sujit K. Mohanty, Steven J. Conrad:
Choosing the most suitable NGS technology to combine with a standardized viral enrichment protocol for obtaining complete avian orthoreovirus genomes from metagenomic samples. - Amy S. Graham, Fadheela Patel, Francesca Little, André J. W. van der Kouwe, Mamadou Kaba, Martha J. Holmes:
Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level. - Natasha N. Kunchur, Joshua J. A. Poole, Jesse Levine, Tillie-Louise Hackett, Rebecca E. Thornhill, Leila B. Mostaço-Guidolin:
Classification of collagen remodeling in asthma using second-harmonic generation imaging, supervised machine learning and texture-based analysis. - Tehrim Motiwala, Babalwa Nyide, Thandeka Khoza:
Molecular dynamic simulations to assess the structural variability of ClpV from Enterobacter cloacae. - Serena Vaglietti, Stefania Boggio Bozzo, Mirella Ghirardi, Ferdinando Fiumara:
Divergent evolution of low-complexity regions in the vertebrate CPEB protein family. - Christina Papangelou, Konstantinos Kyriakidis, Pantelis Natsiavas, Ioanna Chouvarda, Andigoni Malousi:
Reliable machine learning models in genomic medicine using conformal prediction. - Orhun Vural, Leon Jololian:
Machine learning approaches for predicting protein-ligand binding sites from sequence data. - Nandha Kumar Subramani, Subhashree Venugopal:
Identification of novel drug targets and small molecule discovery for MRSA infections. - Subhajit Ghosh, Sukhen Das Mandal, Subarna Thakur:
Biomarker-driven drug repurposing for NAFLD-associated hepatocellular carcinoma using machine learning integrated ensemble feature selection. - Kankana Bhattacharjee, Avik Sengupta, Rahul Kumar, Aryya Ghosh:
Identification of key hub genes in pancreatic ductal adenocarcinoma: an integrative bioinformatics study. - Ibukun John Abulude, Isabel Cristina Rodríguez Luna, Alejandro Sánchez Varela, Andrew Camilli, Daniel E. Kadouri, Xianwu Guo:
Using AlphaFold-Multimer to study novel protein-protein interactions of predation essential hypothetical proteins in Bdellovibrio. - Omar Abdelwahab, Davoud Torkamaneh:
Artificial intelligence in variant calling: a review. - Ishi Keenum, Scott A. Jackson, Emiley A. Eloe-Fadrosh, Lynn M. Schriml:
A standards perspective on genomic data reusability and reproducibility. - Yi-Hsuan Tsai, Prasenjit Mitra, David Taniar, Tun-Wen Pai:
DNA methylation biomarker analysis from low-survival-rate cancers based on genetic functional approaches. - Elijah Kolawole Oladipo, Stephen Feranmi Adeyemo, Ayomiposi Isaiah Oshoneye, Hannah Blessing Akintola, Bolatito Islam Elegbede, Tobiloba Uren Ayoomoba, Dorcas Ayomide Atilade, Omolara Omoboye Adegboye, Abuoma Elizabeth Ejikeme, Chris Olamide Balogun, Kehinde Abolade Aderibigbe, Possible Okikiola Popoola, Victoria Ajike Alabi, Boluwatife Ayobami Irewolede, Gbemi Henry Ano-Edward, Ademola Olabode Ayeleso, Helen Onyeaka:
Harnessing computational immunology to design targeted subunit vaccines for infectious bursal disease in poultry. - Francesco Tomasella, Cinzia Pizzi:
MetaComBin: combining abundances and overlaps for binning metagenomics reads. - Neetu Rani Dhiman, Surbhi Singh, Royana Singh, Anand Kumar, Varun Kumar Singh, Abhishek Pathak, Rameshwar Nath Chaurasia, Vijay Nath Mishra, Niraj Kumar Srivastava, Swati Sahu, Nikhil Pandey, Deepika Joshi:
Urinary based biomarkers identification and genetic profiling in Parkinson's disease: a systematic review of metabolomic studies. - Miriam E. L. Gakpey, Shadrack A. Aidoo, Toheeb A. Jumah, George Hanson, Siyabonga Msipa, Florence N. Mbaoji, Omonijo Bukola, Palesa C. Tjale, Mamadou Sangare, Hedia Tebourbi, Olaitan I. Awe:
Targeting aldose reductase using natural African compounds as promising agents for managing diabetic complications. - Vikas Sharma, Arti Gupta, Mohini Singh, Anshul Singh, Anis Ahmad Chaudhary, Zakir Hussain Ahmed, Salah-ud-din Khan, Sarvesh Rustagi, Sanjay Kumar, Sandeep Kumar:
Phytochemical baicalin potentially inhibits Bcl-2 and VEGF: an in silico approach. - Mikhail Arbatsky, Ekaterina Vasilyeva, Veronika Sysoeva, Ekaterina Semina, Valeri Saveliev, Kseniya Rubina:
Seurat function argument values in scRNA-seq data analysis: potential pitfalls and refinements for biological interpretation. - Veilumuthu Pattapulavar, Sathiyabama Ramanujam, Manisha Shah, Muthukumar Thirunavukkarasu, Sivakumar Arumugam, Ramanathan Karuppasamy, Antony V. Samrot, Deepasree K, Subhashree Venugopal, John Godwin Christopher:
Streptomyces sp. VITGV156 secondary metabolite binds pathogenic protein PBP2a and Beta-lactamase. - Mebrie Zemene Kinde, Bizuayehu Kerisew, Tegegne Eshetu, Abebe Tesfaye Gessese:
Genomic analysis of Listeria monocytogenes strains from dairy products in Ethiopia. - Gourav Choudhir, Faiza Iram, Israil, Mohammad Shahid, Anas Shamsi, Md. Imtaiyaz Hassan, Asimul Islam:
Inhibition potential of margolonone and isomargolonone against the dengue virus protease using molecular modeling approaches. - Julia Kelliher, Leah Y. D. Johnson, Francisca E. Rodriguez, Jaclyn K. Saunders, Marie E. Kroeger, Buck Hanson, Aaron J. Robinson, Winston E. Anthony, Marc W. Van Goethem, Anders Kiledal, Ahmed A. Shibl, Amanda Araujo Serrao de Andrade, Cassandra L. Ettinger, Chhedi Lal Gupta, Chris R. P. Robinson, Cristal Zuniga, Daniel Sprockett, Douglas Terra Machado, Emilie J. Skoog, Iyanu Oduwole, Jason A. Rothman, Kaelan Prime, Katherine R. Lane, Leandro Nascimento Lemos, Lisa Karstens, Mark McCauley, Mitiku Mihiret Seyoum, Moamen M. Elmassry, Mustafa Guzel, Reid Longley, Simon Roux, Thomas M. Pitot, Emiley A. Eloe-Fadrosh:
A cost and community perspective on the barriers to microbiome data reuse. - Ana Stolnicu, Peter Eckhardt-Bellmann, Angelika M. R. Kestler, Hans A. Kestler:
Identification of ordinal relations and alternative suborders within high-dimensional molecular data. - Sanskriti Baranwal, Ricardo Avila Sanchez, Clement-Andi Edet, Erick Chastain, Inimary T. Toby:
Optimizing clustering of CDR3 sequences using natural language processing, Word2Vec, and KMeans. - Praveen Kumar, Vincent T. Metzger, Swastika T. Purushotham, Priyansh Kedia, Cristian Bologa, Christophe G. Lambert, Jeremy J. Yang:
KG2ML: integrating knowledge graphs and positive unlabeled learning for identifying disease-associated genes. - Noor Jamal Alkhateeb, Mamoun Awad:
Advances in protein-protein interaction prediction: a deep learning perspective. - Priscila Galvão Doria, Gisele Vieira Rocha, Vanessa Dybal Bertoni, Roberto de Souza Batista dos Santos, Mariana Araújo-Pereira, Clarissa Gurgel:
Gene expression profile in colon cancer therapeutic resistance and its relationship with the tumor microenvironment. - Omar Abdelwahab, Davoud Torkamaneh:
A Transformers-based framework for refinement of genetic variants. - M. Mohamed Kalith Oli, Jafar Ali Ibrahim Syed Masood:
Identification and validation of tumor microenvironment-related therapeutic targets in gastric cancer using integrated multi-omics and molecular docking approaches. - Andrew H. Lee, Ganesh Talluri, Manan Damani, Brandon Vera Covarrubias, Helena Hanna, Jeremy Chavez, Julian M. Moore, Jacob Baradarian, Michael Molgaard, Beau Nielson, Kalah Walden, Thomas Broderick, Layla Al-Nakkash:
Deep learning software and revised 2D model to segment bone in micro-CT scans. - Emma L. Flynn, Riya Shah, Ian Dunn, Rishal Aggarwal, David Ryan Koes:
PharmacoForge: pharmacophore generation with diffusion models. - Rafael P. Lemos, Diego C. B. Mariano, Sabrina de Azevedo Silveira, Raquel Cardoso de Melo Minardi:
COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices. - Yutaka Nakachi, Jianbin Du, Risa Watanabe, Yutaro Yanagida, Miki Bundo, Kazuya Iwamoto:
MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data. - Leonora Martínez-Núñez:
Structural biology meets typography: using protein structures to inspire creative expression and connect diverse audiences. - Shivani Malik, Ritu Tomer, Akanksha Arora, Gajendra P. S. Raghava:
Identification of multiple prognostic biomarker sets for risk stratification in SKCM. - Susanne Zabel, Philipp Hennig, Kay Nieselt:
Visualizing stability: a sensitivity analysis framework for t-SNE embeddings. - Yuyun Jia, Yanping Cao, Qin Yin, Xueqian Li, Xiu Wen:
Identification of immune and major depressive disorder-related diagnostic markers for early nonalcoholic fatty liver disease by WGCNA and machine learning. - Max van den Boom, Erik Schultes, Thomas Hankemeier:
Structure-based prediction of SARS-CoV-2 variant properties using machine learning on mutational neighborhoods. - Juan Zhou, Huan Wang, Jin Wang, Fuming Zhou:
Discovering biomarkers for chronic sinusitis with nasal polyps: a study integrating bioinformatics analysis and experimental validation of macrophage polarization and metabolism-related genes. - Christopher Golden, David J. Studholme, Rhys A. Farrer:
DIAMOND2GO: rapid Gene Ontology assignment and enrichment detection for functional genomics. - Qingfang Ba, Heng Zhou, Zheming Yuan, Zhijun Dai:
Enhancing genomic prediction in Arabidopsis thaliana with optimized SNP subset by leveraging gene ontology priors and bin-based combinatorial optimization. - Genevieve Laprade, Quinn Lee, Kristin L. Gallik, Michael Nelson, Natalie Woo, Celina Terán Ramírez, Alexis Ricardo Becerril Cuevas, Kevin W. Eliceiri, Corinne Esquibel:
The importance of democratized resources in early-career training for bioimage analysts and bioimaging scientists. - Nihui Shao, Yunfei Guo:
Protein embeddings reveal a continuous molecular landscape of host adaptation in waterfowl parvoviruses. - Dehua Feng, Jingwen Hao, Lingxu Li, Jian Chen, Xinying Liu, Ruijie Zhang, Huirui Han, Tianyi Li, Xuefeng Wang, Xia Li, Lei Yu, Bing Li, Jin Li, Limei Wang:
Drug discovery for chemotherapeutic resistance based on pathway-responsive gene sets and its application in breast cancer. - Iveth Gómez-Morales, Adriana P. Mendizabal, José Alejandro Morales, Teresa Romero-Gutiérrez:
High-dimensional co-expression network analysis reveals persistent TRH gene expression throughout axolotl telencephalon regeneration. - Hiba Orsud, Sumaya Zoughbor, Fatima Aldhaheri, Khalid Hajissa, Manar Refaey, Suad Ajab, Khaled Alswaider, Nora Mohamed, Obaid Alkaabi, Zakeya Al Rasbi:
Multi-marker comparative analysis of 18S, ITS1, and ITS2 primers for human gut mycobiome profiling. - Loganathan Chandramani Priya Dharshini, Abul Kalam Azad Mandal:
Network-based insights into miR-30a-5p-mediated regulation and EGCG targeting in triple-negative breast cancer. - Helya Goharbavang, Artem T. Ashitkov, Athira Pillai, Joshua D. Wythe, Guoning Chen, David Mayerich:
Segmentation and modeling of large-scale microvascular networks: a survey. - Riya Nalwa, Anis Ahmad Chaudhary, Mandeep Chouhan, Prashant Kumar Tiwari, Saurabh Gupta, Hassan Ahmed Rudayni, Vivek Dhar Dwivedi, Sanjay Kumar:
Computational investigation of potential natural compounds as inhibitors of monkeypox virus cysteine proteinase. - Tim Breitenbach, Thomas Dandekar:
Adaptive sampling methods facilitate the determination of reliable dataset sizes for evidence-based modeling. - Xiaoxi Hao, Dingjian Liang, Yimin Shen, Cuimin Sun, Wei Lan:
PreBP: an interpretable, optimized ensemble framework using routine complete blood count for rapid pathogen identification in bacterial pneumonia. - Jingmin Zhang, Tianwei Meng, Weiqi Gao, Xinghua Li, Juan Xu:
Identifying novel therapeutic targets for non-alcoholic fatty liver disease using bioinformatics approaches: from drug repositioning to traditional Chinese medicine. - Antoine A. Ruzette, Nina Kozlova, Kayla A. Cruz, Taru Muranen, Simon F. Nørrelykke:
An image analysis pipeline to quantify the spatial distribution of cell markers in stroma-rich tumors. - Vineet Saravanan, Alexander Kravetz, Fabia Ursula Battistuzzi:
Higher frequency of prokaryotic low complexity regions in core and orthologous genes. - Innocent Sibanda, Geoff Nitschke:
Bioengineering hybrid artificial life. - Daiana Colibasanu, Vlad Groza, Maria Antonietta Occhiuzzi, Fedora Grande, Mihai Udrescu, Lucretia Udrescu:
Drug repositioning pipeline integrating community analysis in drug-drug similarity networks and automated ATC community labeling to foster molecular docking analysis. - Lenin Domínguez-Ramírez, Maricruz Anaya-Ruiz, Paulina Cortés-Hernández:
Quality over quantity: how to get the best results when using docking for repurposing. - Yaan J. Jang:
Editorial: Computational protein function prediction based on sequence and/or structural data. - Anas Al-Okaily, AbdelGhani Tbakhi:
A novel linear indexing method for strings under all internal nodes in a suffix tree. - Jinnan Hu, Donald Freed, Hanying Feng, Hong Chen, Zhipan Li, Haodong Chen:
A novel and accelerated method for integrated alignment and variant calling from short and long reads. - Shrudhi Devi, Gurunathan Jayaraman:
Unraveling the molecular basis of snake venom nerve growth factor: human TrkA recognition through molecular dynamics simulation and comparison with human nerve growth factor. - Sangeetha Muthamilselvan, Natarajan Vaithilingam, Ashok Palaniappan:
BC-predict: mining of signal biomarkers and production of models for early-stage breast cancer subtyping and prognosis. - Suraiya Akhter, John H. Miller:
Bacteriocin prediction through cross-validation-based and hypergraph-based feature evaluation approaches. - Rubén Fernández, L. Francisco Lorenzo-Martín, Víctor Quesada, Xosé R. Bustelo:
Pan-cancer analyses identify oncogenic drivers, expression signatures, and therapeutic vulnerabilities in RHO GTPase pathway genes. - Alexander Hunt, Holger Schulze, Kay Samuel, Robert B. Fisher, Till T. Bachmann:
Stain-free artificial intelligence-assisted light microscopy for the identification of blood cells in microfluidic flow. - Bing He, Teng Xu, Shaowei Xu, Huqiang Fang, Qingshan Yang:
Comparative transcriptome analysis of different tissues of Hylomecon japonica provides new insights into the biosynthesis pathway of triterpenoid saponins. - Zeyu Zou, Ziheng Duan:
SpaLLM: a general framework for spatial domain identification with large language models. - Angela Wang, Elena Xiao, Jason Cheng, Xiaoxi Shen:
Genetic risk predictions using deep learning models with summary data. - Nandha Kumar Subramani, Subhashree Venugopal, Anand Prem Rajan:
An integrated subtractive genomics and immunoinformatic approach for designing a multi-epitope peptide vaccine against methicillin-resistant Staphylococcus aureus. - David Kirchenbuechler, Mariana De Niz, Constadina Arvanitis:
Trail-blazing and keeping pace: building, retaining and expanding image analysis expertise. - Shanyong Jiang, Jingjing Cao, Jianshu Lu, Jianxiao Liang, Lianxin Li, Yanqiang Song, Jincheng Gao, Baoen Jiang:
Identification and functional analysis of hub genes in knee osteoarthritis via bioinformatics and experimental validation. - Mohammed Alrouji, Mohammed S. Alshammari, Sharif Alhajlah, Syed Tasqeeruddin, Khuzin Dinislam, Anas Shamsi, Saleha Anwar:
Computational drug repurposing reveals Alectinib as a potential lead targeting Cathepsin S for therapeutic developments against cancer and chronic pain. - Sreeshma Ravindran Kammarambath, Leona Dcunha, Athira Perunelly Gopalakrishnan, Amal Fahma, Neelam Krishna, Altaf Mahin, Samseera Ummar, Prathik Basthikoppa Shivamurthy, Inamul Hasan Madar, Rajesh Raju:
Role of histone-lysine N-methyltransferase 2D (KMT2D) in MEK-ERK signaling-mediated epigenetic regulation: a phosphoproteomics perspective. - Shangyi Luo, Li Liu, Yang Sun, Jian Shi, Yajing Zhang:
Spatial heterogeneity reveals an evolutionary signature predicting therapeutic response and clinical outcomes in hepatocellular carcinoma. - Nicolina Sciaraffa, Antonino Gagliano, Luigi Augugliaro, Claudia Coronnello:
Optimization of clustering parameters for single-cell RNA analysis using intrinsic goodness metrics. - Chelsy Chesterman, Thomas Desautels, Luz-Jeannette Sierra, Kathryn T. Arrildt, Adam T. Zemla, Edmond Y. Lau, Shivshankar Sundaram, Jason Laliberte, Lynn Chen, Aaron Ruby, Mark Mednikov, Sylvie Bertholet, Dong Yu, Kate Luisi, Enrico Malito, Corey P. Mallett, Matthew J. Bottomley, Robert A. van den Berg, Daniel M. Faissol:
Design of cross-reactive antigens with machine learning and high-throughput experimental evaluation. - Rachel Griffard-Smith, Emily Schueddig, Diane E. Mahoney, Prabhakar Chalise, Devin C. Koestler, Dong Pei:
micRoclean: an R package for decontaminating low-biomass 16S-rRNA microbiome data. - Jose Barba-Montoya, Jack M. Craig, Sudhir Kumar:
Integrating phylogenies with chronology to assemble the tree of life. - Asma Attaoui, Hajer Foddha, Houcemeddine Othman, Hassen Ben Abdennebi, Amel Haj Khelil:
Utility of regional STR marker variations in Tunisian and sub-Saharan populations: insights into forensic and population genetics. - K. Lakshmi, Sundararajan Vino:
Cross-disease transcriptomic meta-analysis and network pharmacology reveal key therapeutic targets in rheumatoid arthritis, systemic lupus erythematosus and multiple sclerosis. - Fouzia Nawab, Wafa Naeem, Sadia Fatima, Muhammad Uzair Khan, Aamir Mehmood, Sadia Nawab, Ishaq Khan, Haseena Nawaz, Hilal Ahmad, Ali Talha Khalil, Ishtiaq Ahmad Khan, Muhammad Irfan, Mohammed Alorini, Syed Ali Khurram, Asif Ali:
Mutational insights and in silico characterization of NEK family kinases in OSCC patients from the Pakistani population. - Jaytha Thomas, Fathimathul Lubaba, Mukhtar Ahmed, Althaf Mahin, Levin John, Athira Perunelly Gopalakrishnan, Suhail Subair, Prathik Basthikoppa Shivamurthy, Rajesh Raju, Sowmya Soman:
CIT kinase phosphorylation as significant regulatory node for cellular checkpoints. - Prashant Kumar Tiwari, Mukesh Kumar, Richa Mishra, Xiaomeng Zhang, Sanjay Kumar:
In silico identification of novel natural compounds as potential KIFC1 inhibitors for the therapeutic intervention of triple-negative breast cancer. - Sandro Gepiro Contaldo, Antonio d'Acierno, Lorenzo Bosio, Francesco Venice, Elisa Li Perottino, Janneth Estefania Hoyos Rea, Giovanna Cristina Varese, Francesca Cordero, Marco Beccuti:
Long-read microbial genome assembly, gene prediction and functional annotation: a service of the MIRRI ERIC Italian node. - Yan Li, Boran Wang, Zhen Liu, Wei Wei, Caiyi Fei, Shi Xu, Tiyun Han, Wei Geng, Zengding Wu:
TRANSAID: a hybrid deep learning framework for translation site prediction with integrated biological feature scoring. - Tianle Xue, Yunpeng Chen, Xiaomeng Li, Zhixiang Zhou, Qiyang Chen:
Correction: Integrative machine learning and bioinformatics analysis to identify cellular senescence-related genes and potential therapeutic targets in ulcerative colitis and colorectal cancer. - Durgadevi Rajendran, Nalini Easwaran:
In silico analysis of Triphala-derived polyphenols as inhibitors of TIR-TIR homodimerization in the inflammatory pathway. - Gayatri Munieswaran, Venkatraman Manickam:
Functional and structural impacts of oncogenic missense variants on human polo-like kinase 1 protein. - Clara Shionyu-Mitusyama, Satoshi Ohmori, Subaru Hirata, Hirokazu Ishida, Tsuyoshi Shirai:
IDRdecoder: a machine learning approach for rational drug discovery toward intrinsically disordered regions. - Damiano Clementel, Alessio Del Conte, Alexander Miguel Monzon, Silvio C. E. Tosatto:
ngx-mol-viewers: Angular components for interactive molecular visualization in bioinformatics. - Maxime Maria, Valentin Guillaume, Simon Guionnière, Nicolas Dacquay, Cyprien Plateau-Holleville, Vincent Larroque, Jean Lardé, Yassine Naimi, Jean-Philip Piquemal, Guillaume Levieux, Nathalie Lagarde, Stéphane Mérillou, Matthieu Montès:
Interactive visualization of large molecular systems with VTX: example with a minimal whole-cell model. - Gaetano Aufiero, Carmine Fruggiero, Nunzio D'Agostino:
inDAGO: a user-friendly interface for seamless dual and bulk RNA-Seq analysis. - Mahshid Khazani Asforooshani, Narjes Noori Goodarzi, Behzad Shahbazi, Nayereh Rezaie Rahimi, Kimia Mahdavian, Mahdi Rohani, Farzad Badmasti:
Exploiting subtractive genomics to identify novel drug targets and new immunogenic candidates against Bordetella pertussis: an in silico study. - Joshua Stephenson, Konda Reddy Karnati:
Recent trends in machine learning and deep learning-based prediction of G-protein coupled receptor-ligand binding affinities. - Shipra Jain, Ritu Tomer, Sumeet Patiyal, Gajendra P. S. Raghava:
NfκBin: a machine learning based method for screening TNF-α induced NF-κB inhibitors. - Sumaiya Binte Shahid, Maleeha Kaikaus, Md. Hasanul Kabir, Mohammad Abu Yousuf, A. K. M. Azad, Asmaa S. Al-Moisheer, Naif Mohammed Alotaibi, Salem A. Alyami, Touhid Bhuiyan, Mohammad Ali Moni:
Novel deep learning for multi-class classification of Alzheimer's in disability using MRI datasets. - Ehsan Saghapour, Rahul Sharma, Delower Hossain, Kevin Song, Zhandos Sembay, Jake Y. Chen:
Temporal GeneTerrain: advancing precision medicine through dynamic gene expression visualization. - Aanya Gupta, Koji Abe, Holden T. Maecker:
Comprehensive analysis of multi-omics vaccine response data using MOFA and Stabl algorithms. - Tianle Xue, Yunpeng Chen, Xiaomeng Li, Zhixiang Zhou, Qiyang Chen:
Integrative machine learning and bioinformatics analysis to identify cellular senescence-related genes and potential therapeutic targets in ulcerative colitis and colorectal cancer. - Xiaohua An, Xiaoxue Huang, Qiujie Yu, Yiyue Tang, Yan Wang, Huasu Chen, Yafei Zhang, Qianhao Huang, Yudi Rao, Guomei Hu, He Zha:
Bioinformatics analysis of lncRNA and mRNA differentially expressed in patients with cervical cancer. - Kleber Padovani de Souza, Rafael Cabral Borges, Roberto Xavier, André C. P. L. F. de Carvalho, Anna Reali, Annie Chateau, Ronnie Alves:
Using reinforcement learning in genome assembly: in-depth analysis of a Q-learning assembler. - Jae-Won Cho, Jingyi Cao, Martin Hemberg:
Single-cell splicing QTL analysis in pancreatic islets. - Qihuan Yao, Zhen Chen, Ye Cao, Huijing Hu:
Enhancing drug-target interaction prediction with graph representation learning and knowledge-based regularization. - Islam Akef Ebeid, Haoteng Tang, Pengfei Gu:
Inferred global dense residue transition graphs from primary structure sequences enable protein interaction prediction via directed graph convolutional neural networks. - Anthony Wong, Sanskruthi Guduri, Tsungyen Chen, Kunal Patel:
Machine learning-guided optimization of triple agonist peptide therapeutics for metabolic disease. - Osasan Stephen Adebayo, George Oche Ambrose, Daramola Olusola, Adefolalu Oluwafemi, Hind A. Alzahrani, Abdulkarim Hasan:
QSAR-guided discovery of novel KRAS inhibitors for lung cancer therapy. - Piyachat Udomwong, Thanathat Pamonsupornwichit, Kanchanok Kodchakorn, Chatchai Tayapiwatana:
ParaDeep: sequence-based deep learning for residue-level paratope prediction using chain-aware BiLSTM-CNN models. - Carlos G. Schrago, Beatriz Mello:
Assessment of phylogenetic informativeness in mitochondrial and nuclear genes for mammalian systematics using sparse learning. - Rafhanah Shazwani Rosli, Mohamed Hadi Habaebi, Md Rafiqul Islam, Mohammed Abdulla Salim Al Hussaini:
Analysis of breast region segmentation in thermal images using U-Net deep neural network variants. - Qiu Wang, Hong Yang, Fang Li, Song Ge, Ling Ji, Xiaofeng Li:
Analysis of histone modifications in key cellular subpopulations in the context of azoospermia using spermatogenic single-cell RNA-seq data. - Raghad Al-Rasheed, Abdulmohsen Al Thubaity, Lolwah Abdullah Alriyees, Abir Abdullah Alamro, Humidah Alanazi, Areej Alhareeri, Bader Almuzzaini, Mamoon Rashid:
In silico analysis of CSF2RB from cancer genomic databases reveals a heterogeneous role in different breast cancer subtypes. - Vineetha Shaji, Akash Anil, Ayisha A. Jabbar, Althaf Mahin, Ahmad Rafi, Amjesh Revikumar, Sowmya Soman, Ganesh Prasad, Sneha M. Pinto, Yashwanth Subbannayya, Abhithaj Jayanandan, Rajesh Raju:
Uncovering human kinase substrates in nipah proteome. - Derek L. Thompson, Hsiang-Yun Wu, Christopher W. Bartlett, William C. Ray:
Editorial: Networks and graphs in biological data: current methods, opportunities and challenges. - Ankita Lawarde, Masuma Khatun, Prakash Lingasamy, Andres Salumets, Vijayachitra Modhukur:
Tumor tissue-of-origin classification using miRNA-mRNA-lncRNA interaction networks and machine learning methods. - Sonar Soni Panigoro, Rafika Indah Paramita, Fadilah Fadilah, Septelia Inawati Wanandi, Aisyah F. Prawiningrum, Linda Erlina, Wahyu Dian Utari, Ajeng Megawati Fajrin:
Germline mutation profiling of breast cancer patients using a non-BRCA sequencing panel. - Kylee K. Rahm, Branden S. Kinghorn, Myanna J. Moody, Ben C. Stone, Kenton C. Strong, Brian S. Kim, Yen Jou Chang, Samantha N. Sleight, Alyssa A. Nitz, David V. Hansen, Matthew H. Bailey:
Cellf-deception: human microglia clone 3 (HMC3) cells exhibit more astrocyte-like than microglia-like gene expression. - Lara Vázquez-González, Carlos A. Peña-Reyes, Alba Regueira-Iglesias, Carlos Balsa-Castro, Inmaculada Tomás, María J. Carreira:
EPheClass: ensemble-based phenotype classifier from 16S rRNA gene sequences. - Gustavo Schottlender, Juan M. Prieto, Marcelo A. Marti, Darío Fernández Do Porto:
Beyond Tanimoto: a learned bioactivity similarity index enhances ligand discovery. - Baptiste Bauvin, Thibaud Godon, Guillaume Bachelot, Claudia Carpentier, Riikka Huusaari, Maxime Déraspe, Juho Rousu, Caroline Quach, Jacques Corbeil:
Extracting a COVID-19 signature from a multi-omic dataset. - Yizhou Wang, Priyanka Bhandary, Kevin Griffin, Jason H. Moore, Xue Li, Zhiping Paul Wang:
Integrative multi-omics study identifies sex-specific molecular signatures and immune modulation in bladder cancer. - Shreyashi Bodaka, Narasaiah Kolliputi:
CoMPHI: a novel composite machine learning approach utilizing multiple feature representation to predict hosts of bacteriophages. - Ali Alghubayshi, Mohammad A. Alshabeeb, Dayanjan S. Wijesinghe, Mohammed Alawadh, Suad Alshammari, Khalifa Alrajeh, Mona A. Alkhairi, Imadul Islam, Ahmed Alaskar:
Genomics-driven drug repurposing and novel targets identification for sickle cell disease in Saudi patients. - Alexander Hunt, Holger Schulze, Kay Samuel, Robert B. Fisher, Till T. Bachmann:
Stain-free artificial intelligence-assisted light microscopy for the identification of leukocyte morphology change in presence of bacteria. - Franz Leonard Böge, Helena U. Zacharias, Stefanie C. Becker, Klaus Jung:
Using deep neural networks and LASSO regression to predict miRNA expression changes based on mRNA data. - Alexandra Lindsey Djomkam Zune, Charles Ochieng' Olwal, Emmanuel Agbeli, Abdoulaye Baniré Diallo, Emmanuella Amoako, Yaw Bediako, Lily Paemka:
Precision medicine on a budget in Africa: using existing genetic data to mitigate adverse drug reactions to conventional cancer drugs. - Ying Liu, Jiayi Cai, Aamir Fahira, Kai Zhuang, Jiaojiao Wang, Zhi Zhang, Lin Yan, Yong Liu, Defang Ouyang, Zunnan Huang:
Unveiling the impact of interferon genes on the immune microenvironment of triple-negative breast cancer: identification of therapeutic targets. - Sofia Ramos, João Gregório, Ana Sofia Fernandes, Nuno Saraiva:
Association between dysregulated expression of Ca2+ and ROS-related genes and breast cancer patient survival. - Shuang Zhao, He Zhang:
Key genes associated with brain metastasis in non-small cell lung cancer: novel insights from bioinformatics analysis. - Manisha Shah, Sivakumar Arumugam:
Food-derived linear vs. rationally designed cyclic peptides as potent TNF-alpha inhibitors: an integrative computational study. - Jishnu Ghosh, Abdullah M. Alshahrani, Aritra Palodhi, Debarghya Bhattacharyya, Subhadip Das, Sunil Kanti Mondal, Abul Kalam, S. Rehan Ahmad, Chittabrata Mal:
Identification and therapeutic investigation of biomarker genes underpinning hepatocellular carcinoma: an in silico study utilising molecular docking and dynamics simulation. - Yi Zhang, Yongqian Liu, Wei Meng, Xiaobo Yu, Xiaojun Xu:
Integrative transcriptomic analysis reveals microglial metabolic-inflammatory crosstalk of HK2-HSPA5-TNF axis after intracerebral hemorrhage. - Jianfeng Zhang, Mujun Chen, Dianzeng Yang, Yanjie Jia:
The bacteriostatic regulation of luteolin from honeysuckle by protein network interaction. - Xiangjun Wang, Panpan Jin, Juan Xu, Junyi Li, Mengzhen Ji:
Integrative machine learning and transcriptomic analysis identifies key molecular targets in MNPN-associated oral squamous cell carcinoma pathogenesis. - Jie Sun, Robert Morrison, Soyeon Kim, Kairuo Yan, Hyun Jung Park:
Quantitative measures to assess the quality of cellular indexing of transcriptomes and epitopes by sequencing data. - Jeremiah I. Abok, Jeremy S. Edwards, Jeremy J. Yang:
TICTAC: target illumination clinical trial analytics with cheminformatics. - Andrew J. Maritan, Frank J. Stewart:
Essential nucleic acid omics: a theoretical foundation for early-stage users. - Marina Leer, George A. Soultoukis, Markus Jähnert, Masoome Oveisi, Dirk Walther, Timothy J. Schulz:
pubCounteR: an R package for interrogating published literature for experimentally-derived gene lists within a user-defined biological context. - Behnam Hasannejad-Asl, Farkhondeh Pooresmaeil, Sareh azadi, Ali Najafi, Ali Esmaeili, Saeid Bagheri-Mohammadi, Bahram Kazemi:
Computational drug discovery of potential 5α-reductase phytochemical inhibitors and hair growth promotion using in silico techniques. - Mengyao Sha, Jun Chen, Haifeng Hou, Huaihui Dou, Yan Zhang:
Integrated single-cell and bulk RNA dequencing to identify and validate prognostic genes related to T Cell senescence in acute myeloid leukemia. - Alexandre Pedro Selvatti, Naoko Takezaki:
Internal fossil constraints have more effect on the age estimates of crown Palaeognathae than different phylogenomic data type. - Mohammed Naveez Valathoor, Subhashree Venugopal, Anand Prem Rajan:
Subtractive genomic approach to uncover novel drug targets in Salmonella typhimurium and computational screening of food-based polyphenols as inhibitors. - Jack M. Craig, Whitney L. Fisher, Allan S. Thomas, S. Blair Hedges, Sudhir Kumar:
Completing a molecular timetree of Afrotheria. - Pearl John, C. Sudandiradoss:
Neurogenic locus notch homolog protein 1 (NOTCH 1) SNP informatics coupled with intrinsically disordered regions and post-translational modifications reveals the complex structural crosstalk of Lung Adenocarcinoma (LUAD). - Ryan M. Tobin, Shikha Singh, Sudhir Kumar, Sayaka Miura:
GenoPath: a pipeline to infer tumor clone composition, mutational history, and metastatic cell migration events from tumor DNA sequencing data. - Yesid Aristizabal, Yamil Liscano, José Oñate López:
Understanding the selectivity in silico of colistin and daptomycin toward gram-negative and gram-positive bacteria, respectively, from the interaction with membrane phospholipids. - Grigorios Koulouras, Yingrong Xu:
Protein cleaver: an interactive web interface for in silico prediction and systematic annotation of protein digestion-derived peptides. - Zhaorong Li, Juan I. Fuxman Bass:
ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets. - João C. Setubal, Alberto Paccanaro:
Editorial: Expert opinions in genomic analysis. - Chunhui Xu, Yang Yu, Govardhan Khadakkar, Jiacheng Xie, Dong Xu, Qiuming Yao:
Multimodal knowledge expansion widget powered by plant protein phosphorylation database and ChatGPT. - Micaela Villacrés, Alec Avila, Karina Beatriz Jimenes Vargas, António Machado, José M. Alvarez-Suarez, Eduardo Tejera:
Discovering molecules and plants with potential activity against gastric cancer: an in silico ensemble-based modeling analysis. - Roman Perik-Zavodskii, Olga Perik-Zavodskaia, Marina Volynets, Saleh Alrhmoun, Sergey Sennikov:
TCRscape: a single-cell multi-omic TCR profiling toolkit. - Minghao Wang, Yu Wang, Yitong Li, Chengyi Zhang, Canjun Li, Nan Bi:
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma. - Ayesha Sajjad, Ihteshamul Haq, Rabia Syed, Faheem Anwar, Muhammad Hamza, Muhammad Musharaf, Tehmina Kiani, Faisal Nouroz:
In-silico molecular analysis and blocking of the viral G protein of Nipah virus interacting with ephrin B2 and B3 receptor by using peptide mass fingerprinting. - Yi-Chun Wang, Daniel Bulte, Michael Brady:
Bridging the gap between hepatocellular carcinoma management guidelines and personalised medicine: a Bayesian network study. - Konstantinos Perperidis, Themis P. Exarchos, Aristidis G. Vrahatis, Panagiotis Vlamos, Marios G. Krokidis:
Computational analysis of transcriptome data and mapping of functional networks in Parkinson's disease. - Shubham Choudhury, Naman Kumar Mehta, Gajendra P. S. Raghava:
CytoLNCpred-a computational method for predicting cytoplasm associated long non-coding RNAs in 15 cell-lines. - Yuya Sato, Toru Asahi, Kosuke Kataoka:
Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data. - Boris Tchatchoua Ngassam, Huilin Niu, Sunny Pang, Valeryia Shydlouskaya, Tallulah S. Andrews:
Applications of AI to single-cell and spatial transcriptomics: current state-of-the-art and challenges. - Veronica Remori, Michela Prest, Mauro Fasano:
Sequence-based prioritization of i-Motif candidates in the human genome. - Delower Hossain, Ehsan Saghapour, Jake Y. Chen:
NeSyDPP-4: discovering DPP-4 inhibitors for diabetes treatment with a neuro-symbolic AI approach. - Patricia Agudelo-Romero, Talya Conradie, Jose Antonio Caparros-Martin, David Martino, Anthony Kicic, Stephen Stick, Christopher Hakkaart, Abhinav Sharma:
Advancing bioinformatics capacity through Nextflow and nf-core: lessons from an early-to mid-career researchers-focused program at The Kids Research Institute Australia. - Vachiranee Limviphuvadh, Thimo Ruethers, Minh N. Nguyen, Dean R. Jerry, Benjamin P. C. Smith, Yulan Wang, Yansong Miao, Anand Kumar Andiappan, Andreas L. Lopata, Sebastian Maurer-Stroh:
Fish isoallergens and variants: database compilation, in silico allergenicity prediction challenges, and epitope-based threshold optimization. - Giulia Ghisleni, Christian Stolte, Megan Gozzard, Lea Von Soosten, Antonia Bruno:
Why science needs art. - Emanuell Rodrigues de Souza, Higor Almeida Cordeiro Nogueira, Ronaldo da Silva Francisco Junior, Ana Beatriz Garcia, Enrique Medina-Acosta:
Integrated multi-optosis model for pan-cancer candidate biomarker and therapy target discovery. - Srineevas Sriram, Chandresh Palanichamy, Subash Palaniappan Thirumoorthi, Manshi Kumari Gupta, C. Sudandiradoss:
REST missense mutations reveal disrupted Re1 motif binding and co-repressor interactions in uterine fibroids. - Lifeng Niu, Yanli Wang, Yao Gao, Jun Zhang:
Altered circRNAs: a novel potential mechanism for the functions of extracellular vesicles derived from platelet-rich plasma. - Wafa Alanazi, Di Meng, Gianluca Pollastri:
DeepPredict: a state-of-the-art web server for protein secondary structure and relative solvent accessibility prediction. - Arsenij Ustjanzew, Federico Marini, Saskia Wagner, Arthur Wingerter, Roger Sandhoff, Jörg Faber, Claudia Paret:
Predicting GD2 expression across cancer types by the integration of pathway topology and transcriptome data.
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