Latest Computational Biology Research Papers
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- Integrated single-cell and spatial transcriptomic analyses identify TRIP6 as a prognostic and EMT-associated biomarker in colorectal cancerQiwei Cui, Xiaohong Gao, Xiaoqing Wu, Dongwei Zhang · Frontiers in Cell and Devel... · Jul 22, 2026
Background Colorectal cancer (CRC) is characterized by profound molecular heterogeneity and complex tumor–microenvironment interactions, which contribute to invasion, metastasis, and variable clinical outcomes. More effective prognostic bio…
- Patient-derived organoids in functional precision oncology: from experimental models to clinical decision-makingAmanda Caruso, A Delvecchio, R Memeo, M Lanzino et al. · Frontiers in Endocrinology · Jul 22, 2026
Despite major advances in high-throughput genomics, proteomics, and multimodal imaging, a substantial gap persists between molecular tumor characterization and clinically actionable therapeutic decision-making, partly due to the limitations…
- EMERGING ROLE OF MULTI-OMICS APPROACHES IN TUMOR CLASSIFICATIONSumana Pawar · International Journal of Dr... · Jul 21, 2026
Tumor classification plays a vital role in proper diagnosis, prognosis, and treatment planning of cancer. Tumors are currently classified in many different ways, but these traditional approaches do not account for the great molecular comple…
- Research and application advances in real-time single-cell functional analysisYingjie Yue, Xinyu Liu, Xijiao Yu · Discover Nano · Jul 20, 2026
Real-time single-cell functional analysis (RT-SCFA) continuously interrogates living single cells at subcellular spatial resolution and second-to-millisecond temporal resolution, enabling in situ profiling of secretion/efflux, redox stress,…
- Convergent genomic trajectories shape adaptation to life on land across animal lineagesGemma I. Martínez‐Redondo, Klara Eleftheriadi, Judit Salces-Ortiz, Nuria Escudero et al. · Nature Communications · Jul 18, 2026
How animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared genomic mechanisms underlie these transitio…
- Single-cell technologies in mRNA cancer vaccinesEkaterina V. Ovcharenko, М. Р. Патышева, Kirill M. Kirilenko, А. А. Ибрагимова et al. · npj Vaccines · Jul 18, 2026
The fast evolution of mRNA-based cancer therapeutics requires advanced frameworks to overcome the challenges of tumor heterogeneity and the immunosuppressive tumor immune microenvironment. In this context, single-cell technologies enable ch…
- scYeast: a biological-knowledge-guided foundation model on yeast single-cell transcriptomicsXingcun Fan, Wenxing Liao, Luchi Xiao, Xuefeng Yan et al. · Synthetic and Systems Biote... · Jul 17, 2026
Abstract Though large-scale pre-trained models are vital for foundational cell modeling, most focus on human or mouse systems, neglecting model organisms like yeast ( Saccharomyces cerevisiae ) and often failing to use existing biological p…
- Mass-spectrometry-based single-cell and subcellular spatial omics via gel-assisted sample embedding and expansionYat Ho Chan, Maddison C. Hibbard, Helen P. Dobbelmann, Ruixuan Gao · QRB Discovery · Jul 16, 2026
An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button....
- Specificity-driven cell-gene graph learning identifies rare cell states in single-cell and spatial transcriptomic dataJinjin Huang, Xuanzhe Xia, Feng Luo, 屈良鹄 et al. · Advanced Biotechnology · Jul 16, 2026
Detecting rare cell populations that drive development, differentiation, and disease-associated transformation remains a central challenge in biology and medicine. Although these populations often represent promising targets for interventio…
- Multiscale Modeling of Embryonic Morphogenesis from Fertilization to OrganogenesisDebanik Deb, Orishma Parida, Laasya Naduthota, Bandan Chakrabortty · npj Systems Biology and App... · Jul 15, 2026
Embryonic development transforms a single cell into a structured multicellular organism through coordinated molecular, cellular, and tissue-level processes. In this review, we discuss multiscale modeling studies spanning early embryogenesis…
- Targeting the PRMT1 axis in cancer: from epigenetic plasticity to contextual therapeutic interventionsShahper Nazeer Khan, Aamir Ahmad, Mohd Haris Siddiqui · Frontiers in Oncology · Jul 14, 2026
Protein arginine methyltransferase 1 (PRMT1), the predominant Type I arginine methyltransferase, is reported to play the key role in regulating cancer epigenetics. Its activity directs gene expression, chromatin structure and transcriptiona…
- Machine learning-driven identification of DLL3 as a molecular target and development of a DLL3-binding cyclic peptide for glioblastomaDan Xu, Daqing Huang, Zhijie Li, Yan Yan et al. · Frontiers in Oncology · Jul 14, 2026
Background Glioblastoma (GBM) remains the most aggressive primary brain tumor and is associated with a dismal prognosis despite maximal multimodal therapy. Targeted radionuclide therapy requires a tumor-selective, cell-surface-accessible mo…
- Decoding Complex Biological Networks: Demonstrating a Next-Generation Quantum Deep Learning Pipelineinquantio · Zenodo (CERN European Organ... · Jul 13, 2026
A study published on bioRxiv presents the first proof-of-concept workflow that combines non-linear autoencoders (deep representation learning) with the Quantum Approximate Optimization Algorithm (QAOA) to detect functional modules within bi…
- rbims: an R package for integrative functional profiling and pathway-level discrimination in metagenome-assembled genomesKarla P López-Martínez, Stephanie Hereira-Pacheco, Diana Hernández-Oaxaca, Frida López-Ruiz et al. · Frontiers in Bioinformatics · Jul 13, 2026
Metagenomics enables the recovery of metagenome-assembled genomes (MAGs), providing access to the metabolic potential of uncultured microbial communities that drive ecosystem function and biogeochemical cycles. However, as MAGs datasets inc…
- Decoding Complex Biological Networks: Demonstrating a Next-Generation Quantum Deep Learning Pipelineinquantio · Zenodo (CERN European Organ... · Jul 13, 2026
A study published on bioRxiv presents the first proof-of-concept workflow that combines non-linear autoencoders (deep representation learning) with the Quantum Approximate Optimization Algorithm (QAOA) to detect functional modules within bi…
- Global research landscape and trends of single-cell sequencing in sexually transmitted infections: a comprehensive bibliometric analysis from 2015 to 2025Cuixiu Wu, Yuanshuo Guo, Na Cui, Y Gao et al. · Frontiers in Reproductive H... · Jul 13, 2026
Background Single-cell sequencing offers new insights into sexually transmitted infections (STIs) research, but there remains a lack of systematic bibliometric overview. Here, we summarize and quantify the developmental dynamics, research h…
- From the Editor's DeskSumati Gaumat · Journal of Environmental Bi... · Jul 13, 2026
Publishing a Special Issue on advancing research is not only inspiring, but also an enriching experience. This Editorial column gives a bird's eye view of the topic. It's a great delight to introduce this Special Issue, which highlights cut…
- How WRKY transcription factors fine-tune specificity in plant stress responses: from W-box to regulatory codeSrushtideep Angidi, Khizar Razzaq · Molecular Biology Reports · Jul 10, 2026
Abstract WRKY transcription factors are among the largest plant-specific transcription factor families and play central roles in coordinating gene expression during biotic and abiotic stress. Despite decades of research, a fundamental parad…
- Selaginella sellowii gene regulatory networks reveal distinct transcriptional strategies for dehydration stress and recoveryJingyi Zhang, Gabriela Cabrales-Orona, Gerardo Alejo‐Jacuinde, Luis Herrera-Estrella et al. · Scientific Reports · Jul 10, 2026
Vegetative desiccation tolerance (VDT) enables resurrection plants to withstand extreme water loss, yet its system-level regulation remains incompletely understood. Here, we interrogated the VDT landscape in Selaginella sellowii using time-…
- Single-cell sequencing in precision management of chronic myeloid leukemiaXinyi Li, R. Chen, Yiyong Huang, Xingyi Xiao et al. · Journal of Translational Ge... · Jul 10, 2026
Single-cell sequencing technology provides a high-resolution perspective for the precision diagnosis and treatment of chronic myeloid leukemia (CML). Cellular and molecular heterogeneity in CML is closely associated with tyrosine kinase inh…
- Integrated multi-omics and deep learning analysis reveals neurotransmitter metabolism regulatory mechanisms of Tianwang Buxin Dan完玛草, Rangyuzhen Cai, Xi Zhang, Xiaojuan Li · Frontiers in Neuroscience · Jul 8, 2026
Background Tianwang Buxin Dan is a classical Traditional Chinese Medicine formula with documented clinical use in treating neuropsychiatric disorders, yet its molecular mechanisms remain incompletely understood. Methods We developed an inte…
- FastPedia-ML: An Interpretable Machine-Learning Framework for Pediatric Leukemia Subtype Classification using Gene-Expression DataR Samundi, J Vijayarani · International Journal of En... · Jul 8, 2026
Pediatric Acute Myeloid Leukemia (pAML) is a heterogeneous disease with complicated genomic variants that make it difficult to subclassify the disease properly. The paper suggests a strong and explainable machine learning model applied to t…
- An integrated subtractive genomics and immunoinformatics approach for designing a universal multi-epitope vaccine against Brucella spp.Rhitam Biswas, Swapno Surabhi Sinha, Aditi Roy, Sudha Ramaiah et al. · Frontiers in Bioinformatics · Jul 7, 2026
Introduction Brucella spp. are Gram-negative bacteria accountable for brucellosis in immunocompromised individuals and livestock. Due to the slow-growing latent phenotype, current antibiotics are insufficient to treat the infection. The lac…
- From single cell analysis to 3D micro physiological systems: microfluidic tools integrating cancer cell targets for delineating natural killer cell biologyMaria V. Hangad, H F, Sam K. P. Kung, Francis Lin · Microsystems & Nanoengineering · Jul 6, 2026
Natural killer cell is a critical cell type in our immune system. Its therapeutic potential in the development of novel cancer immunotherapy has been emerging. Microfluidic technologies capable of manipulating small volumes of fluid through…
- Complementary structure of statistical significance and predictive relevance in explainable machine learning–based transcriptomic tissue classification of Hanwoo cattleDogyeong Lee, Junyoung Lee, Inchul Choi, Dajeong Lim · Frontiers in Genetics · Jul 6, 2026
Understanding tissue-specific transcriptomic structures in livestock is essential for elucidating the molecular basis of economically important traits. Conventional differential gene expression analysis efficiently identifies genes with lar…
- Artificial intelligence for genomic science: a scoping review of concepts, architectures, applications, and open challengesWellington Francisco Rodrigues, Mariana T. D. Parise, Doglas Parise, Lucas Moraes dos Santos et al. · Frontiers in Bioinformatics · Jul 3, 2026
Introduction Artificial intelligence (AI) is becoming central to genomics and multi-omics, but its concepts, architectures, applications, evaluation standards, and translational requirements remain fragmented. This scoping review mapped how…
- Epitranscriptomic regulation by m6A in immunity and autoimmune disorders: emerging mechanisms and clinical perspectivesMadiha Maqsood, C. Zhan, Muhammad Hassan, X Z Li et al. · Frontiers in Immunology · Jul 3, 2026
Immune-mediated diseases arise from intricate interactions among genetic, environmental, and epigenetic factors that disrupt immune homeostasis. In recent years, epigenetic mechanisms have been widely explored as critical factors in autorea…
- Vardetector: a pure Python package to detect DNA called mutations in aligned RNA readsJulij Šelb, Luka Dejanović, Katja Mohorčič, Matija Rijavec et al. · Scientific Reports · Jun 27, 2026
We develop a freely-available Python package Vardetector (https://github.com/julijselb/vardetector/tree/main/vardetector) used for detecting DNA called mutations in aligned RNA reads. We benchmark it by comparing it to industry standard var…
- Genomic Fundamentals and Applications in Asian Swamp Eel (Monopterus albus): A ReviewYingbing Su, Yao Wu, 易提林, Hanwen Yuan et al. · Fishes · Jun 25, 2026
The Asian swamp eel (Monopterus albus), a commercially important freshwater aquaculture species in China and Southeast Asia, has attracted growing scientific interest owing to its natural protogynous hermaphroditism and substantial economic…
- Pharmacogenomics and Epigenetic Regulation Transforming Pediatric Precision TherapeuticsShakta Mani Satyam, Sainath Prabhakar, Tanya Densil, Husham Taha Mohammed et al. · Journal of Personalized Med... · Jun 19, 2026
Pediatric drug therapy remains fundamentally challenged by profound interindividual variability driven by dynamic development, genetic, and environmental factors. Although dosing strategies based on age, body weight, or body surface area re…