Native Preprint Pilot

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  1. bioRxiv

    Spatialsnake: a flexible workflow for spatial transcriptomics analysis across platforms

    Lin, Z, Zhang, Z, Huang, N, Lu, Z, Xu, S

    Preprint source: bioRxiv: Bioinformatics

  2. bioRxiv

    Interpreting Short Tandem Repeat Variations with Genomic Foundation Models in Olive

    Xia, F, Pakdel, M. H, Mazinani, M. H, Asadi, A, Zeng, Y, Zhang, J, Shariati, V, Anisimova, M

    Preprint source: bioRxiv: Bioinformatics

  3. bioRxiv

    CellMethMarker provides an integrated database of human cell- and tissue-type-specific DNA methylation markers

    Sun, X, Peng, Y, Yi, Y, Fu, L, Liu, F, Xie, Y, Dai, Q, Gu, H, Shi, J, Wang, H, Zhang, F

    Preprint source: bioRxiv: Bioinformatics

  4. bioRxiv

    Informed, scalable and unified transport couplings for single-cell alignment and downstream inference with scBIOT

    Zhang, H, Qin, P

    Preprint source: bioRxiv: Bioinformatics

  5. bioRxiv

    HOMED enables hierarchical and multimodal optimization of DNA methylation deconvolution across tissues

    Liu, Y, Chen, Y, Du, Y, Garmire, L

    Preprint source: bioRxiv: Bioinformatics

  6. bioRxiv

    DSSNA: Automated Nucleic Acid Structure Analysis in Molecular Dynamics

    Gorelov, S, Konevega, A, Shvetsov, A

    Preprint source: bioRxiv: Bioinformatics

  7. bioRxiv

    Evaluation of Cross-slice Imputation for Spatial Proteomics

    Bondar, G. A, Bozorgui, B, Korkut, A, Halder, A

    Preprint source: bioRxiv: Bioinformatics

  8. bioRxiv

    Ground-truth evaluation of sparse autoencoder features on spatial, single-cell and language-model embeddings

    Shahsavand, A, Forghani, S, Akbarzadeh, S, Mahdavi Sabet, F

    Preprint source: bioRxiv: Bioinformatics

  9. bioRxiv

    mito-overview: a mitochondrial report software

    Gai, X, Ahuja, K, LOPES, E. N

    Preprint source: bioRxiv: Bioinformatics

  10. bioRxiv

    Scooby-2: fine-tuning AlphaGenome for single-cell genomic track prediction

    Hingerl, J. C, Gagneur, J

    Preprint source: bioRxiv: Bioinformatics

  11. bioRxiv

    Joint localization and testing reveals spatial context of differential expression

    Stotzem, N, Chang, S, Cai, N, Casale, F. P

    Preprint source: bioRxiv: Bioinformatics

  12. bioRxiv

    Efficient biological design via genomic in-context learning

    Brixi, G, Hao, Y. A, Nori, D, Merchant, A, Widatalla, T, King, S, Shalvarjian, K, Park, D, Hie, B

    Preprint source: bioRxiv: Bioinformatics

  13. bioRxiv

    Transcriptomic similarity guides source selection beyond tissue lineage

    Jiang, L, Pang, J, Luo, B, Wu, X, Li, X, Zhang, H

    Preprint source: bioRxiv: Bioinformatics

  14. bioRxiv

    Agentic Discovery Transfer Enables Cross-Cancer Discovery at Scale

    Cheng, L, Shireman, J, GOGATE, A, Stangis, M, Cai, Y, Xie, Y, Khatri, P, Dey, M, Kendziorski, C

    Preprint source: bioRxiv: Bioinformatics

  15. bioRxiv

    Building synthetic cell-cell synapses using engineered scaffold protein condensates

    Shin, N. Y, Mitra, G, Grodsky, A. M, Ruff, K. M, Chauhan, G, Pappu, R. V, Lim, W. A

    Preprint source: bioRxiv: Synthetic Biology

  16. bioRxiv

    NanoPro - a Framework for Probiotically-Guided Nanovector Therapy

    Michels, A, Haseki, A, Ashraf, M, Lam, A, Grant, K. R, Lu, A, Vincent, R. L, Im, J, Singer, Z. S, Ballister, E. R, Danino, T

    Preprint source: bioRxiv: Synthetic Biology

  17. bioRxiv

    Expanding the therapeutic window of bacteria for cancer therapy

    Im, J, Komaranchath, M, Windemuth, S, Kim, H, Hu, X, Adapa, A, Ashraf, M, Cummins, K. A, Coker, C, Jang, Y, Jin, H, Leong, K. W, Drapkin, R, Bruce, J. N, Canoll, P, Danino, T

    Preprint source: bioRxiv: Synthetic Biology

  18. bioRxiv

    CEP-IP with CMRF in SEA-AD Microglia: A Mitochondrial Co-expression Module Linked to Cognition

    Wong, K. K

    Preprint source: bioRxiv: Bioinformatics

  19. bioRxiv

    GLOM TGITO: multiscale protein modelling and multiview landscape-guided sequence discovery

    Xiong, Y, Tirta, Y. K, Wang, S, Hu, Z, Ma, W, Yuan, S

    Preprint source: bioRxiv: Bioinformatics

  20. bioRxiv

    PHACTn enables training-free, context-independent inference of nucleotide variant tolerance across the genome

    Yildirim, C, Kuru, N, Adebali, O

    Preprint source: bioRxiv: Bioinformatics

  21. bioRxiv

    Single-cell RNA-seq of amniotic fluid provides unique insight into fetal development

    Grima, C. V, Atukorala, I, Beard, S, Guleria, S, Neil, L, Hannan, N, Pal, B, Maksimovic, J, Hui, L, Oshlack, A

    Preprint source: bioRxiv: Bioinformatics

  22. bioRxiv

    Verifiable Agentic Science on Public Infrastructure

    Baker, D, Cain, S, van den Beek, M, Chilton, J, Callan, D, Weaver, S, Coraor, N, Beavers, K, Goecks, J, Schatz, M. C, Gruening, B, Kosakovsky Pond, S. L, Nekrutenko, A

    Preprint source: bioRxiv: Bioinformatics

  23. bioRxiv

    From {triangleup}{triangleup}G Prediction to Mutation Prioritization with Conformal Prediction

    Barducci, G, Sanavia, T, Fariselli, P

    Preprint source: bioRxiv: Bioinformatics

  24. bioRxiv

    Fixing the Measurement Model Before the Selection Heuristics: Optimiser Repairs for Living-Cell Self-Driving Laboratories

    Brimo, N, Serdaroglu, D. C

    Preprint source: bioRxiv: Bioinformatics

  25. bioRxiv

    PepPr: De Novo peptide sequencing with peptide priors

    Khan, S, Klaproth-Andrade, D, Bruns, Y, Wilhelm, M, Gagneur, J

    Preprint source: bioRxiv: Bioinformatics

  26. bioRxiv

    Benchmarking strain-level profiling of Escherichia coli in short-read gut metagenomes

    Galbraith, M, Williams, D, Shaw, L. P, Lipworth, S, Stoesser, N

    Preprint source: bioRxiv: Bioinformatics

  27. bioRxiv

    Neopep: Reinforcement Learning From Machine-Learned Force Field Energy for Non-Canonical Peptide Structure Prediction

    Jagannathan, D, Kim, P. M

    Preprint source: bioRxiv: Bioinformatics

  28. bioRxiv

    Multiplex-GCN Predicts Clinically Actionable Tumor Microenvironment Subtypes in Pancreatic Cancer

    Bose, S, Upama, P. B, Ahamed, S. I

    Preprint source: bioRxiv: Bioinformatics

  29. bioRxiv

    'PhyTaxR', a set of phytoplankton taxonomic curation tools in R

    Rayon Vina, F, Finkel, Z. V, Irwin, A. J

    Preprint source: bioRxiv: Bioinformatics

  30. bioRxiv

    Reference normalizations of Effort-To-Compress across length, alphabet size, and composition

    Jang, H, Sohn, J.-y, Huang, Z

    Preprint source: bioRxiv: Bioinformatics

  31. bioRxiv

    A community audit of error control in crosslinking mass spectrometry

    Fischer, L, Amaral, B. C, Birklbauer, M. J, Bruce, J. E, Carvalho, P. C, Chalkley, R. J, Clasen, M. A, Dorfer, V, Gozzo, F. C, Heck, A. J. R, Hoopmann, M. R, Iacobucci, C, Keller, A, Kolbowski, L, Lenz, S, Lima, D. B, Liu, F, Mechtler, K, Moritz, R. L, Mueller, F, Ruta, J, Schriemer, D. C, Shteynberg, D. D, Trnka, M. J, Viner, R, Rappsilber, J

    Preprint source: bioRxiv: Bioinformatics

  32. bioRxiv

    Single-Nucleus Profiling Reveals Neuronal Metabolic Collapse During the Transition to Alzheimer's Disease Dementia

    Lu, S, Enduru, N, Citu, C, Tung, C.-H, Zhao, Z

    Preprint source: bioRxiv: Bioinformatics

  33. bioRxiv

    Binning-based Methods for Model Fitting and Data Splitting Improve Machine Learning Imbalanced Regression

    Abdulnabi, H, Westwood, J. T

    Preprint source: bioRxiv: Bioinformatics

  34. bioRxiv

    Beyond profiles: supervised repeat annotation using protein embeddings

    Qiu, K, Ludwiczak, J, Lupas, A. N, Dunin-Horkawicz, S

    Preprint source: bioRxiv: Bioinformatics

  35. bioRxiv

    Data coherence over data volume drives generalisable genome-based prediction of microbial carbon utilisation

    Kishore, D, Ranjan, P, Neely, C, Cashman, M, Sakkaff, Z, Riehl, W. J, Joachimiak, M. P, Edirisinghe, J. N, Faria, J. P, Weisenhorn, P, Cohen, M. B, Pelletier, D. A, Cottingham, R. W, Henry, C. S, Doktycz, M. J, Arkin, A. P, Dehal, P. S

    Preprint source: bioRxiv: Bioinformatics

  36. bioRxiv

    Oyster: A Neural Network for Modeling Genomic Sequences with Exact Position-Specific k-mer Contributions

    Abdulnabi, H, Westwood, J. T

    Preprint source: bioRxiv: Bioinformatics

  37. bioRxiv

    NK-RCPP: a receptor-conditioned computational workflow for prioritizing neurokinin-receptor peptide candidates

    Zhou, X, Zhang, H, Ning, K

    Preprint source: bioRxiv: Bioinformatics

  38. bioRxiv

    Hypatia: Comparative Isoform Profiling Across Cell Populations from Long-Read Single-Cell Transcriptomes

    Pan, T, Shiau, C.-K. S, Lu, L, Wang, C, Wang, M, He, Y, Bhimaraj, A, Brat, D. J, Huse, J. T, Li, J. J, Gao, R

    Preprint source: bioRxiv: Bioinformatics

  39. bioRxiv

    Integrated Transcriptomic and Structural Prioritization of Sulforaphane Targets in Neurodegeneration: A Multi-Dataset In Silico Study

    Ugur, S, Onal-Suzek, T

    Preprint source: bioRxiv: Bioinformatics

  40. bioRxiv

    Multi-resolution humanness scoring of antibodies via a region-isolated language model

    Liu, H, Chen, P, Zhou, S, Wei, B, Deng, S, Zhang, L, Liu, X, Zhou, S, Han, L, Ye, L

    Preprint source: bioRxiv: Bioinformatics

  41. bioRxiv

    MultiFlow: coupled flow matching for predicting single-cell multiomic perturbation responses in unseen cellular contexts

    Wang, H, Zhang, C, Zhang, M, Nie, X, Liu, Q

    Preprint source: bioRxiv: Bioinformatics

  42. bioRxiv

    Compact CRISPR-based genetic circuitry using a miniature genome-integrated Cas12m protein

    Joshi, S. H.-N, Jenkins, C, Ulaeto, D, Gorochowski, T. E

    Preprint source: bioRxiv: Synthetic Biology

  43. bioRxiv

    VesiScope: A stand-alone tool for the automatic detection, quantification and size analysis of GUVs from phase contrast microscopy images

    Cecchi, D, Lasala, A, Poli, F, De Remigis, E, Moccia, S, Palagi, S

    Preprint source: bioRxiv: Synthetic Biology

  44. bioRxiv

    Learning the structural diversity in random protein sequence space

    Buchel, F, Neuwirthova, T, Tureckiova, T, Fuertes, G, Benda, A, Panek, D, Fricek, M, AlQuraishi, M, Hlouchova, K

    Preprint source: bioRxiv: Synthetic Biology

  45. bioRxiv

    Generative design of functional disordered regions in a developmental transcription factor

    Denes, L. T, Emenecker, R, Wang, N, Chirumamilla, D, Mohotti, R, Holehouse, A. S, Holt, L. J, Lionnet, T

    Preprint source: bioRxiv: Synthetic Biology

  46. arXiv

    A unified coarse-grained neural network potential for the dynamics of biomolecular complexes

    Antonio Mirarchi, Stephen E. Farr, Adrià Peréz, Gianni De Fabritiis

    Preprint source: arXiv: Biomolecules

  47. arXiv

    HGPRGDel: GPR-Aware Learning and Ranking for Growth-Coupled Gene Deletion Design

    Ziwei Yang, Takeyuki Tamura

    Preprint source: arXiv: Quantitative Methods

  48. arXiv

    Accurate structural modelling of protein-glycan recognition with GlycoWeave

    Huifeng Zhao, Jintu Zhang, Yifei Xiao, Youqiao Qian, Silong Zhai, Zichang Jin, Li Wang, Yuchao Wang, Hang Dong, Yifan Zhao, Zhenxing Wu, Hongyan Du, Yuansheng Huang, Bowei Zhao, Xiaorui Wang, Shukai Gu, Jike Wang, Zhongjun Li, Zhongtang Li, Tingjun Hou, Yu Kang

    Preprint source: arXiv: Biomolecules

  49. arXiv

    pyTransRate: 1 reference-free quality assessment of de novo transcriptome assemblies with current aligners and quantifiers

    Matthew MacManes

    Preprint source: arXiv: Quantitative Methods

  50. arXiv

    Stationary Action Principles for Neuronal Growth

    Nathan Brodeur, Cristian Staii

    Preprint source: arXiv: Quantitative Methods

  51. bioRxiv

    VenusGenome: Genome-Aware Masked Autoencoding for Microbial Genome Representation Learning

    Zhang, L, Zhang, Y, Tan, Y, Jiang, F, Zhong, B, Cheng, X, Hong, L, Li, M, Yu, Y

    Preprint source: bioRxiv: Bioinformatics

  52. bioRxiv

    OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow

    Zheng, Y, Liu, X, Yi, Y, Sun, X, Liu, F, Yan, X, Man, C.-H, Gu, H, Wang, X, Zhang, F

    Preprint source: bioRxiv: Bioinformatics

  53. bioRxiv

    Cellular context defines brain-specific functions of genes associated with neurodevelopmental disorders

    Djokic, M, Karunanithi, S, Welzel, M, Kielisch, F, Luck, K

    Preprint source: bioRxiv: Bioinformatics

  54. bioRxiv

    In Silico Design and Evaluation of CRISPR Cytosine Base Editing Strategy for Potential Correction of the ASPA Variant Associated with Canavan Disease

    Verma, A, Natrajan, E

    Preprint source: bioRxiv: Bioinformatics

  55. bioRxiv

    Identification of gene kinetics patterns improves RNA velocity and cell fate prediction using JuloVelo

    Tung, K.-C, Tu, Y.-H, Hsieh, K.-Y, Juan, H.-F, Huang, H.-C

    Preprint source: bioRxiv: Bioinformatics

  56. bioRxiv

    Regularized logistic regression-based gene selection for functional analysis of heterogeneous scRNA-seq macrophage populations in muscle aging and regeneration.

    Costa, T. M, Lopes, M. B, Neves, J, Sousa-Victor, P, Vinga, S

    Preprint source: bioRxiv: Bioinformatics

  57. bioRxiv

    Winnow-tax: sensitive and precise taxonomic profiling of low-coverage organisms in shotgun metagenomes

    Sun, S, Fodor, A. A

    Preprint source: bioRxiv: Bioinformatics

  58. bioRxiv

    Evaluation design shapes estimates of cross-donor generalization in single-cell classification of cell-type

    Chen, X, Li, J, Battle, A

    Preprint source: bioRxiv: Bioinformatics

  59. bioRxiv

    BLOOM: Biologically Informed Flow Matching for Transcriptomic Virtual Embryo Modeling

    Liang, Z, Li, S, Li, B, Huang, Y, Yu, L

    Preprint source: bioRxiv: Bioinformatics

  60. bioRxiv

    FlyAnatoView: Visualization of Drosophila Single-cell RNA-seq Datasets on Anatomographs

    Hu, Y, Kalina, J, Veal, A, Ewen-Campen, B, Porter, T, Song, J, Luo, Y, Huang, K, Goutte-Gattat, D, Brown, N. H, Papatheodorou, I, Perrimon, N

    Preprint source: bioRxiv: Bioinformatics

  61. bioRxiv

    Xenograft supervision and joint methylation-fragment-end encoding define a reusable molecular scoring layer for cell-free tumor DNA

    Zhang, X, Sun, X, Wang, R, Zhao, N, Liu, F, Li, X, Huang, J, Sun, J, Li, H, Lou, S, Wang, H, Zhao, H, Shu, H, Zhen, P, Gu, H, Shi, J, Wang, T, Zhang, F

    Preprint source: bioRxiv: Bioinformatics

  62. bioRxiv

    RNA-SpecFlow: RNA-Conditioned Spectral Flow for Histology Synthesis

    Liu, Y, He, W

    Preprint source: bioRxiv: Bioinformatics

  63. bioRxiv

    Mimic: A Unified Neural Network Architecture for Modelling Genomic Sequences and Module-level Comparison

    Abdulnabi, H, Westwood, J. T

    Preprint source: bioRxiv: Bioinformatics

  64. bioRxiv

    MPFIL: Multi-Level Protein Feature Integration for Predicting Mutation-Induced Protein-Protein Binding Affinity Changes

    Zhang, H, Liu, Y, Yu, L, Guo, M

    Preprint source: bioRxiv: Bioinformatics

  65. bioRxiv

    CATFISHR: integration of transcriptome and inferred CNV profiles for comprehensive malignant cell identification

    Shukla, P, Mannino, M, Hofer, M, Lattmann, E. R, Haunerdinger, V, Turko, P, Levesque, M. P

    Preprint source: bioRxiv: Bioinformatics

  66. bioRxiv

    Metric-driven Pre-acquisition Diagnostics for Automated Microscopy Ultraviolet Surface Excitation (MUSE)

    Nunez, M, Davies, B

    Preprint source: bioRxiv: Bioinformatics

  67. bioRxiv

    ProtCell: a foundation model for single-cell proteomics

    Hu, B, Li, Z, Jiang, Q, Yin, Q, Liu, Z, Jiang, R

    Preprint source: bioRxiv: Bioinformatics

  68. bioRxiv

    How Much Can AI Virtual Cells Gain from Unified Perturbational Modeling?

    Wei, Z, Ye, Y, Cui, S, Ma, W, You, Y

    Preprint source: bioRxiv: Bioinformatics

  69. bioRxiv

    BenchMHC: a reproducible framework for peptide-MHC presentation prediction

    Borck, T, Chabrol, M, Colombo, D, Imbert, A, Perier-Dulhoste, M, Volzhenin, K, Lang, M, Lopez Carranza, S. N

    Preprint source: bioRxiv: Bioinformatics

  70. bioRxiv

    Best Practices for Pre-Processing Large-Scale ATAC-Seq Data: Why Epidemiological Studies Demand Greater Stringency

    Wells, P. M, Flores-Payan, M, Chioza, B, Burrage, J, Babtie, A, Marzi, S. J, Schalkwyk, L. C, YouthGEMS Consortium,, Dempster, E, Mill, J, Hannon, E. J

    Preprint source: bioRxiv: Bioinformatics

  71. bioRxiv

    Integrative Single-Cell Transcriptomics and Explainable AI for Disease Mechanism and Biomarker Discovery in Triple-Negative Breast Cancer

    Huda, T, BISWAS, S

    Preprint source: bioRxiv: Bioinformatics

  72. bioRxiv

    Asking the Data: Conversational Interrogation of LC-MS/MS Proteomics Data Sets with an LLM Agent

    da Silva de Araujo, C, Keirsebelik, M, Silas Rodrigues, A. C, Leda Valverde, A, Maciel-de-Freitas, R. d. S, Guimaraes, M. Z. P, Junqueira, M

    Preprint source: bioRxiv: Bioinformatics

  73. bioRxiv

    Dimensionality Reduction for Cyclic Compositional Data

    Swarna, N. P, Emhemed, J, Pachter, L

    Preprint source: bioRxiv: Bioinformatics

  74. bioRxiv

    Benchmarking Large Language Models for Transcriptomic Data Analysis and Visualization: Multi-Model Workflow Evaluation

    Iyer, A, Subedi, A, Butler, K. S, Krishnakumar, R

    Preprint source: bioRxiv: Bioinformatics

  75. bioRxiv

    AltereGO: Prediction of Protein Function by Multimodal Fusion of Protein Language Models.

    Amburn, J. A, Stempel, J. C, Chang-Gonzalez, A. C, Moth, C. W, Meiler, J, Smith, M. D, Smith, J. C

    Preprint source: bioRxiv: Bioinformatics

  76. bioRxiv

    Perturbation-based propagation of bacterial composition uncertainty improves robustness and reproducibility of microbiome differential abundance analysis.

    Andrews, M. E, Vincennie, T, Koprivica, M, Browning, M, Bracco, S, Mullan, M, Wright, A. T, Crawford, F, Mouzon, B

    Preprint source: bioRxiv: Bioinformatics

  77. bioRxiv

    Phenologs at knowledge-graph scale: a mouse-to-slime-mold catalog of candidate genes for thousands of human diseases

    Odell, A, Korn, D. R, Laraway, B. J, Richmond, P. A, Matentzoglu, N, Schaper, K, Mungall, C. J, Haendel, M. A

    Preprint source: bioRxiv: Bioinformatics

  78. bioRxiv

    Building virtual cell dynamics that evolve with biological measurements

    Zhang, Z, Wang, Z, Tian, Q, Zhou, B, Zhou, T, Nie, Q, Zhou, P

    Preprint source: bioRxiv: Bioinformatics

  79. bioRxiv

    Species phylogenetics using intraprotein residue dependence inferred with protein foundation models

    Alibutud, R. F, Mowlaei, M. E, Kumar, S

    Preprint source: bioRxiv: Bioinformatics

  80. bioRxiv

    Targeting PRMT5 Across Cancers and AI-Driven Discovery of Candidate Compounds

    Rana, S, Hossan, M. S, Rafi, A. A, Hagidok, D. D, Kumer, A, Talukder, M. E. K, Ali, M. C, Al-Amin, R. A

    Preprint source: bioRxiv: Bioinformatics

  81. bioRxiv

    DAPE-PD: Diffusion adaptation of genomic foundation model enables tailored-generation of cis-regulatory DNA

    Echavarria Galindo, M, Gong, S, Zhan, Y, Wang, S, Kong, L, LAI, Y

    Preprint source: bioRxiv: Synthetic Biology

  82. bioRxiv

    Genetic control couples TGFβ-independent pluripotent stem cell renewal to deterministic forward programming across germ layers

    Bottini, S, Amodeo, F, Avnoor, D, De Gregorio, M, Arigoni, M, Bachinger, F, Barrett, P, Mack, D. L, Porporato, P. E, Defilippi, P, Vallier, L, Smith, A. S, Balmas, E, Bertero, A

    Preprint source: bioRxiv: Synthetic Biology

  83. arXiv

    Structure, Not Sequence: Tracking and Validating Folding Mechanisms in ESMFold's Trunk with Sparse Autoencoders

    Bohan Liu, Xiaohan Fan, Wenqian Ye, Aidong Zhang

    Preprint source: arXiv: Quantitative Methods

  84. arXiv

    Dynamic heart rate variability for classification of arrhythmia burden

    Brian Kang, Michael Wacker, Steven S. Kang

    Preprint source: arXiv: Quantitative Methods

  85. arXiv

    Multiscale MIGHT: Modeling Local and Systemic Particle Transport in the Cardiovascular System

    Theofilos Symeonidis, Timo Jakumeit, Fardad Vakilipoor, Robert Schober, Maximilian Schäfer

    Preprint source: arXiv: Quantitative Methods

  86. arXiv

    Escaping cells dilute CRISPR screen responses unequally across cell types

    Xuanrui Huang

    Preprint source: arXiv: Quantitative Methods

  87. arXiv

    mdRNAcat: A Molecular Dynamics RNA Catalog of REST2 Conformational Ensembles

    Anton E. Dorn, Emile de Bruyn, Fabrice von der Lehr, Philipp Knechtges, Stefan Kesselheim, Alexander Schug

    Preprint source: arXiv: Biomolecules

  88. arXiv

    Multivariate Augmented Prediction-Powered Survival Inference for EHR Association Studies With Limited Chart Review

    Xicheng Xie, Katherine Fiona Simpson, Hyojung Jang, Theresa L. Walunas, Lili Zhao

    Preprint source: arXiv: Quantitative Methods

  89. bioRxiv

    Curated neurodegeneration axis signals are sensitive to cell composition and analytic choices: an adversarial re-analysis of a transcriptomic scoring pipeline

    Ghosh, N, Sinha, K

    Preprint source: bioRxiv: Bioinformatics

  90. bioRxiv

    Building computational benchmarks: an Omnibenchmark reimplementation of a single-cell preprocessing pipeline evaluation

    Choudhury, A, Kitak, T, Carrillo, B, Busch, P, Emons, M, Gunz, S, Koderman, M, Luo, S, Mallona, I, Meara, A, Wissel, D, Robinson, M. D

    Preprint source: bioRxiv: Bioinformatics

  91. bioRxiv

    scTGCL: A Transformer-Based Graph Contrastive Learning Approach for Efficiently Clustering Single-Cell RNA-seq Data

    Khan, M. S. A, Kabir, M. H, Faisal, M. M

    Preprint source: bioRxiv: Bioinformatics

  92. bioRxiv

    BROOQS: Quartet-based Resolution of Level-1 Hybridization Cycles without Tests of Symmetry

    Arasti, S, Mirarab, S

    Preprint source: bioRxiv: Bioinformatics

  93. bioRxiv

    Mathematical AI Predicts 40% and 57% Influenza Vaccine Effectiveness Against H1N1 and H3N2, Respectively, for the 2026--2027 U.S. Season

    Wang, X. X, Wei, G

    Preprint source: bioRxiv: Bioinformatics

  94. bioRxiv

    ASPIRE: the Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems

    McLaughlin, R. J, Chen, S, Nag, A, Noonan, A. J. C, Bartolomeu, C, Borden, S. A, Lam, S, Myers, R, Hallam, S. J

    Preprint source: bioRxiv: Bioinformatics

  95. bioRxiv

    Generative augmentation recovers prognostic disease signatures from underpowered transcriptomic datasets

    Sethi, T, Anand, A, Pratiti, M, Ali, S. Y, Kamra, S, Verma, S, Singh, S, Bajaj, T

    Preprint source: bioRxiv: Bioinformatics

  96. bioRxiv

    flodl-bio: First Rust data, transformers and model layer for entire deep learning on biological sequences

    Sablok, G, de Stefanis, F

    Preprint source: bioRxiv: Bioinformatics

  97. bioRxiv

    Prediction transfer does not imply reliability transfer in single-cell foundation models

    Park, H. J, Sriram, A, Luo, T, Zhang, L

    Preprint source: bioRxiv: Bioinformatics

  98. bioRxiv

    Paired activity learning supports systematic identification of mutant-selective EGFR inhibitors

    Zhu, J, Kong, W, Huang, L, Song, Z. Z, Ying, H, Kurppa, K. J, Miihkinen, M, Zhu, S.-J, Aittokallio, T

    Preprint source: bioRxiv: Bioinformatics

  99. bioRxiv

    A Pipeline for Predicting Variant Associations with Complex Disorders via Functional Annotations

    Gualdi, F, Darani, Z, Malpetti, D, Scutari, M, Mangili, F

    Preprint source: bioRxiv: Bioinformatics

  100. bioRxiv

    Mapping bioimage-analysis software adoption in microscopy

    Shakespeare, T, Saraiva, B. M, Cunha, I, Jacobs, C, Jacquemet, G, Henriques, R

    Preprint source: bioRxiv: Bioinformatics

  101. bioRxiv

    Pathway-Based Analysis of Essential Metabolic Enzymes as Drug Targets

    Bhat, D. S, Singh, B

    Preprint source: bioRxiv: Bioinformatics

  102. bioRxiv

    Auto-AVS: A Novel Framework for Automated Autophagic Vacuole Simulation

    Bleta, S, Dunning, P, Ross, A, Backues, S. K, Spantidi, O

    Preprint source: bioRxiv: Bioinformatics

  103. bioRxiv

    Cornealia: automated collective order analysis reveals density-dependent reorganization of donor corneal endothelium

    Rostami, M, Asim, S, Steele, M, Kyauk, D. S, Moul, L, Haarman, S, Richard, A, Peh, G, Moore, D, Rizwan, M, Mehta, J. S, Han, S. J

    Preprint source: bioRxiv: Bioinformatics

  104. bioRxiv

    NeCS-Flow: Necrosis-Guided Contrast-Enhanced MRI Synthesis with Rectified-Flow Refinement

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    Can Folding Models Tell Binders from Bluffers? Evidence from POISK: The Patent-Derived Antibody Dataset

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    An evidence-governed agent harness for spatial transcriptomics prioritizes ICAM-1 as a target in lung fibrosis

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    Using XCiMS to Quantify the Benefits of Ion Mobility Spectrometry for Untargeted Metabolomics

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    RFind-sc maps single cells onto biological axes defined by external gene signatures

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    AntiOxiPred: Predicting Antioxidant Peptides using Machine Learning Techniques and BLAST

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    Predicting Protein-Protein Interactions Using Vectorized Sequence Descriptors and Machine Learning Classifiers

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    Characterization of heterogeneous bioinformatics training needs in the AI era

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    Machine learning classification of fibromyalgia from blood transcriptomes: confounder benchmarking and implications for endometriosis-associated pain

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    Influenza A virus H5Nx genotypes assigned by genetic similarity are incongruent with global phylogenies

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    TAFFISH: shell-native command-level reproducibility for bioinformatics

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    False discovery rate control enables trustworthy deep-learning-based de novo peptide sequencing

    Liang, Z, Dai, C, Ling, T, Yang, T, Yang, Y, Leng, Y, Xie, L, He, Y, He, F, Wang, Y, Chang, C

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    Polymorphic Structures of an Artificial Nucleocapsid Evolved from a Circularly Permuted Bacterial Protein Cage

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    Benchmarking miRNA Target Prediction Methods

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    Mathematical genomics of SRY proteins and their associated HMG-Box domains across mammals

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    Large-scale integrated single-cell analysis reveals molecular subtypes and microenvironmental remodeling in cutaneous T cell lymphoma

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    A Pan-Cancer Benchmark of Clustering Strategies for Patient-Specific Gene Regulatory Networks

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    ALHENA, an H&E encoder distilled from transcriptomic foundation models for multi-scale slide analysis

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    Centered cross-context perturbation transfer on the public 2025 Virtual Cell Challenge benchmark

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    ScienceRSI: Recursive Scientific Self-Improvement

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    Cardiomyocyte Identity Crisis Without Regenerative Re-entry: A Multi-Scale Atlas of Incomplete Dedifferentiation and Intercellular Communication Rewiring in the Infarcted Human Heart

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    In-silico Tandem Mass Spectral Libraries for the Blood Exposome and Metabolomics Workbench Databases: Application of Gemini Large Language Model

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    AlphaGenome informed machine learning for pathogenicity prediction of germline mutations

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    Non-canonical proteoforms of the human fusiform gyrus in Alzheimers disease

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  131. arXiv

    Multiscale Topology-Regulated Nonlinear Dynamics for Protein B-Factor Prediction and Single-Cell Type Classification

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    ProtAgent: Post-Training Compact Protein Tool Agents with Interaction-Level Credit Assignment

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    MechGate: combining mechanism-derived measures of permeation and efflux to screen small molecule drugs targeting Escherichia coli

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    Probabilistic uncertainty in virtual spatial transcriptomics from histology is largely redundant with the predicted mean

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    Scalable subclonal reconstruction of cancer cells in DNA sequencing data using a penalized likelihood model

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    spaTransfer: transfer learning for single-cell and spatial transcriptomics data using non-negative matrix factorization

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    Overcoming segmentation bottlenecks in brain tissue for spatial proteomic inference at population scale

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    BRIDGE prioritizes human and mouse gene correspondences using functional and disease evidence

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    corrdeconv corrects deconvolution's misreading of disease cell states as abundance, overturning benchmarks and outperforming every published deconvolution method

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    Haplotype-based fine-mapping of variant associations for complex traits

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    Agent K: An Agent-Orchestrated Pipeline for Mapping Genes to Biosynthetic Pathway towards Metabolite Discovery

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    A physics-informed neural network framework for inferring infinitesimal phase response curves from finite-pulse circadian recordings

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    Sequence-only antigen context improves modeling of antibody hypervariable regions

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    Alignment-free sequence composition based features can distinguish paralogous proteins

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    A robust mutation spectrum analysis framework for high-depth error-corrected sequencing data

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    DNA methylation reveals molecular heterogeneity and urate excretion-associated subtypes of gout

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    Multi-scale microenvironment covariance for unsupervised spatial domain identification

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    The GA4GH Workflow Execution Service: A Standard API for Workflow Execution and Management in Genomics

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    Language models annotate mass cytometry clusters within the range where human experts disagree

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    Two opposite failure modes in alignment-based conservation scores, one inflating and one concealing constraint, are computable before the score is used

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    Alignment-free discovery of conserved RNA structures in the human genome

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    Fine-Grained and Reliable Cell Classification from Pathology Images

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    Viral host assignment across the tree of life with VHAMSTeR

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    Expanding gmx_MMPBSA capabilities for end-state binding free energy calculations with GROMACS and AMBER

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    Thermodynamic, Electrochemical and Practical Constraints on Electromicrobial Formate Assimilation

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    What Transfers Across Protein Pockets? Experience Reuse in Molecular Optimization for Agentic Structure-Based Drug Design

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    A genetically informed atlas of transcriptomic programs from massive human RNA-seq compendia

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    Projected Gradient Descent for Hallucination-Based Protein Binder Design

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    Different, same, or arrhythmic: an empirically informed benchmark of differential rhythmicity methods

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    OmniRE-seq: A Dual-Method Framework for Decoding RNA Editing Dynamics in Disease and Therapy

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    UnibindMD: An Integrated AI and Molecular Dynamics Platform for De Novo Peptide Binder Design

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    Averaging in gene perturbation benchmarks hides perturbation-strength variation: Consequences for model evaluation

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    Data mining of global sequence datasets markedly expands known diversity within the Tobamovirus genus

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    Denoising single-cell ATAC-seq data with Shannon entropy

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    Information contracts determine what inverse perturbation benchmarks measure

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    Whole-genome sequencing reveals tumor T-cell infiltration associated with immunotherapy outcomes

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    Reference-free isoform discovery links unannotated RNA processing to disease risk

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    CAI-Vax: Computational Design of Personalized mRNA Cancer Vaccine Constructs After Antigen Selection

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    RiboDFM: Robust RNA sequence design using backbone-conditioned discrete flow matching

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    Cuticulome.org: a centralized database of proteins in arthropod cuticles

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    AI-guided discovery of natural pocket proteins for portable small-molecule sensing

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    Astrolabe: Programmable all-atom biomolecular design through cross-context coordination and structural intervention

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    Streamline CNV - A Handy Nextflow Pipeline for Chromosomal Copy Number Variation Analysis

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    BUDDY: An interactive web platform to accelerate the functional modeling of human missense variants using Saccharomyces cerevisiae orthologs

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    Mechanism-guided Discovery of Fluoroacetate Dehalogenase (FAcD) Variants for Enzymatic PFAS Defluorination

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    Self-extending DNA recording with stochastic and programmed writing

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    Metabolic engineering of Yarrowia lipolytica for higher fatty alcohol production

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    Dysregulated mechanoregulation of load-induced bone adaptation in prematurely aged mice: insights from a micro-multiphysics agent-based model

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    NI2+ AND ZN2+-BINDING DNA MOTIFS REVEALED IN DNA APTAMERS TO AFRICAN SWINE FEVER VIRUS

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    Automated Knowledge Graph Construction for CAR T Cell Receptor Design via Hybrid Text Mining

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    Behavioral Mapping of Hierarchical Dynamical Models Accelerates Bayesian Parameter Inference

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    RiboBridge: protein-conditioned de novo RNA binder structure design

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    Supercoiling Drives DNA-Protein Co-Condensation

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    Pose: a pure-NumPy, chirality-aware, structural engine for building and manipulating the molecular structures of proteins, nucleic acids, and small organic molecules

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    LiverHomo: An Integrated and Interactive Human Liver Single-Cell Atlas with Protein Interaction and Cell-Cell Communication Networks

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    Using Arabian Sea Coastal Water as a Model to Study Plasmid-mediated AMR Dissemination driven by Anthropogenic Impacts

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    CDSeq2 integrates individual-level cell-type expression deconvolution with recoverability-guided prioritization

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    A prediction-interval framework for identifying outlier control cohorts in lifespan studies

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    Foundation Models Improve Perturbation Response Prediction

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    Unimeth: A unified transformer framework for accurate DNA methylation detection from nanopore reads

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    A moving target: non-stationary selection governs unsupervised prediction of viral fitness

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    Characterization of selective pressures acting on protein sites with Deep Learning

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    CCTP-Atlas: Compartment-Resolved Ciliary Transcriptional Dysregulation in Tetralogy of Fallot, A Six-Dataset Integrative Meta-Analysis

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    A translational transcriptomic signature of vaccine reactogenicity for the evaluation of novel formulations

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    De novo transformer modeling improves recovery of genetic cell types from sparse single-cell RNA sequencing

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    CellWHISPER disentangles direct cell-cell communication from structural proximity

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    Differential Gene Expression in the Tropical House Cricket and Its Iridovirus in Healthy versus Diseased Specimens

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    How AlphaFold 3 helps with multiscale drug discovery

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    Predicting Pre-treatment Resistance or Post-treatment Effect? A Systematic Benchmarking of Single-Cell Drug Response Models

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