bioinformatics papers | Gist.Science

Bioinformatics sits at the exciting intersection where biology meets data science, using powerful computer tools to decode the vast complexity of living systems. From mapping the human genome to tracking how viruses evolve, this field transforms raw biological information into actionable insights that drive modern medicine and research forward without requiring a supercomputer to understand the basics.

On Gist.Science, we ensure you never miss a breakthrough by processing every new preprint in this category directly from bioRxiv. Our team provides both plain-language explanations and detailed technical summaries for each paper, making cutting-edge discoveries accessible to everyone regardless of their background.

Below are the latest bioinformatics papers added from bioRxiv, ready for you to explore with clarity and depth.

💻 bioinformatics

POTTR: Identifying Recurrent Trajectories in Evolutionary and Developmental Processes using Posets

This paper introduces POTTR, a novel combinatorial algorithm that utilizes incomplete partially ordered sets (posets) and a conflict graph approach to solve the NP-hard maximum k-common induced incomplete subposet problem, thereby identifying statistically significant recurrent genetic trajectories and conserved differentiation routes across diverse biological datasets while effectively resolving uncertainties inherent in tumor phylogenies and lineage tracing.

Käufler, S. C., Schmidt, H., Jürgens, M., Klau, G. W., Sashittal, P., Raphael, B.2026-02-26

💻 bioinformatics

MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements

This paper introduces MaxGeomHash, a novel parallelizable and permutation-invariant sketching algorithm that generates variable-size random samples of distinct k-mers with sub-linear complexity, offering a balanced trade-off between storage efficiency and similarity estimation accuracy compared to existing fixed-size (MinHash) and linear-size (FracMinHash) methods.

Hera, M. R., Koslicki, D., Martinez, C.2026-02-25

💻 bioinformatics

PMGen: From Peptide-MHC Structure Prediction to Peptide Generation

PMGen is an integrated framework that leverages AlphaFold2 with novel strategies to achieve state-of-the-art structural prediction for variable-length peptide-MHC complexes, thereby enabling high-fidelity structure-guided peptide design and the generation of large-scale datasets to train advanced immunological models.

Asgary, A. H., Aleyasin, A., Mehl, J. A., Fallah, S., Aintablian, H., Ludewig, B., Mishto, M., Liepe, J., Soeding, J.2026-02-25

💻 bioinformatics

PaNDA: Efficient Optimization of Phylogenetic Diversity in Networks

This paper introduces PaNDA, a software package featuring a novel polynomial-time algorithm to efficiently maximize phylogenetic diversity in phylogenetic networks with bounded scanwidth, while also extending the diversity definition to semi-directed networks and proving the NP-hardness of the optimization problem in that context.

Holtgrefe, N., van Iersel, L., Meuwese, R., Murakami, Y., Schestag, J.2026-02-25

💻 bioinformatics

Protein Compositional Ratio Representation (PCRR)Systematically Improves Human Disease Prediction

This study demonstrates that modeling plasma proteomics data as compositional systems using pairwise protein ratios significantly outperforms traditional abundance-based approaches in predicting human diseases, achieving substantial accuracy gains in Alzheimer's subtypes and across a broad spectrum of conditions in the UK Biobank.

Madduri, A. V., Ellis, R. J., Patel, C. J.2026-02-25

💻 bioinformatics

KuPID: Kmer-based Upstream Preprocessing of Long Reads forIsoform Discovery

KuPID is a kmer-based preprocessing tool for long RNAseq reads that accelerates novel isoform discovery by using kmer sketching to pseudo-align reads and filter out extraneous data, thereby significantly improving both pipeline speed and accuracy.

Borowiak, M., Yu, Y. W.2026-02-25

💻 bioinformatics

GaugeFixer: overcoming parameter non-identifiability in models of sequence-function relationships

The paper introduces GaugeFixer, a scalable Python package that resolves parameter non-identifiability in sequence-function models through linear-time gauge-fixing, enabling the biologically meaningful interpretation of complex landscapes with millions of parameters.

Marti-Gomez, C., McCandlish, D. M., Kinney, J. B.2026-02-25

💻 bioinformatics

Generating Structurally Diverse Therapeutic Peptides with GFlowNet

This paper demonstrates that GFlowNet outperforms traditional reinforcement learning methods like GRPO in generating structurally diverse therapeutic peptides by inherently achieving uniform sequence sampling through proportional reward sampling, thereby eliminating the need for explicit diversity penalties and preventing mode collapse.

Wijaya, E.2026-02-25

💻 bioinformatics

Distilling Protein Language Models with Complementary Regularizers

This paper demonstrates that distilling a large protein language model into compact students using two complementary protein-specific regularizers—uncertainty-aware position weighting and calibration-aware label smoothing—significantly improves inference speed, memory efficiency, and sample efficiency on scarce data, enabling high-quality domain adaptation on consumer-grade hardware.

Wijaya, E.2026-02-25

💻 bioinformatics

ARCH3D: A foundation model for global genome architecture

This paper introduces ARCH3D, a foundation model for global genome architecture that utilizes a novel masked locus modeling task to capture genome-wide spatial structures and enable the reconstruction of complex chromosomal interactions, ultimately serving as a structural basis for simulating genome behavior.

Galioto, N., Stansbury, C., Gorodetsky, A. A., Rajapakse, I.2026-02-25

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