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Bioinformatics

EIM: An effective solution for improving multi-modal large language models

Yuting Bai, Tonghua Su, Zixing Bai

published 11 Aug 2025

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Bag-of-words is competitive with sum-of-embeddings language-inspired representations on protein inference

Frixos Papadopoulos, Tilman Sanchez-Elsner, Mahesan Niranjan, Ashley I. Heinson

published 06 Aug 2025

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Analysis and comparison of the bacterial σ⁵⁴ regulon: Evidence of phylogenetic trends in gene regulation

Maricela Carrera-Reyna, Edna Cruz-Flores, Enrique Merino

published 01 Aug 2025

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Apparent differences between human and chimp proteomes are reduced when considering human population: Human specific variants are enriched in disordered and compositionally biased regions

Pablo Mier, Miguel A. Andrade-Navarro, Enrique Morett

published 31 Jul 2025

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A long-term localization and mapping system for autonomous inspection robots in large-scale environments using 3D LiDAR sensors

Wandeng Mao, Liang Jiang, Shanfeng Liu, Shengzhe Xi, Hua Bao

published 31 Jul 2025

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Positional distribution of transcription factor binding sites in the human genome

Chun-Ping Yu, Zhi Thong Soh, Maloyjo Joyraj Bhattacharjee, Wen-Hsiung Li

published 30 Jul 2025

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Multi-modal deep learning for intelligent landscape design generation: A novel CBS3-LandGen model

Mingzhen Lu, Lili Shi

published 24 Jul 2025

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cONcat: Computational reconstruction of concatenated fragments from long Oxford Nanopore reads

Alexander J. Petri, Mai Thi-Huyen Nguyen, Anjali Rajwar, Erik Benson, Kristoffer Sahlin

published 24 Jul 2025

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The genetic context of bla_IMP varies among bacterial families from One Health sources

Susan Vaughn Grooters, Dixie F. Mollenkopf, Thomas E. Wittum

published 23 Jul 2025

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Bioinformatics and modelling studies of FhuD, the periplasmic siderophore binding protein from the plant pathogen Erwinia amylovora

Sharda Bharti, Lavinia Carlini, Alfonso Esposito, Stefano Benini

published 23 Jul 2025

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Off-target sequence variations driven by the intrinsic properties of the Cas–sgRNA–DNA complex in genome editing

Celine Kurniawan, Takeshi Itoh

published 18 Jul 2025

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Longitudinal sequencing of cardiometabolic multimorbidity among older adults and association with subsequent dementia onset

Corey L. Nagel, Siting Chen, Heather G. Allore, Anda Botoseneanu, Jason T. Newsom, Nick Bishop, David A. Dorr, Jeffrey Kaye, Ana R. Quiñones

published 10 Jul 2025

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A high quality genome of the common swamp pitcher plant (Nepenthes mirabilis) using PacBio HiFi sequencing

Christopher J. Jackson, Todd G.B. McLay, Gareth D. Holmes, Theodore R. Allnutt, Alastair S. Robinson

published 10 Jul 2025

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