Bioinform.

Publications

volume 40, number 2, 2024

volume 40, number 3, 2024

Florian J. Gisdon, Mariella Zunker, Jan Niclas Wolf, Kai Prüfer, Jörg Ackermann, Christoph Welsch, Ina Koch
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes. Bioinform. 40 (3) (2024)
Shreyas Arvindekar, Aditi S. Pathak, Kartik Majila, Shruthi Viswanath
Optimizing representations for integrative structural modeling using Bayesian model selection. Bioinform. 40 (3) (2024)
David Ferreiro, Catarina Branco, Miguel Arenas
Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation. Bioinform. 40 (3) (2024)
Jiqing Wu, Viktor H. Koelzer
spatial transcriptomic editing at single-cell resolution. Bioinform. 40 (3) (2024)
Zuher Jahshan, Leonid Yavits
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment. Bioinform. 40 (3) (2024)
Hannah-Marie Martiny, Nikiforos Pyrounakis, Thomas Nordahl Petersen, Oksana Lukjancenko, Frank Aarestrup, Philip T. L. C. Clausen, Patrick Munk
ARGprofiler - a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets. Bioinform. 40 (3) (2024)
Woosung Jeon, Dongsup Kim
AbFlex: designing antibody complementarity determining regions with flexible CDR definition. Bioinform. 40 (3) (2024)
Chiung-Ting Wu, Dongping Du, Lulu Chen, Rujia Dai, Chunyu Liu, Guoqiang Yu, Saurabh Bhardwaj, Sarah J. Parker, Zhen Zhang, Robert Clarke, David M. Herrington, Yue Wang
CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution. Bioinform. 40 (3) (2024)
Milind Misra, Jeffy Jeffy, Charis Liao, Stephanie Pickthorn, Kshitij Wagh, Alon Herschhorn
HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies. Bioinform. 40 (3) (2024)
Guillermo Dufort y Álvarez, Martí Xargay-Ferrer, Alba Pagès-Zamora, Idoia Ochoa
EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization. Bioinform. 40 (3) (2024)
Correction to: OncoThreads: visualization of large-scale longitudinal cancer molecular data. Bioinform. 40 (3) (2024)
Yiyang Yu, Shivani Muthukumar, Peter K. Koo
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow. Bioinform. 40 (3) (2024)
Jun Xue, Bingyi Wang, Hongchao Ji, Weihua Li
RT-Transformer: retention time prediction for metabolite annotation to assist in metabolite identification. Bioinform. 40 (3) (2024)
Arik Ermshaus, Michael Piechotta, Gina Rüter, Ulrich Keilholz, Ulf Leser, Manuela Benary
preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology. Bioinform. 40 (3) (2024)
J. Harry Caufield, Harshad Hegde, Vincent Emonet, Nomi L. Harris, Marcin P. Joachimiak, Nicolas Matentzoglu, Hyeongsik Kim, Sierra A. T. Moxon, Justin T. Reese, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. Bioinform. 40 (3) (2024)
Zhengyang Guo, Yang Wang, Guangshuo Ou
Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison. Bioinform. 40 (3) (2024)
Hamza Biyuzan, Mohamed-Akram Masrour, Lucas Grandmougin, Frédéric Payan, Dominique Douguet
SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space. Bioinform. 40 (3) (2024)
Jose L. Figueroa III, Eliza Dhungel, Madeline Bellanger, Cory R. Brouwer, Richard Allen White III
MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life. Bioinform. 40 (3) (2024)
Emese I Végh, Katerina Douka
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS. Bioinform. 40 (3) (2024)
Xiangxin Zhan, Yanbin Yin, Han Zhang
BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework. Bioinform. 40 (3) (2024)
Melpomeni Kasapi, Kexin Xu, Timothy M. D. Ebbels, Declan P. O'Regan, James S. Ware, Joram M. Posma
LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies. Bioinform. 40 (3) (2024)
Kristofer Sandås, Jacob Lewerentz, Edvin Karlsson, Linda Karlsson, David Sundell, Kotryna Simonyté-Sjödin, Andreas Sjödin
Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification. Bioinform. 40 (3) (2024)
Haoliang Xue, Mélina Gallopin, Camille Marchet, Ha N. Nguyen, Yunfeng Wang, Antoine Lainé, Chloé Bessiere, Daniel Gautheret
-mer count matrix dimension reduction. Bioinform. 40 (3) (2024)
Oliver Cheng, Min Hao Ling, Changqing Wang, Shuyi Wu, Matthew E. Ritchie, Jonathan Göke, Noorul Amin, Nadia M. Davidson
Flexiplex: a versatile demultiplexer and search tool for omics data. Bioinform. 40 (3) (2024)
Jaroslaw Chilimoniuk, Krystyna Grzesiak, Jakub Kala, Dominik Nowakowski, Adam Kretowski, Rafal Kolenda, Michal Ciborowski, Michal Burdukiewicz
imputomics: web server and R package for missing values imputation in metabolomics data. Bioinform. 40 (3) (2024)

volume 40, number 4, 2024

volume 40, number 5, 2024

Wenmin Zhang, Tianyuan Lu, Robert Sladek, Yue Li, Hamed S. Najafabadi, Josée Dupuis
SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals. Bioinform. 40 (5) (2024)

volume 40, number 6, 2024

volume 40, number 7, 2024

volume 40, number 8, 2024

Andrew Dickson, Mohammad R. K. Mofrad
Fine-tuning protein embeddings for functional similarity evaluation. Bioinform. 40 (8) (2024)