- Helena Balabin, Charles Tapley Hoyt, Colin Birkenbihl, Benjamin M. Gyori, John A. Bachman, Alpha Tom Kodamullil, Paul G. Plöger, Martin Hofmann-Apitius, Daniel Domingo-Fernández:
STonKGs: a sophisticated transformer trained on biomedical text and knowledge graphs. Bioinform. 38(6): 1648-1656 (2022) - Athanasios Baltzis, Leila Mansouri, Suzanne Jin, Björn E. Langer, Ionas Erb, Cédric Notredame:
Highly significant improvement of protein sequence alignments with AlphaFold2. Bioinform. 38(22): 5007-5011 (2022) - Hmrishav Bandyopadhyay, Zihao Deng, Leiting Ding, Sinuo Liu, Mostofa Rafid Uddin, Xiangrui Zeng, Sima Behpour, Min Xu:
Cryo-shift: reducing domain shift in cryo-electron subtomograms with unsupervised domain adaptation and randomization. Bioinform. 38(4): 977-984 (2022) - Xiaoqiong Bao, Kaiyu Zhu, Xuefei Liu, Zhihang Chen, Ziwei Luo, Qi Zhao, Jian Ren, Zhixiang Zuo:
MeRIPseqPipe: an integrated analysis pipeline for MeRIP-seq data based on Nextflow. Bioinform. 38(7): 2054-2056 (2022) - Luca Barbon, Victoria Offord, Elizabeth J. Radford, Adam P. Butler, Sebastian S. Gerety, David J. Adams, Hong Kee Tan, Andrew J. Waters:
Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments. Bioinform. 38(4): 892-899 (2022) - Amélie Barozet, Kevin Molloy, Marc Vaisset, Christophe Zanon, Pierre Fauret, Thierry Siméon, Juan Cortés:
MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations. Bioinform. 38(2): 552-553 (2022) - Giacomo Baruzzo, Giulia Cesaro, Barbara Di Camillo:
Identify, quantify and characterize cellular communication from single-cell RNA sequencing data with scSeqComm. Bioinform. 38(7): 1920-1929 (2022) - Genis Bayarri, Pau Andrio, Adam Hospital, Modesto Orozco, Josep Lluis Gelpí:
BioExcel Building Blocks REST API (BioBB REST API), programmatic access to interoperable biomolecular simulation tools. Bioinform. 38(12): 3302-3303 (2022) - Yasser Mohseni Behbahani, Simon Crouzet, Elodie Laine, Alessandra Carbone:
Deep Local Analysis evaluates protein docking conformations with locally oriented cubes. Bioinform. 38(19): 4505-4512 (2022) - Bahareh Behkamal, Mahmoud Naghibzadeh, Andrea Pagnani, Mohammad Reza Saberi, Kamal Al Nasr:
LPTD: a novel linear programming-based topology determination method for cryo-EM maps. Bioinform. 38(10): 2734-2741 (2022) - Nikola Benes, Lubos Brim, Ondrej Huvar, Samuel Pastva, David Safránek, Eva Smijáková:
AEON.py: Python library for attractor analysis in asynchronous Boolean networks. Bioinform. 38(21): 4978-4980 (2022) - Christopher Bennett, Micah Thornton, Chanhee Park, Gervaise Henry, Yun Zhang, Venkat S. Malladi, Daehwan Kim:
SeqWho: reliable, rapid determination of sequence file identity using k-mer frequencies in Random Forest classifiers. Bioinform. 38(7): 1830-1837 (2022) - Erik N. Bergstrom, Mousumy Kundu, Noura Tbeileh, Ludmil B. Alexandrov:
Examining clustered somatic mutations with SigProfilerClusters. Bioinform. 38(13): 3470-3473 (2022) - Victor Bernal, Venustiano Soancatl-Aguilar, Jonas Bulthuis, Victor Guryev, Peter Horvatovich, Marco Grzegorczyk:
GeneNetTools: tests for Gaussian graphical models with shrinkage. Bioinform. 38(22): 5049-5054 (2022) - Judith Bernett, Dominik Krupke, Sepideh Sadegh, Jan Baumbach, Sándor P. Fekete, Tim Kacprowski, Markus List, David B. Blumenthal:
Robust disease module mining via enumeration of diverse prize-collecting Steiner trees. Bioinform. 38(6): 1600-1606 (2022) - Martina Bevilacqua, Lisanna Paladin, Silvio C. E. Tosatto, Damiano Piovesan:
ProSeqViewer: an interactive, responsive and efficient TypeScript library for visualization of sequences and alignments in web applications. Bioinform. 38(4): 1129-1130 (2022) - Giovanni Birolo, Andrea Telatin:
BamToCov: an efficient toolkit for sequence coverage calculations. Bioinform. 38(9): 2617-2618 (2022) - Sebastian Bittrich, Yana Rose, Joan Segura, Robert Lowe, John D. Westbrook, Jose M. Duarte, Stephen K. Burley:
RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB. Bioinform. 38(5): 1452-1454 (2022) - Daniele Bizzarri, Marcel J. T. Reinders, Marian Beekman, P. Eline Slagboom, Erik van den Akker:
MiMIR: R-shiny application to infer risk factors and endpoints from Nightingale Health's 1H-NMR metabolomics data. Bioinform. 38(15): 3847-3849 (2022) - Antoine Bodein, Marie-Pier Scott-Boyer, Olivier Périn, Kim-Anh Lê Cao, Arnaud Droit:
timeOmics: an R package for longitudinal multi-omics data integration. Bioinform. 38(2): 577-579 (2022) - Gregory J. Boggy, G. W. McElfresh, Eisa Mahyari, Abigail B. Ventura, Scott G. Hansen, Louis J. Picker, Benjamin N. Bimber:
BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data. Bioinform. 38(10): 2791-2801 (2022) - Galina Boldina, Paul Fogel, Corinne Rocher, Charles Bettembourg, George Luta, Franck Augé:
A2Sign: Agnostic Algorithms for Signatures - a universal method for identifying molecular signatures from transcriptomic datasets prior to cell-type deconvolution. Bioinform. 38(4): 1015-1021 (2022) - José Bonet, Mandi Chen, Marc Dabad, Simon Heath, Abel Gonzalez-Perez, Núria López-Bigas, Jens Lagergren:
DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data. Bioinform. 38(5): 1235-1243 (2022) - James K. Bonfield:
CRAM 3.1: advances in the CRAM file format. Bioinform. 38(6): 1497-1503 (2022) - Jonathan R. Bowles, Caroline Hoppe, Hilary L. Ashe, Magnus Rattray:
Scalable inference of transcriptional kinetic parameters from MS2 time series data. Bioinform. 38(4): 1030-1036 (2022) - Peter J. Bradbury, Terry M. Casstevens, Sarah E. Jensen, L. C. Johnson, Z. R. Miller, Brandon Monier, M. C. Romay, B. Song, Edward S. Buckler:
The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinform. 38(15): 3698-3702 (2022) - Nadav Brandes, Dan Ofer, Yam Peleg, Nadav Rappoport, Michal Linial:
ProteinBERT: a universal deep-learning model of protein sequence and function. Bioinform. 38(8): 2102-2110 (2022) - Tim Breitenbach, Matthias Jürgen Schmitt, Thomas Dandekar:
Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing. Bioinform. 38(17): 4162-4171 (2022) - Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, Roman Bauer:
BioDynaMo: a modular platform for high-performance agent-based simulation. Bioinform. 38(2): 453-460 (2022) - Kenneth I Brewer, Glenn J. Gaffield, Malavika Puri, Ronald R. Breaker:
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria. Bioinform. 38(2): 533-535 (2022)