Bioinformatics 2024: all accepted papers
- Fast multiple sequence alignment via multi-armed bandits ↗Kayvon Mazooji, Ilan Shomorony1 citation
- Fast polypharmacy side effect prediction using tensor factorization ↗Oliver Lloyd, Yi Liu, Tom R. Gaunt1 citation
- FastTENET: an accelerated TENET algorithm based on manycore computing in Python ↗Rakbin Sung, Hyeonkyu Kim, Junil Kim et al.1 citation
- GEEES: inferring cell-specific gene–enhancer interactions from multi-modal single-cell data ↗Shuyang Chen, Sündüz Keleş1 citation
- GTAM: A Molecular Pretraining Model with Geometric Triangle Awareness ↗Xiaoyang Hou, Tian Zhu, Milong Ren et al.1 citation
- GUANIN: an all-in-one GUi-driven analyzer for NanoString interactive normalization ↗Julián Montoto-Louzao, Alberto Gómez‐Carballa, Xabier Bello et al.1 citation
- HCS—hierarchical algorithm for simulation of omics datasets ↗Piotr Stomma, Witold Remigiusz Rudnicki1 citation
- Highly efficient clustering of long-read transcriptomic data with GeLuster ↗Junchi Ma, Xiaoyu Zhao, Enfeng Qi et al.1 citation
- KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction ↗Haoliang Xue, Mélina Gallopin, Camille Marchet et al.1 citation
- KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs ↗Dhruv Khatri, Shivani A. Yadav, Chaitanya A. Athale1 citation
- Knowledge mining of brain connectivity in massive literature based on transfer learning ↗Xiaokang Chai, Sile An, Simeng Chen et al.1 citation
- M2ara : unraveling metabolomic drug responses in whole-cell MALDI mass spectrometry bioassays ↗Thomas Enzlein, Alexander Geisel, Carsten Hopf et al.1 citation
- Metadata-guided feature disentanglement for functional genomics ↗Alexander Rakowski, Remo Monti, Viktoriia Huryn et al.1 citation
- Modeling multi-stage disease progression and identifying genetic risk factors via a novel collaborative learning method ↗Duo Xi, Minjianan Zhang, Muheng Shang et al.1 citation
- MotGen: a closed-loop bacterial motility control framework using generative adversarial networks ↗BoGeum Seo, DoHee Lee, Heung Jin Jeon et al.1 citation
- OneSC: a computational platform for recapitulating cell state transitions ↗Da Peng, Patrick Cahan1 citation
- Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling ↗Srijay Deshpande, Sokratia Georgaka, Michael Haley et al.1 citation
- PERFUMES: pipeline to extract RNA functional motifs and exposed structures ↗Arnaud Chol, Roman Sarrazin‐Gendron, Éric Lécuyer et al.1 citation
- Polyphonia: detecting inter-sample contamination in viral genomic sequencing data ↗Lydia Andreyevna Krasilnikova, Christopher H. Tomkins-Tinch, Alton C. Gayton et al.1 citation
- PostFocus: automated selective post-acquisition high-throughput focus restoration using diffusion model for label-free time-lapse microscopy ↗Kwan-Ling Wu, Melisa J. Montalvo, Prashant S. Menon et al.1 citation
- Quantitative analysis of the dexamethasone side effect on human-derived young and aged skeletal muscle by myotube and nuclei segmentation using deep learning ↗Seonghwan Park, Min Young Kim, Min Young Kim et al.1 citation
- RUCova: Removal of Unwanted Covariance in mass cytometry data ↗Rosario Astaburuaga-García, Thomas Sell, Samet Mutlu et al.1 citation
- SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality ↗Xin Liu, Jieni Hu, Jie Zheng1 citation
- SampleExplorer: using language models to discover relevant transcriptome data ↗Wee Loong Chin, Timo Lassmann1 citation
- Sensommatic: an efficient pipeline to mine and predict sensory receptor genes in the era of reference-quality genomes ↗Louise Ryan, Colleen Lawless, Graham M. Hughes1 citation
- Shu: visualization of high-dimensional biological pathways ↗Jorge Carrasco Muriel, Nicholas Luke Cowie, Shannara Kayleigh Taylor Parkins et al.1 citation
- SimService: a lightweight library for building simulation services in Python ↗T. J. Sego1 citation
- Subset scanning for multi-trait analysis using GWAS summary statistics ↗Rui Cao, EVAN A. OLAWSKY, Edward McFowland et al.1 citation
- The 2024 ISCB Accomplishments by a Senior Scientist Award—Dr Tandy Warnow ↗Mallory L Wiper1 citation
- The 2024 ISCB Innovator Award—Dr Su-In Lee ↗Mallory L Wiper1 citation
- Uncertainty quantification in high-dimensional linear models incorporating graphical structures with applications to gene set analysis ↗Xiangyong Tan, Xiao Zhang, Yuehua Cui et al.1 citation
- Weighted centroid trees: a general approach to summarize phylogenies in single-labeled tumor mutation tree inference ↗Hamed Vasei, Mohammad-Hadi Foroughmand-Araabi, Amir Daneshgar1 citation
- ceas: an R package for Seahorse data analysis and visualization ↗Rachel J. House, James Eapen, Hui Shen et al.1 citation
- easySCF: a tool for enhancing interoperability between R and Python for efficient single-cell data analysis ↗Haoyun Zhang, Wentao Zhang, Shuai Zhao et al.1 citation
- pyTWMR: transcriptome-wide Mendelian randomization in python ↗Sergey Oreshkov, Kaido Lepik, Federico Andrea Santoni1 citation
- rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments ↗Jonathan L. Price, Omer Ziv, Malte L. Pinckert et al.1 citation
- scCross: efficient search for rare subpopulations across multiple single-cell samples ↗Alexander Gerniers, Siegfried Nijssen, Pierre Dupont1 citation
- 3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures ↗Victoria Ruiz‐Serra, Samuel Valentini, Sergi Madroñero et al.
- A multi-bin rarefying method for evaluating alpha diversities in TCR sequencing data ↗Mo Li, Xing Hua, Shuai Cheng Li et al.
- ADTGP: correcting single-cell antibody sequencing data using Gaussian process regression ↗Alex C.H. Liu, Steven M. Chan
- ALLSTAR: inference of reliAble causaL ruLes between Somatic muTAtions and canceR phenotypes ↗Dario Simionato, Antonio Collesei, Federica Miglietta et al.
- BindCompare: a novel integrated protein–nucleic acid binding analysis platform ↗Pranav Mahableshwarkar, Jasmine Shum, Mukulika Ray et al.
- Chapter 1 Introduction to bioinformatics ↗Nitin Sharma, Manika Choudhary, Vikas Kumar
- Chapter 2 Biological databases and bioinformatics tools ↗Varruchi Sharma, Imran Sheikh, Vikas Kushwaha et al.
- Chapter 3 Fundamentals of bioinformatics ↗Varruchi Sharma, Poonam Bansal, Imran Sheikh et al.
- Chapter 5 Recent advances in the discovery of drug molecules: trends, scope, and relevance ↗Ramesh Chand Thakur, Akshay Sharma, Renuka Sharma
- ClusterMatch aligns single-cell RNA-sequencing data at the multi-scale cluster level via stable matching ↗Teer Ba, Miao Hao, Lirong Zhang et al.
- Crypt4GH-JS: securely storing sensitive data online with client-side encryption ↗Fabienne Thelen, Jannis Hochmuth, Sven Griep et al.
- ECCB2024: The 23rd European Conference on Computational Biology ↗Anu Kukkonen-Macchi, Sampsa Hautaniemi, Katharina F. Heil et al.
- Eliater: a Python package for estimating outcomes of perturbations in biomolecular networks ↗Sara Mohammad-Taheri, Pruthvi Prakash Navada, Charles Tapley Hoyt et al.
- Enabling Population Protein Dynamics Through Bayesian Modeling ↗Sylvain Lehmann, Jérôme Vialaret, Audrey Gabelle et al.
- GINSA: an accumulator for paired locality and next-generation small ribosomal subunit sequence data ↗Eric Odle, Samuel E. Kahng, Siratee Riewluang et al.
- GRIEVOUS: your command-line general for resolving cross-dataset genotype inconsistencies ↗James V. Talwar, Adam Klie, Meghana S. Pagadala et al.
- Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks ↗Sam F. L. Windels, Daniel Tello Velasco, Mikhail Rotkevich et al.
- ISMB 2024 Proceedings ↗Tijana Milenković, Yann Ponty
- ITree: a user-driven tool for interactive decision-making with classification trees ↗Hubert Sokołowski, Marcin Czajkowski, Anna Czajkowska et al.
- Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence ↗Jason Y. Cain, Jacob I. Evarts, Jessica S. Yu et al.
- Integrative annotation scores of variants for impact on RNA binding protein activities ↗Jingqi Duan, Audrey P. Gasch, Sündüz Keleş
- Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique ↗Hang Yang, Xiaoxin Lu, Jiaxing Chang et al.
- MiPRIME: an integrated and intelligent platform for mining primer and probe sequences of microbial species ↗Zhiming Zhang, Jing Fei Ren, Lili Ren et al.
- Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions ↗Ruoqian Liu, Yue Wang, Dan Cheng
- New GO-based measures in multiple network alignment ↗Kimia Yazdani, Reza Mousapour, Wayne B. Hayes
- OpenVariant: a toolkit to parse and operate multiple input file formats ↗David Martínez-Millán, Federica Brando, Miguel L. Grau et al.
- Optimal sequencing budget allocation for trajectory reconstruction of single cells ↗Noa Moriel, Edvin Memet, Mor Nitzan
- PONYTA: prioritization of phenotype-related genes from mouse KO events using PU learning on a biological network ↗Jun Hyeong Kim, Bonil Koo, Sun Kim
- Peer Review Report For: From the establishment of a national bioinformatics society to the development of a national bioinformatics infrastructure [version 1; peer review: 3 approved with reservations] ↗Bogdan Andrei Mirauta, Cătălina Zenoaga-Barbăroşie, Monica I. Abrudan et al.
- Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems ↗Mauro Silberberg, Henning Hermjakob, Rahuman S. Malik‐Sheriff et al.
- Probabilistic pathway-based multimodal factor analysis ↗Alexander Immer, Stefan G. Stark, Francis Jacob et al.
- PySNV for complex intra-host variation detection ↗Liandong Li, Haoyi Fu, Wentai Ma et al.
- RTF: an R package for modelling time course data ↗Eva Brombacher, Clemens Kreutz
- Regional analysis to delineate intrasample heterogeneity with RegionalST ↗Yue Lyu, Chong Wu, Wei Sun et al.
- SWGTS—a platform for stream-based host DNA depletion ↗Philipp Spohr, Max Ried, Laura C. Kühle et al.
- Supervised learning of enhancer–promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning ↗Dylan Barth, Richard Van, Jonathan Cardwell et al.
- SurvBal: compositional microbiome balances for survival outcomes ↗Ying Li, Teresa Lee, Kai Marin et al.
- TARO: tree-aggregated factor regression for microbiome data integration ↗Aditya K. Mishra, Iqbal Mahmud, Philip L. Lorenzi et al.
- TRAITER: transformer-guided diagnosis and prognosis of heart failure using cell nuclear morphology and DNA damage marker ↗Hiromu Hayashi, Toshiyuki Ko, Zhehao Dai et al.
- The 2024 ISCB Overton Prize Award—Dr Martin Steinegger ↗Mallory L Wiper
- VSS-Hi-C: variance-stabilized signals for chromatin contacts ↗Neda Shokraneh, Faezeh Bayat, Maxwell W. Libbrecht
- biotextgraph: graphical summarization of functional similarities from textual information ↗Noriaki Sato, Yaozhong Zhang, Zuguang Gu et al.
- cloudrna SP Ades : isoform assembly using bulk barcoded RNA sequencing data ↗Dmitry Meleshko, Andrey D. Prjbelski, Mikhail Raiko et al.
- cypress: an R/Bioconductor package for cell-type-specific differential expression analysis power assessment ↗Shilin Yu, Guanqun Meng, Wen Tang et al.
- greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets ↗Sheikh Nizamuddin, H. T. Marc Timmers
- quaqc: efficient and quick ATAC-seq quality control and filtering ↗Benjamin J.-M. Tremblay, Julia I. Qüesta
- snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics ↗Kim L. Vertacnik, Oksana V. Vernygora, Julian R. Dupuis
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