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TopicPaper titleYearURL
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AlignmentFlexible seed size enables ultra-fast and accurate read alignment2022https://www.biorxiv.org/content/10.1101/2021.06.18.449070v3
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AlignmentLarge multiple sequence alignments with a root-to-leaf regressive method2019https://www.nature.com/articles/s41587-019-0333-6
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AlignmentVargas: heuristic-free alignment for assessing linear and graph read aligners2020https://academic.oup.com/bioinformatics/article/36/12/3712/5823884
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AlignmentLocality-sensitive hashing for the edit distance2020https://academic.oup.com/bioinformatics/article/35/14/i127/5529166
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AlignmentProbMinHash – A Class of Locality-Sensitive Hash Algorithms for the (Probability) Jaccard Similarity2020https://ieeexplore.ieee.org/abstract/document/9185081
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AlignmentOn the Hardness of Sequence Alignment on De Bruijn Graphs2022https://www.liebertpub.com/doi/10.1089/cmb.2022.0411
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AlignmentPangenomics enables genotyping of known structural variants in 5202 diverse genomes2021https://www.science.org/doi/epdf/10.1126/science.abg8871
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AlignmentBlock aligner: fast and flexible pairwise sequence alignment with SIMD-accelerated adaptive blocks2021https://www.biorxiv.org/content/10.1101/2021.11.08.467651v1
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AlignmentA fast bit-vector algorithm for approximate string matching based on DP1999https://dl.acm.org/doi/10.1145/316542.316550
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AlignmentIntroducing difference recurrence relations for faster semi-global alignment of long sequences2017https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2014-8
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AlignmentAn O(NP) Sequence Comparison Algorithm1989https://www.sciencedirect.com/science/article/abs/pii/002001909090035V?via%3Dihub
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AlignmentSpeeding up DP algorithms for finding optimal lattice paths1989https://epubs.siam.org/doi/10.1137/0149094
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AlignmentParameterized syncmer schemes improve long-read mapping2022https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010638
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AlignmentAlgorithms for Colinear Chaining with Overlaps and Gap Costs2022https://www.liebertpub.com/doi/10.1089/cmb.2022.0266
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AlignmentProgressive Cactus is a multiple-genome aligner for the thousand-genome era2020https://www.nature.com/articles/s41586-020-2871-y
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Alignment / Protein StructureProtein Structural Alignments From Sequence2020https://web.archive.org/web/20201209214217id_/https://www.biorxiv.org/content/biorxiv/early/2020/11/04/2020.11.03.365932.full.pdf
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Analysison the approximation of the kolmogorow complexity for DNA sequences2017
https://www.researchgate.net/profile/Diogo-Pratas/publication/317104968_On_the_Approximation_of_the_Kolmogorov_Complexity_for_DNA_Sequences/links/5accd4e14585154f3f3f2461/On-the-Approximation-of-the-Kolmogorov-Complexity-for-DNA-Sequences.pdf
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AnalysisSeed-chain-extend alignment is accurate and runs in close to O(m log n) time for similar sequences: a rigorous average-case analysis2022https://www.biorxiv.org/content/10.1101/2022.10.14.512303v1
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Applied MLDNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome2021https://academic.oup.com/bioinformatics/article/37/15/2112/6128680
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Applied MLDirect antimicrobial resistance prediction from clinical MALDI-TOF mass spectra using machine learning2022https://www.nature.com/articles/s41591-021-01619-9
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Applied ML / DNA language modelingDNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome2021https://academic.oup.com/bioinformatics/article/37/15/2112/6128680
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Applied ML / homology detectionTM-Vec: template modeling vectors for fast homology detection and alignment2022https://web.archive.org/web/20220731175100id_/https://www.biorxiv.org/content/biorxiv/early/2022/07/27/2022.07.25.501437.full.pdf
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Applied ML / Pathogenicity ClassificationDeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks2020https://pubmed.ncbi.nlm.nih.gov/31298694/
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Applied ML / Pathogenicity ClassificationInterpretable detection of novel human viruses from genome sequencing data2021https://academic.oup.com/nargab/article/3/1/lqab004/6125551
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Applied ML / Pathogenicity ClassificationDeep learning-based real-time detection of novel pathogens during sequencing2021https://pubmed.ncbi.nlm.nih.gov/34297793/
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Applied ML / Pathogenicity ClassificationDetecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collection2022https://academic.oup.com/bioinformatics/article/38/Supplement_2/ii168/6702016
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Applied ML / protein alignmentDEDAL: A deep learning-based model that learns to align protein sequences and detect homologs2022https://www.nature.com/articles/s41592-022-01700-2
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Applied ML / protein function predictionStructure-based protein function prediction using graph convolutional networks2021https://www.nature.com/articles/s41467-021-23303-9
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Applied ML / protein structureEvolutionary-scale prediction of atomic level protein structure with a language model2022https://www.biorxiv.org/content/10.1101/2022.07.20.500902v3.abstract
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Applied ML / protein structure predictionAlphaFold: A highly accurate protein folding algorithm2021https://www.nature.com/articles/s41586-021-03819-2
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Applied ML / reference-free enrichmentAMAISE: a machine learning approach to index-free sequence enrichment2022https://www.nature.com/articles/s42003-022-03498-3
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Applied ML / Treatment response PredictionRecurrent somatic mutations as predictors of immunotherapy response2022https://doi.org/10.1038/s41467-022-31055-3
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Applied ML / Treatment response PredictionA mutation-based gene set predicts survival benefit after immunotherapy across multiple cancers and reveals the immune response landscape2022https://doi.org/10.1186/s13073-022-01024-y
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Applied ML/spatial transcriptomicsIntegrative spatial analysis of cell morphologies and transcriptional states with MUSE2022https://www.nature.com/articles/s41587-022-01251-z
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Applied ML/spatial transcriptomicsDeep learning and alignment of spatially resolved single-cell transcriptomes with Tangram2021https://www.nature.com/articles/s41592-021-01264-7
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Approximate mappingStrobealign: flexible seed size enables ultra-fast and accurate read alignment2022https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02831-7
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Approximate mappingSTAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions2021https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02490-0
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Approximate mappingmapquik: Efficient low-divergence mapping of long reads in minimizer space2022https://www.biorxiv.org/content/10.1101/2022.12.23.521809v1?s=31
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Approximate mappingSourmash Branchwater Enables Lightweight Petabyte-Scale Sequence Search2022https://www.biorxiv.org/content/10.1101/2022.11.02.514947v1
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Approximate mappingGSearch: Ultra-Fast and Scalable Microbial Genome Search by combining Kmer Hashing with Hierarchical Navigable Small World Graphs2022https://www.biorxiv.org/content/10.1101/2022.10.21.513218v1
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Approximate MappingRawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes2022https://www.biorxiv.org/content/10.1101/2023.01.22.525080v1
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AssemblyVerkko: telomere-to-telomere assembly of diploid chromosomes2022https://www.biorxiv.org/content/10.1101/2022.06.24.497523v1
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AssemblyMinimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer2021https://www.sciencedirect.com/science/article/pii/S240547122100332X
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CompressionMasked Minimizers: Unifying sequence sketching methods2022https://www.biorxiv.org/content/10.1101/2022.10.18.512430v1
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CompressionEfficient minimizer orders for large values of k using minimum decycling sets2022https://www.biorxiv.org/content/10.1101/2022.10.18.512682v1
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CompressionEulertigs: minimum plain text representation of k-mer sets without repetitions in linear time2022https://www.biorxiv.org/content/10.1101/2022.05.17.492399v3
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CompressionkmcEx: memory-frugal and retrieval-efficient encoding of counted k-mers2019https://academic.oup.com/bioinformatics/article/35/23/4871/5481953
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CompressionHigh efficiency referential genome compression algorithm2019https://academic.oup.com/bioinformatics/article-abstract/35/12/2058/5165377
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CompressionQuark enables semi-reference-based compression of RNA-seq data2017https://academic.oup.com/bioinformatics/article/33/21/3380/3920524
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CompressionREINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets2020https://academic.oup.com/bioinformatics/article/36/Supplement_1/i177/5870500
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Data StructuresExtremely-fast construction and querying of compacted and colored de Bruijn graphs with GGCAT*2022https://www.biorxiv.org/content/10.1101/2022.10.24.513174v1
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Data StructuresKMC 2: fast and resource-frugal k-mer counting2015https://academic.oup.com/bioinformatics/article/31/10/1569/177467
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Data StructuresSimulating the DNA String Graph in Succinct Space2019https://arxiv.org/pdf/1901.10453.pdf
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Data StructuresFaster Repetition-Aware Compressed Suffix Trees based on Block Trees2019https://arxiv.org/abs/1902.03274
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Data StructuresSpace-efficient merging of succinct de Bruijn graphs2019https://arxiv.org/abs/1902.02889
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Data StructuresXor Filters: Faster and Smaller Than Bloom and Cuckoo Filters2020https://dl.acm.org/doi/fullHtml/10.1145/3376122
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Data Structures / ImmunotherapyNeoSplice: a bioinformatics method for prediction of splice variant neoantigens2022https://doi.org/10.1093/bioadv/vbac032
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Genomic variationReference flow: reducing reference bias using multiple population genomes2021https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02229-3
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Genomic variationA draft human pangenome reference2022https://www.biorxiv.org/content/10.1101/2022.07.09.499321v1.abstract
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Genomic variationA general framework for estimating the relative pathogenicity of human genetic variants2014https://www.nature.com/articles/ng.2892
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Medical geneticsMixed-model association for biobank-scale datasets2018https://www.nature.com/articles/s41588-018-0144-6
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Medical geneticsGenetic mechanisms of critical illness in COVID-192020https://www.nature.com/articles/s41586-020-03065-y
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Medical geneticsGenetic regulatory variation in populations informs transcriptome analysis in rare disease2019https://science.sciencemag.org/content/366/6463/351.abstract
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Medical genetics / Mendelian RandomizationAppraising the causal role of smoking in multiple diseases: A systematic review and meta-analysis of Mendelian randomization studies2022https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(22)00335-8/fulltext
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Medical genetics / Polygenic Risk ScoresDeveloping and evaluating polygenic risk prediction models for stratified disease prevention2018https://www.nature.com/articles/nrg.2016.27
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MicrobiomeData Augmentation for Compositional Data: Advancing Predictive Models of the Microbiome2022https://arxiv.org/abs/2205.09906
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MicrobiomeAccurate identification of bacteriophages from metagenomic data using Transformer2022https://pubmed.ncbi.nlm.nih.gov/35769000/
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MicrobiomembImpute: an accurate and robust imputation method for microbiome data2021https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02400-4
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RNA-Seq Analysis (spatial, scRNAseq)Spatial transcriptomics at subspot resolution with BayesSpace2021https://www.nature.com/articles/s41587-021-00935-2
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RNA-Seq Analysis (spatial, scRNAseq)Cell2location maps fine-grained cell types in spatial transcriptomics2022https://doi.org/10.1038/s41587-021-01139-4
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