Publications

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# Co-First authors;

Journal Publications

• Song L*, Langmead B, Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification, Genome Biol. 2024 Apr 25;25(1):106. [PubMed] (Best Paper Award at RECOMB2024) (*:corresponding author)
• Yu X, Song L#, …, Wang X, Pan-cancer γδ TCR analysis uncovers clonotype diversity and prognostic potential, Cell Reports Medicine, 2024 Oct 4. [Full text]
• Zhou Y, Song L and Li H, Full resolution HLA and KIR genes annotation for human genome assemblies, Genome Res. 2024 Jun 5:gr.278985.124. [PubMed]
• Song L, Bai G, Liu XS, Li B and Li H, Efficient and accurate KIR and HLA genotyping with massive parallel sequencing data. Genome Res. 2023 Jun;33(6):923-931. [PubMed]
• Yang L, Wang J, Altreuter J, Jhaveri A, …, Song L, …, Liu Y, Liu XS, Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA. Nat Protoc. 2023 Jun 30. [PubMed]
• Song L, Ouyang Z, Cohen D, Yang C, …, Liu XS, Comprehensive characterizations of immune receptor repertoire in tumors and cancer immunotherapy studies. Cancer Immunol Res. 2022 Jul 1;10(7):788-799. [PubMed]
• Song L, Cohen, D, Ouyang, Z, Cao, Y, Hu, X and Liu, XS, TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nat Methods. 2021 Jun;18(6):627-630. [PubMed]
• Zhang H, Song L#, …, Liu XS, Li H, Fast alignment and preprocessing of chromatin profiles with Chromap. Nat Commun. 2021 Nov 12;12(1):6566. [PubMed]
• Song L, Sabunciyan S, Yang G and Florea L, A multi-sample approach increases the accuracy of transcript assembly. Nat Commun. 2019 Nov 1;10(1):5000. [PubMed]
• Zhang J, Hu X, …, Song L, …, Liu XS, Immune receptor repertoires in pediatric and adult acute myeloid leukemia. Genome Med. 2019 Nov 26;11(1):73. [PubMed]
• You Y, Song L, Nonyane, BAS, Price, LB, Silbergeld EK, Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities, PLoS One. 2018 Mar 6;13(3):e0193820. [PubMed]
• Miller JR, Zhou P, Mudge J, …, Song L, …, Silverstein KAT, Hybrid assembly with long and short reads improves discovery of gene family expansions, BMC Genomics. 2017;18(1):541. [PubMed]
• Song L, Sabunciyan S and Florea L, CLASS2: accurate and efficient splice variant annotation from RNA-seq reads, Nucleic Acids Res. 2016;44(10):e98. [PubMed]
• Song L, Shankar D and Florea L, Rascaf: improving genome assembly with RNA-seq data, Plant Genome. 2016;9(3). [PubMed]
• Kim D, Song L#, Breitweiser FP and Salzberg SL, Centrifuge: rapid and sensitive classification of metagenomic sequences, Genome Res. 2016; 26(12): 1721-1729. [PubMed]
• Song L and Florea L, Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads, Gigascience. 2015;4:48. [PubMed]
• Song L, Florea L and Langmead B, Lighter: fast and memory-efficient sequencing error correction without Counting, Genome Biol. 2014;15(11):509. [PubMed]
• Song L and Florea L, CLASS: constrained transcript assembly of RNA-seq reads, Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing - RECOMB-SEQ 2013, BMC Bioinformatics 14(Suppl 5):S14. [PubMed]
• Florea L, Song L and Salzberg SL, Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues, F1000 Research 2013, 2:188. [Full text]

Preprints

• Abdullah L, Emilani F, Vaidya C, …, Song L, …, Huang Y, Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infection, Biorxiv, 2024. [Full text]