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Li Song, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Zhang H, Song L, Wang X, Cheng H, Wang C, Meyer CA, Liu T, Tang M, Aluru S, Yue F, Liu XS, Li H. Fast alignment and preprocessing of chromatin profiles with Chromap. Nat Commun. 2021 11 12; 12(1):6566. PMID: 34772935; PMCID: PMC8589834.
    Citations: 5     Fields:    Translation:HumansCells
  2. Song L, Cohen D, Ouyang Z, Cao Y, Hu X, Liu XS. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nat Methods. 2021 06; 18(6):627-630. PMID: 33986545; PMCID: PMC9328942.
    Citations: 21     Fields:    
  3. Zhang J, Hu X, Wang J, Sahu AD, Cohen D, Song L, Ouyang Z, Fan J, Wang B, Fu J, Gu S, Sade-Feldman M, Hacohen N, Li W, Ying X, Li B, Liu XS. Immune receptor repertoires in pediatric and adult acute myeloid leukemia. Genome Med. 2019 11 26; 11(1):73. PMID: 31771646.
    Citations: 19     Fields:    Translation:HumansCells
  4. Song L, Sabunciyan S, Yang G, Florea L. A multi-sample approach increases the accuracy of transcript assembly. Nat Commun. 2019 11 01; 10(1):5000. PMID: 31676772.
    Citations: 8     Fields:    Translation:Humans
  5. 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; 13(3):e0193820. PMID: 29509797.
    Citations: 3     Fields:    Translation:HumansAnimalsCellsPHPublic Health
  6. Miller JR, Zhou P, Mudge J, Gurtowski J, Lee H, Ramaraj T, Walenz BP, Liu J, Stupar RM, Denny R, Song L, Singh N, Maron LG, McCouch SR, McCombie WR, Schatz MC, Tiffin P, Young ND, Silverstein KAT. Hybrid assembly with long and short reads improves discovery of gene family expansions. BMC Genomics. 2017 07 19; 18(1):541. PMID: 28724409.
    Citations: 19     Fields:    Translation:AnimalsCells
  7. Song L, Shankar DS, Florea L. Rascaf: Improving Genome Assembly with RNA Sequencing Data. Plant Genome. 2016 11; 9(3). PMID: 27902792.
    Citations: 16     Fields:    
  8. Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 2016 12; 26(12):1721-1729. PMID: 27852649; PMCID: PMC5131823.
    Citations: 373     Fields:    Translation:Cells
  9. Song L, Sabunciyan S, Florea L. CLASS2: accurate and efficient splice variant annotation from RNA-seq reads. Nucleic Acids Res. 2016 06 02; 44(10):e98. PMID: 26975657; PMCID: PMC4889935.
    Citations: 24     Fields:    Translation:HumansAnimalsCells
  10. Song L, Florea L. Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. Gigascience. 2015; 4:48. PMID: 26500767.
    Citations: 138     Fields:    
  11. Song L, Florea L, Langmead B. Lighter: fast and memory-efficient sequencing error correction without counting. Genome Biol. 2014; 15(11):509. PMID: 25398208; PMCID: PMC4248469.
    Citations: 88     Fields:    Translation:Humans
  12. Florea L, Song L, Salzberg SL. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000Res. 2013; 2:188. PMID: 24555089; PMCID: PMC3892928.
    Citations: 185     Fields:    
  13. Song L, Florea L. CLASS: constrained transcript assembly of RNA-seq reads. BMC Bioinformatics. 2013; 14 Suppl 5:S14. PMID: 23734605.
    Citations: 13     Fields:    Translation:HumansCells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.