Fast alignment and preprocessing of chromatin profiles with Chromap.
Zhang H, Song L, Wang X, Cheng H, Wang C, Meyer CA, Liu T, Tang M, Aluru S, Yue F, Liu XS, Li H.
Nat Commun. 2021 11 12. 12(1):6566. PMID: 34772935
Bibliography
TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data.
Song L, Cohen D, Ouyang Z, Cao Y, Hu X, Liu XS.
Nat Methods. 2021 06. 18(6):627-630. PMID: 33986545
Immune receptor repertoires in pediatric and adult acute myeloid leukemia.
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.
Genome Med. 2019 11 26. 11(1):73. PMID: 31771646
A multi-sample approach increases the accuracy of transcript assembly.
Song L, Sabunciyan S, Yang G, Florea L.
Nat Commun. 2019 11 01. 10(1):5000. PMID: 31676772
Genomic differences between nasal Staphylococcus aureus from hog slaughterhouse workers and their communities.
You Y, Song L, Nonyane BAS, Price LB, Silbergeld EK.
PLoS One. 2018. 13(3):e0193820. PMID: 29509797
Hybrid assembly with long and short reads improves discovery of gene family expansions.
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.
BMC Genomics. 2017 07 19. 18(1):541. PMID: 28724409
Rascaf: Improving Genome Assembly with RNA Sequencing Data.
Song L, Shankar DS, Florea L.
Plant Genome. 2016 11. 9(3). PMID: 27902792
Centrifuge: rapid and sensitive classification of metagenomic sequences.
Kim D, Song L, Breitwieser FP, Salzberg SL.
Genome Res. 2016 12. 26(12):1721-1729. PMID: 27852649
CLASS2: accurate and efficient splice variant annotation from RNA-seq reads.
Song L, Sabunciyan S, Florea L.
Nucleic Acids Res. 2016 06 02. 44(10):e98. PMID: 26975657
Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads.
Song L, Florea L.
Gigascience. 2015. 4:48. PMID: 26500767