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RSeQC: quality control of RNA-seq experiments.
Wang L, Wang S, Li W. Wang L, et al. Among authors: wang s. Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27. Bioinformatics. 2012. PMID: 22743226
CrossMap: a versatile tool for coordinate conversion between genome assemblies.
Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L. Zhao H, et al. Among authors: wang j, wang l. Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730. Epub 2013 Dec 18. Bioinformatics. 2014. PMID: 24351709 Free PMC article.
HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.
Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP. Yan H, et al. Among authors: wang l. BMC Bioinformatics. 2014 Aug 15;15(1):280. doi: 10.1186/1471-2105-15-280. BMC Bioinformatics. 2014. PMID: 25128017 Free PMC article.
Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer.
Sowalsky AG, Xia Z, Wang L, Zhao H, Chen S, Bubley GJ, Balk SP, Li W. Sowalsky AG, et al. Among authors: wang l. Mol Cancer Res. 2015 Jan;13(1):98-106. doi: 10.1158/1541-7786.MCR-14-0273. Epub 2014 Sep 4. Mol Cancer Res. 2015. PMID: 25189356 Free PMC article.
MACE: model based analysis of ChIP-exo.
Wang L, Chen J, Wang C, Uusk├╝la-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W. Wang L, et al. Among authors: wang c. Nucleic Acids Res. 2014 Nov 10;42(20):e156. doi: 10.1093/nar/gku846. Epub 2014 Sep 23. Nucleic Acids Res. 2014. PMID: 25249628 Free PMC article.
PVAAS: identify variants associated with aberrant splicing from RNA-seq.
Wang L, Nie JJ, Kocher JP. Wang L, et al. Bioinformatics. 2015 May 15;31(10):1668-70. doi: 10.1093/bioinformatics/btv001. Epub 2015 Jan 7. Bioinformatics. 2015. PMID: 25573917 Free PMC article.
Quality control of RNA-seq experiments.
Li X, Nair A, Wang S, Wang L. Li X, et al. Among authors: wang s, wang l. Methods Mol Biol. 2015;1269:137-46. doi: 10.1007/978-1-4939-2291-8_8. Methods Mol Biol. 2015. PMID: 25577376
Measure transcript integrity using RNA-seq data.
Wang L, Nie J, Sicotte H, Li Y, Eckel-Passow JE, Dasari S, Vedell PT, Barman P, Wang L, Weinshiboum R, Jen J, Huang H, Kohli M, Kocher JP. Wang L, et al. BMC Bioinformatics. 2016 Feb 3;17:58. doi: 10.1186/s12859-016-0922-z. BMC Bioinformatics. 2016. PMID: 26842848 Free PMC article.
CircularLogo: A lightweight web application to visualize intra-motif dependencies.
Ye Z, Ma T, Kalmbach MT, Dasari S, Kocher JA, Wang L. Ye Z, et al. Among authors: wang l. BMC Bioinformatics. 2017 May 22;18(1):269. doi: 10.1186/s12859-017-1680-2. BMC Bioinformatics. 2017. PMID: 28532394 Free PMC article.
Characterization and identification of long non-coding RNAs based on feature relationship.
Wang G, Yin H, Li B, Yu C, Wang F, Xu X, Cao J, Bao Y, Wang L, Abbasi AA, Bajic VB, Ma L, Zhang Z. Wang G, et al. Among authors: wang f, wang l. Bioinformatics. 2019 Sep 1;35(17):2949-2956. doi: 10.1093/bioinformatics/btz008. Bioinformatics. 2019. PMID: 30649200
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