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Characterization of HPV and host genome interactions in primary head and neck cancers.
Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; Cancer Genome Atlas Network. Parfenov M, et al. Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15544-9. doi: 10.1073/pnas.1416074111. Epub 2014 Oct 13. Proc Natl Acad Sci U S A. 2014. PMID: 25313082 Free PMC article.
A probabilistic framework for aligning paired-end RNA-seq data.
Hu Y, Wang K, He X, Chiang DY, Prins JF, Liu J. Hu Y, et al. Among authors: liu j. Bioinformatics. 2010 Aug 15;26(16):1950-7. doi: 10.1093/bioinformatics/btq336. Epub 2010 Jun 23. Bioinformatics. 2010. PMID: 20576625 Free PMC article.
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM, MacLeod JN, Chiang DY, Prins JF, Liu J. Wang K, et al. Among authors: liu j. Nucleic Acids Res. 2010 Oct;38(18):e178. doi: 10.1093/nar/gkq622. Epub 2010 Aug 27. Nucleic Acids Res. 2010. PMID: 20802226 Free PMC article.
Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P; RGASP Consortium. Engström PG, et al. Nat Methods. 2013 Dec;10(12):1185-91. doi: 10.1038/nmeth.2722. Epub 2013 Nov 3. Nat Methods. 2013. PMID: 24185836 Free PMC article.
Cytoplasmic synthesis of endogenous Alu complementary DNA via reverse transcription and implications in age-related macular degeneration.
Fukuda S, Varshney A, Fowler BJ, Wang SB, Narendran S, Ambati K, Yasuma T, Magagnoli J, Leung H, Hirahara S, Nagasaka Y, Yasuma R, Apicella I, Pereira F, Makin RD, Magner E, Liu X, Sun J, Wang M, Baker K, Marion KM, Huang X, Baghdasaryan E, Ambati M, Ambati VL, Pandey A, Pandya L, Cummings T, Banerjee D, Huang P, Yerramothu P, Tolstonog GV, Held U, Erwin JA, Paquola ACM, Herdy JR, Ogura Y, Terasaki H, Oshika T, Darwish S, Singh RK, Mozaffari S, Bhattarai D, Kim KB, Hardin JW, Bennett CL, Hinton DR, Hanson TE, Röver C, Parang K, Kerur N, Liu J, Werner BC, Sutton SS, Sadda SR, Schumann GG, Gelfand BD, Gage FH, Ambati J. Fukuda S, et al. Among authors: liu j, liu x. Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):e2022751118. doi: 10.1073/pnas.2022751118. Proc Natl Acad Sci U S A. 2021. PMID: 33526699 Free PMC article.
Biclustering in gene expression data by tendency.
Liu J, Wang J, Wang W. Liu J, et al. Proc IEEE Comput Syst Bioinform Conf. 2004:182-93. doi: 10.1109/csb.2004.1332431. Proc IEEE Comput Syst Bioinform Conf. 2004. PMID: 16448012
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