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RResolver: efficient short-read repeat resolution within ABySS.
Nikolić V, Afshinfard A, Chu J, Wong J, Coombe L, Nip KM, Warren RL, Birol I. Nikolić V, et al. Among authors: nip km. BMC Bioinformatics. 2022 Jun 21;23(1):246. doi: 10.1186/s12859-022-04790-z. BMC Bioinformatics. 2022. PMID: 35729491 Free PMC article.
Complete genomic landscape of a recurring sporadic parathyroid carcinoma.
Kasaian K, Wiseman SM, Thiessen N, Mungall KL, Corbett RD, Qian JQ, Nip KM, He A, Tse K, Chuah E, Varhol RJ, Pandoh P, McDonald H, Zeng T, Tam A, Schein J, Birol I, Mungall AJ, Moore RA, Zhao Y, Hirst M, Marra MA, Walker BA, Jones SJ. Kasaian K, et al. Among authors: nip km. J Pathol. 2013 Jul;230(3):249-60. doi: 10.1002/path.4203. J Pathol. 2013. PMID: 23616356
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.
Swanson L, Robertson G, Mungall KL, Butterfield YS, Chiu R, Corbett RD, Docking TR, Hogge D, Jackman SD, Moore RA, Mungall AJ, Nip KM, Parker JD, Qian JQ, Raymond A, Sung S, Tam A, Thiessen N, Varhol R, Wang S, Yorukoglu D, Zhao Y, Hoodless PA, Sahinalp SC, Karsan A, Birol I. Swanson L, et al. Among authors: nip km. BMC Genomics. 2013 Aug 14;14:550. doi: 10.1186/1471-2164-14-550. BMC Genomics. 2013. PMID: 23941359 Free PMC article.
Kleat: cleavage site analysis of transcriptomes.
Birol I, Raymond A, Chiu R, Nip KM, Jackman SD, Kreitzman M, Docking TR, Ennis CA, Robertson AG, Karsan A. Birol I, et al. Among authors: nip km. Pac Symp Biocomput. 2015:347-58. Pac Symp Biocomput. 2015. PMID: 25592595 Free PMC article.
Reduced adenosine-to-inosine miR-455-5p editing promotes melanoma growth and metastasis.
Shoshan E, Mobley AK, Braeuer RR, Kamiya T, Huang L, Vasquez ME, Salameh A, Lee HJ, Kim SJ, Ivan C, Velazquez-Torres G, Nip KM, Zhu K, Brooks D, Jones SJ, Birol I, Mosqueda M, Wen YY, Eterovic AK, Sood AK, Hwu P, Gershenwald JE, Robertson AG, Calin GA, Markel G, Fidler IJ, Bar-Eli M. Shoshan E, et al. Among authors: nip km. Nat Cell Biol. 2015 Mar;17(3):311-21. doi: 10.1038/ncb3110. Epub 2015 Feb 16. Nat Cell Biol. 2015. PMID: 25686251 Free PMC article.
Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection.
Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN; ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants; Kellen MR, Chen K, Norman TC, Friend SH, Guinney J, Stolovitzky G, Haussler D, Margolin AA, Stuart JM, Boutros PC. Lee AY, et al. Genome Biol. 2018 Nov 6;19(1):188. doi: 10.1186/s13059-018-1539-5. Genome Biol. 2018. PMID: 30400818 Free PMC article.
33 results