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Items: 1 to 50 of 64

1.

CytoConverter: a web-based tool to convert karyotypes to genomic coordinates.

Wang J, LaFramboise T.

BMC Bioinformatics. 2019 Sep 11;20(1):467. doi: 10.1186/s12859-019-3062-4.

2.

Impact of germline CTC1 alterations on telomere length in acquired bone marrow failure.

Shen W, Kerr CM, Przychozen B, Mahfouz RZ, LaFramboise T, Nagata Y, Hanna R, Radivoyevitch T, Nazha A, Sekeres MA, Maciejewski JP.

Br J Haematol. 2019 Jun;185(5):935-939. doi: 10.1111/bjh.15862. Epub 2019 Mar 19.

PMID:
30891747
3.

Correction: A 32 kb Critical Region Excluding Y402H in CFH Mediates Risk for Age-Related Macular Degeneration.

Sivakumaran TA, Igo RP Jr, Kidd JM, Itsara A, Kopplin LJ, Chen W, Hagstrom SA, Peachey NS, Francis PJ, Klein ML, Chew EY, Ramprasad VL, Tay WT, Mitchell P, Seielstad M, Stambolian DE, Edwards AO, Lee KE, Leontiev DV, Jun G, Wang Y, Tian L, Qiu F, Henning AK, LaFramboise T, Sen P, Aarthi M, George R, Raman R, Das MK, Vijaya L, Kumaramanickavel G, Wong TY, Swaroop A, Abecasis GR, Klein R, Klein BEK, Nickerson DA, Eichler EE, Iyengar SK.

PLoS One. 2018 Dec 20;13(12):e0209943. doi: 10.1371/journal.pone.0209943. eCollection 2018.

4.

The DNMT1-associated lincRNA DACOR1 reprograms genome-wide DNA methylation in colon cancer.

Somasundaram S, Forrest ME, Moinova H, Cohen A, Varadan V, LaFramboise T, Markowitz S, Khalil AM.

Clin Epigenetics. 2018 Oct 22;10(1):127. doi: 10.1186/s13148-018-0555-3.

5.

Germline loss-of-function SAMD9 and SAMD9L alterations in adult myelodysplastic syndromes.

Nagata Y, Narumi S, Guan Y, Przychodzen BP, Hirsch CM, Makishima H, Shima H, Aly M, Pastor V, Kuzmanovic T, Radivoyevitch T, Adema V, Awada H, Yoshida K, Li S, Sole F, Hanna R, Jha BK, LaFramboise T, Ogawa S, Sekeres MA, Wlodarski MW, Cammenga J, Maciejewski JP.

Blood. 2018 Nov 22;132(21):2309-2313. doi: 10.1182/blood-2017-05-787390. Epub 2018 Oct 15. No abstract available.

PMID:
30322869
6.

Mitochondrial genomics in the cancer cell line encyclopedia and a scoring method to effectively pair cell lines for cytoplasmic hybridization.

Grandhi S, Gould L, Wang J, Grandhi A, LaFramboise T.

Mitochondrion. 2019 May;46:256-261. doi: 10.1016/j.mito.2018.07.005. Epub 2018 Jul 31.

PMID:
30075297
7.

Consequences of mutant TET2 on clonality and subclonal hierarchy.

Hirsch CM, Nazha A, Kneen K, Abazeed ME, Meggendorfer M, Przychodzen BP, Nadarajah N, Adema V, Nagata Y, Goyal A, Awada H, Asad MF, Visconte V, Guan Y, Sekeres MA, Olinski R, Jha BK, LaFramboise T, Radivoyevitch T, Haferlach T, Maciejewski JP.

Leukemia. 2018 Aug;32(8):1751-1761. doi: 10.1038/s41375-018-0150-9. Epub 2018 May 24.

PMID:
29795413
8.

Colon Cancer-Upregulated Long Non-Coding RNA lincDUSP Regulates Cell Cycle Genes and Potentiates Resistance to Apoptosis.

Forrest ME, Saiakhova A, Beard L, Buchner DA, Scacheri PC, LaFramboise T, Markowitz S, Khalil AM.

Sci Rep. 2018 May 9;8(1):7324. doi: 10.1038/s41598-018-25530-5.

9.

Unexpected cancer-predisposition gene variants in Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome patients without underlying germline PTEN mutations.

Yehia L, Ni Y, Sesock K, Niazi F, Fletcher B, Chen HJL, LaFramboise T, Eng C.

PLoS Genet. 2018 Apr 23;14(4):e1007352. doi: 10.1371/journal.pgen.1007352. eCollection 2018 Apr.

10.

Identifying DNA methylation biomarkers for non-endoscopic detection of Barrett's esophagus.

Moinova HR, LaFramboise T, Lutterbaugh JD, Chandar AK, Dumot J, Faulx A, Brock W, De la Cruz Cabrera O, Guda K, Barnholtz-Sloan JS, Iyer PG, Canto MI, Wang JS, Shaheen NJ, Thota PN, Willis JE, Chak A, Markowitz SD.

Sci Transl Med. 2018 Jan 17;10(424). pii: eaao5848. doi: 10.1126/scitranslmed.aao5848.

11.

Detection and quantification of mitochondrial DNA deletions from next-generation sequence data.

Bosworth CM, Grandhi S, Gould MP, LaFramboise T.

BMC Bioinformatics. 2017 Oct 16;18(Suppl 12):407. doi: 10.1186/s12859-017-1821-7.

12.

The REPAIR Project: Examining the Biological Impacts of Sub-Background Radiation Exposure within SNOLAB, a Deep Underground Laboratory.

Thome C, Tharmalingam S, Pirkkanen J, Zarnke A, Laframboise T, Boreham DR.

Radiat Res. 2017 Oct;188(4.2):470-474. doi: 10.1667/RR14654.1. Epub 2017 Jul 19.

PMID:
28723273
13.

Genomic determinants of chronic myelomonocytic leukemia.

Patel BJ, Przychodzen B, Thota S, Radivoyevitch T, Visconte V, Kuzmanovic T, Clemente M, Hirsch C, Morawski A, Souaid R, Saygin C, Nazha A, Demarest B, LaFramboise T, Sakaguchi H, Kojima S, Carraway HE, Ogawa S, Makishima H, Sekeres MA, Maciejewski JP.

Leukemia. 2017 Dec;31(12):2815-2823. doi: 10.1038/leu.2017.164. Epub 2017 May 30.

PMID:
28555081
14.

Heteroplasmic shifts in tumor mitochondrial genomes reveal tissue-specific signals of relaxed and positive selection.

Grandhi S, Bosworth C, Maddox W, Sensiba C, Akhavanfard S, Ni Y, LaFramboise T.

Hum Mol Genet. 2017 Aug 1;26(15):2912-2922. doi: 10.1093/hmg/ddx172.

15.

Selected mitochondrial DNA landscapes activate the SIRT3 axis of the UPRmt to promote metastasis.

Kenny TC, Hart P, Ragazzi M, Sersinghe M, Chipuk J, Sagar MAK, Eliceiri KW, LaFramboise T, Grandhi S, Santos J, Riar AK, Papa L, D'Aurello M, Manfredi G, Bonini MG, Germain D.

Oncogene. 2017 Aug;36(31):4393-4404. doi: 10.1038/onc.2017.52. Epub 2017 Apr 3.

16.

Molecular features of early onset adult myelodysplastic syndrome.

Hirsch CM, Przychodzen BP, Radivoyevitch T, Patel B, Thota S, Clemente MJ, Nagata Y, LaFramboise T, Carraway HE, Nazha A, Sekeres MA, Makishima H, Maciejewski JP.

Haematologica. 2017 Jun;102(6):1028-1034. doi: 10.3324/haematol.2016.159772. Epub 2017 Mar 2.

17.

Visually Meaningful Histopathological Features for Automatic Grading of Prostate Cancer.

Niazi MKK, Keluo Yao, Zynger DL, Clinton SK, Chen J, Koyuturk M, LaFramboise T, Gurcan M.

IEEE J Biomed Health Inform. 2017 Jul;21(4):1027-1038. doi: 10.1109/JBHI.2016.2565515. Epub 2016 May 10. Erratum in: IEEE J Biomed Health Inform. 2017 Sep;21(5):1473-1474.

PMID:
28113734
18.

Recurrent genetic defects on chromosome 5q in myeloid neoplasms.

Hosono N, Makishima H, Mahfouz R, Przychodzen B, Yoshida K, Jerez A, LaFramboise T, Polprasert C, Clemente MJ, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Sanada M, Cui E, Verma AK, McDevitt MA, List AF, Saunthararajah Y, Sekeres MA, Boultwood J, Ogawa S, Maciejewski JP.

Oncotarget. 2017 Jan 24;8(4):6483-6495. doi: 10.18632/oncotarget.14130.

19.

Germline compound heterozygous poly-glutamine deletion in USF3 may be involved in predisposition to heritable and sporadic epithelial thyroid carcinoma.

Ni Y, Seballos S, Fletcher B, Romigh T, Yehia L, Mester J, Senter L, Niazi F, Saji M, Ringel MD, LaFramboise T, Eng C.

Hum Mol Genet. 2017 Jan 15;26(2):243-257. doi: 10.1093/hmg/ddw382.

20.

Dynamics of clonal evolution in myelodysplastic syndromes.

Makishima H, Yoshizato T, Yoshida K, Sekeres MA, Radivoyevitch T, Suzuki H, Przychodzen B, Nagata Y, Meggendorfer M, Sanada M, Okuno Y, Hirsch C, Kuzmanovic T, Sato Y, Sato-Otsubo A, LaFramboise T, Hosono N, Shiraishi Y, Chiba K, Haferlach C, Kern W, Tanaka H, Shiozawa Y, Gómez-Seguí I, Husseinzadeh HD, Thota S, Guinta KM, Dienes B, Nakamaki T, Miyawaki S, Saunthararajah Y, Chiba S, Miyano S, Shih LY, Haferlach T, Ogawa S, Maciejewski JP.

Nat Genet. 2017 Feb;49(2):204-212. doi: 10.1038/ng.3742. Epub 2016 Dec 19.

PMID:
27992414
21.

Phase I/II study of azacitidine and capecitabine/oxaliplatin (CAPOX) in refractory CIMP-high metastatic colorectal cancer: evaluation of circulating methylated vimentin.

Overman MJ, Morris V, Moinova H, Manyam G, Ensor J, Lee MS, Eng C, Kee B, Fogelman D, Shroff RT, LaFramboise T, Mazard T, Feng T, Hamilton S, Broom B, Lutterbaugh J, Issa JP, Markowitz SD, Kopetz S.

Oncotarget. 2016 Oct 11;7(41):67495-67506. doi: 10.18632/oncotarget.11317.

22.

Pluribus-Exploring the Limits of Error Correction Using a Suffix Tree.

Savel D, LaFramboise T, Grama A, Koyuturk M.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Nov-Dec;14(6):1378-1388. doi: 10.1109/TCBB.2016.2586060. Epub 2016 Jun 29.

23.

Oncogenic PIK3CA mutations reprogram glutamine metabolism in colorectal cancer.

Hao Y, Samuels Y, Li Q, Krokowski D, Guan BJ, Wang C, Jin Z, Dong B, Cao B, Feng X, Xiang M, Xu C, Fink S, Meropol NJ, Xu Y, Conlon RA, Markowitz S, Kinzler KW, Velculescu VE, Brunengraber H, Willis JE, LaFramboise T, Hatzoglou M, Zhang GF, Vogelstein B, Wang Z.

Nat Commun. 2016 Jun 20;7:11971. doi: 10.1038/ncomms11971.

24.

Correction: PCR-Free Enrichment of Mitochondrial DNA from Human Blood and Cell Lines for High Quality Next-Generation DNA Sequencing.

Gould MP, Bosworth CM, McMahon S, Grandhi S, Grimberg BT, LaFramboise T.

PLoS One. 2016 May 31;11(5):e0156884. doi: 10.1371/journal.pone.0156884. eCollection 2016.

25.

PCR-Free Enrichment of Mitochondrial DNA from Human Blood and Cell Lines for High Quality Next-Generation DNA Sequencing.

Gould MP, Bosworth CM, McMahon S, Grandhi S, Grimberg BT, LaFramboise T.

PLoS One. 2015 Oct 21;10(10):e0139253. doi: 10.1371/journal.pone.0139253. eCollection 2015. Erratum in: PLoS One. 2016 May 31;11(5):e0156884.

26.

Whole-exome sequencing enhances prognostic classification of myeloid malignancies.

Ruffalo M, Husseinzadeh H, Makishima H, Przychodzen B, Ashkar M, Koyutürk M, Maciejewski JP, LaFramboise T.

J Biomed Inform. 2015 Dec;58:104-113. doi: 10.1016/j.jbi.2015.10.003. Epub 2015 Oct 8.

27.

Germline and somatic SDHx alterations in apparently sporadic differentiated thyroid cancer.

Ni Y, Seballos S, Ganapathi S, Gurin D, Fletcher B, Ngeow J, Nagy R, Kloos RT, Ringel MD, LaFramboise T, Eng C.

Endocr Relat Cancer. 2015 Apr;22(2):121-30. doi: 10.1530/ERC-14-0537.

28.

Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing.

Liu Y, Koyutürk M, Maxwell S, Xiang M, Veigl M, Cooper RS, Tayo BO, Li L, LaFramboise T, Wang Z, Zhu X, Chance MR.

BMC Genomics. 2014 Aug 16;15:685. doi: 10.1186/1471-2164-15-685.

29.

DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads.

Yavaş G, Koyutürk M, Gould MP, McMahon S, LaFramboise T.

BMC Genomics. 2014 Mar 5;15:175. doi: 10.1186/1471-2164-15-175.

30.

Mutational patterns in the breast cancer mitochondrial genome, with clinical correlates.

McMahon S, LaFramboise T.

Carcinogenesis. 2014 May;35(5):1046-54. doi: 10.1093/carcin/bgu012. Epub 2014 Jan 18.

31.

Integrative eQTL-based analyses reveal the biology of breast cancer risk loci.

Li Q, Seo JH, Stranger B, McKenna A, Pe'er I, Laframboise T, Brown M, Tyekucheva S, Freedman ML.

Cell. 2013 Jan 31;152(3):633-41. doi: 10.1016/j.cell.2012.12.034. Review.

32.

Accurate estimation of short read mapping quality for next-generation genome sequencing.

Ruffalo M, Koyutürk M, Ray S, LaFramboise T.

Bioinformatics. 2012 Sep 15;28(18):i349-i355. doi: 10.1093/bioinformatics/bts408.

33.

Activation of the AXL kinase causes resistance to EGFR-targeted therapy in lung cancer.

Zhang Z, Lee JC, Lin L, Olivas V, Au V, LaFramboise T, Abdel-Rahman M, Wang X, Levine AD, Rho JK, Choi YJ, Choi CM, Kim SW, Jang SJ, Park YS, Kim WS, Lee DH, Lee JS, Miller VA, Arcila M, Ladanyi M, Moonsamy P, Sawyers C, Boggon TJ, Ma PC, Costa C, Taron M, Rosell R, Halmos B, Bivona TG.

Nat Genet. 2012 Jul 1;44(8):852-60. doi: 10.1038/ng.2330.

34.

Characterizing mutational heterogeneity in a glioblastoma patient with double recurrence.

Nickel GC, Barnholtz-Sloan J, Gould MP, McMahon S, Cohen A, Adams MD, Guda K, Cohen M, Sloan AE, LaFramboise T.

PLoS One. 2012;7(4):e35262. doi: 10.1371/journal.pone.0035262. Epub 2012 Apr 20.

35.

Epigenomic enhancer profiling defines a signature of colon cancer.

Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, Saiakhova A, Bartels CF, Balasubramanian D, Myeroff L, Lutterbaugh J, Jarrar A, Kalady MF, Willis J, Moore JH, Tesar PJ, Laframboise T, Markowitz S, Lupien M, Scacheri PC.

Science. 2012 May 11;336(6082):736-9. doi: 10.1126/science.1217277. Epub 2012 Apr 12.

36.

Calling amplified haplotypes in next generation tumor sequence data.

Dewal N, Hu Y, Freedman ML, Laframboise T, Pe'er I.

Genome Res. 2012 Feb;22(2):362-74. doi: 10.1101/gr.122564.111. Epub 2011 Nov 16.

37.

A 32 kb critical region excluding Y402H in CFH mediates risk for age-related macular degeneration.

Sivakumaran TA, Igo RP Jr, Kidd JM, Itsara A, Kopplin LJ, Chen W, Hagstrom SA, Peachey NS, Francis PJ, Klein ML, Chew EY, Ramprasad VL, Tay WT, Mitchell P, Seielstad M, Stambolian DE, Edwards AO, Lee KE, Leontiev DV, Jun G, Wang Y, Tian L, Qiu F, Henning AK, LaFramboise T, Sen P, Aarthi M, George R, Raman R, Das MK, Vijaya L, Kumaramanickavel G, Wong TY, Swaroop A, Abecasis GR, Klein R, Klein BE, Nickerson DA, Eichler EE, Iyengar SK.

PLoS One. 2011;6(10):e25598. doi: 10.1371/journal.pone.0025598. Epub 2011 Oct 12. Erratum in: PLoS One. 2018 Dec 20;13(12):e0209943.

38.

Losing balance: Hardy-Weinberg disequilibrium as a marker for recurrent loss-of-heterozygosity in cancer.

Wilkins K, LaFramboise T.

Hum Mol Genet. 2011 Dec 15;20(24):4831-9. doi: 10.1093/hmg/ddr422. Epub 2011 Sep 14.

39.

Comparative analysis of algorithms for next-generation sequencing read alignment.

Ruffalo M, LaFramboise T, Koyutürk M.

Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477. Epub 2011 Aug 19.

PMID:
21856737
40.

Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis.

LaFramboise T, Dewal N, Wilkins K, Pe'er I, Freedman ML.

PLoS Genet. 2010 Sep 2;6(9):e1001086. doi: 10.1371/journal.pgen.1001086.

41.

CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression.

Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T, Tesar P, Wei CL, Scacheri PC.

PLoS Genet. 2010 Jul 15;6(7):e1001023. doi: 10.1371/journal.pgen.1001023.

42.

Dual specificity phosphatase 6 (DUSP6) is an ETS-regulated negative feedback mediator of oncogenic ERK signaling in lung cancer cells.

Zhang Z, Kobayashi S, Borczuk AC, Leidner RS, Laframboise T, Levine AD, Halmos B.

Carcinogenesis. 2010 Apr;31(4):577-86. doi: 10.1093/carcin/bgq020. Epub 2010 Jan 22.

43.

Power to detect selective allelic amplification in genome-wide scans of tumor data.

Dewal N, Freedman ML, LaFramboise T, Pe'er I.

Bioinformatics. 2010 Feb 15;26(4):518-28. doi: 10.1093/bioinformatics/btp694. Epub 2009 Dec 23.

44.

COKGEN: a software for the identification of rare copy number variation from SNP microarrays.

Yavaş G, Koyutürk M, Ozsoyoğlu M, Gould MP, Laframboise T.

Pac Symp Biocomput. 2010:371-82.

45.

An optimization framework for unsupervised identification of rare copy number variation from SNP array data.

Yavas G, Koyutürk M, Ozsoyoğlu M, Gould MP, LaFramboise T.

Genome Biol. 2009;10(10):R119. doi: 10.1186/gb-2009-10-10-r119. Epub 2009 Oct 23.

46.

Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances.

LaFramboise T.

Nucleic Acids Res. 2009 Jul;37(13):4181-93. doi: 10.1093/nar/gkp552. Epub 2009 Jul 1.

47.

Predicting drug susceptibility of non-small cell lung cancers based on genetic lesions.

Sos ML, Michel K, Zander T, Weiss J, Frommolt P, Peifer M, Li D, Ullrich R, Koker M, Fischer F, Shimamura T, Rauh D, Mermel C, Fischer S, Stückrath I, Heynck S, Beroukhim R, Lin W, Winckler W, Shah K, LaFramboise T, Moriarty WF, Hanna M, Tolosi L, Rahnenführer J, Verhaak R, Chiang D, Getz G, Hellmich M, Wolf J, Girard L, Peyton M, Weir BA, Chen TH, Greulich H, Barretina J, Shapiro GI, Garraway LA, Gazdar AF, Minna JD, Meyerson M, Wong KK, Thomas RK.

J Clin Invest. 2009 Jun;119(6):1727-40. doi: 10.1172/JCI37127. Epub 2009 May 18.

48.

Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns.

Schnetz MP, Bartels CF, Shastri K, Balasubramanian D, Zentner GE, Balaji R, Zhang X, Song L, Wang Z, Laframboise T, Crawford GE, Scacheri PC.

Genome Res. 2009 Apr;19(4):590-601. doi: 10.1101/gr.086983.108. Epub 2009 Feb 27.

49.

A flexible rank-based framework for detecting copy number aberrations from array data.

LaFramboise T, Winckler W, Thomas RK.

Bioinformatics. 2009 Mar 15;25(6):722-8. doi: 10.1093/bioinformatics/btp063. Epub 2009 Jan 28.

50.

The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3' mRNA processing factors.

Rozenblatt-Rosen O, Nagaike T, Francis JM, Kaneko S, Glatt KA, Hughes CM, LaFramboise T, Manley JL, Meyerson M.

Proc Natl Acad Sci U S A. 2009 Jan 20;106(3):755-60. doi: 10.1073/pnas.0812023106. Epub 2009 Jan 9.

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