2015

Al-Tassan, NA, Whiffin N, Hosking FJ, Palles C, Farrington SM, Dobbins SE, Harris R, Gorman M, Tenesa A, Meyer BF, Salma M. Wakil SM, Kinnersley B, Campbell H, Martin L, Smith CG,  Idziaszczyk S, Barclay E,  Maughan TS, Kaplan R, Kerr R, Kerr D,Buchannan DD, Win AK, Hopper J, Jenkins M, Lindor NM,Newcomb PA, Gallinger S, Conti D, Schumacher F, Casey G,  Dunlop MG, Tomlinson IP, Cheadle JP, & Houlston RS. A new GWAS and meta-analysis with 1000Genomes imputation identifies novel risk variants for colorectal cancer. Sci. Rep. 2015 5, 10442

Katainen R, Dave K, Pitkänen E, Palin K,  Kivioja T, Välimäki N, Gylfe A, Ristolainen H, Hänninen UA, Cajuso T, Kondelin J, Tanskanen T, Mecklin JP, Järvinen H,  Renkonen-Sinisalo H, Lepistö A, Kaasinen E, Kilpivaara O, Tuupanen S, Enge M,  Taipale J & Aaltonen LA. CTCF/cohesin-binding sites are frequently mutated in cancer. Nat Genet. 2015 Jun 8.

Kondelin J, Tuupanen S, Gylfe AE, Aavikko M, Renkonen-Sinisalo L, Järvinen H, Böhm J, Mecklin JP, Andersen CL, Vahteristo P, Pitkänen E, Aaltonen LA. 3′-UTR poly(T/U) repeat of EWSR1 is altered in microsatellite
unstable colorectal cancer with nearly perfect sensitivity. Fam Cancer. 2015 May 1.

Tanskanen T, Gylfe AE,  Katainen R,  Taipale M, Renkonen-Sinisalo L,  Järvinen H, Mecklin JP, Böhm J,  Kilpivaara O,  Pitkänen E,  Palin K,  Vahteristo P,  Tuupanen S, Aaltonen LA. Systematic search for rare variants in Finnish early-onset colorectal cancer patients. Cancer Genet. 2015 Jan-Feb;208(1-2):35-40.

Jäger R, Migliorini G, Henrion M, Kandaswamy R, Speedy HE, Heindl A,Whiffin N, Carnicer MJ, Broome L, Dryden N,Nagano T, Schoenfelder S, Enge M, Yuan Y, Taipale J, Fraser P, Fletcher O, Houlston RS. Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci. Nat Commun 2015 Feb 19;6:6178.

Chubb D, Broderick P, Frampton M, Kinnersley B, Sherborne A, Penegar S, Lloyd A, Ma YP, Dobbins SE, Houlston RS. Genetic Diagnosis of High-Penetrance Susceptibility for Colorectal Cancer (CRC) Is Achievable for a High Proportion of Familial CRC by Exome Sequencing. J Clin Oncol 2015 Feb 10;33(5):426-32.

Hubner NC, Nguyen LN, Hornig NC, Stunnenberg HG. A Quantitative Proteomics Tool To Identify DNA-Protein Interactions in Primary Cells or Blood. J Proteome Res 2015 Feb 6;14(2):1315-29.

Manor O and Segal E. GenoExp: a web tool for predicting gene expression levels from single nucleotide polymorphisms. Bioinformatics, 2015, Jan 30: 1–3.

2014

Wingender E, Schoeps T, Haubrock M and Dönitz J. TFClass: a classification of human transcriptionfactors and their rodent orthologs. Nucleic Acids Res 2015 Jan 28;43:D97-D102

Iliou MS, da Silva-Diz V, Carmona FJ, Ramalho-Carvalho J,  Heyn H,  Villanueva A,  Munoz P and Esteller M. Impaired DICER1 function promotes stemness and metastasis in colon cancer. Oncogene (2014) 33, 4003–4015

Scales M, Jäger R,  Migliorini G,  Houlston RS, Henrion MYR. visPIG – A Web Tool for Producing Multi-Region, Multi-Track, Multi-Scale Plots of Genetic Data. PLoS One 2014 Sept 10;9(9):07497

Lewis A, Freeman-Mills L, de la Calle-Mustienes E, Giraldez-Perez RM, Davis H, Jaeger E, Becker M, Hubner NC, Nguyen LN, Zeron-Medina J, Bond G, Stunnenberg HG, Carvajal JJ, Gomez-Skarmeta JL, Leedham S, Tomlinson I. A Polymorphic Enhancer near GREM1 Influences Bowel Cancer Risk through Differential CDX2 and TCF7L2 Binding. Cell reports 2014 8(4) 983-90

Tuupanen S, Hänninen UA, Kondelin J, von Nandelstadh P, Cajuso T, Gylfe AE, Katainen R, Tanskanen T, Ristolainen H, Böhm J, Mecklin J-P, Järvinen H, Renkonen-Sinisalo L, Andersen CL, Taipale M, Taipale J, Vahteristo P, Lehti K, Pitkänen E, Aaltonen LA. Identification of 33 candidate oncogenesby screening for base-specific mutations. Br J Cancer 2014 Aug 12.

Ongen H,  Andersen CL, Bramsen JB, Oster B, Rasmussen MH, Ferreira PG, Sandoval J, Vidal E, Whiffin N, Planchon A, Padioleau I, Bielser D, Romano L, Tomlinson I, Houlston RS, Esteller M, Orntoft TF & Dermitzakis ET. Putative cis-regulatory drivers in colorectal cancer. Nature 2014 512: 87-90.

Menafra R,  Brinkman AB,  Matarese F,  Franci G, Bartels SJJ,  Nguyen L,  Shimbo T, Wade PA,  Hubner NC, Stunnenberg HG. Genome-Wide Binding of MBD2 Reveals Strong Preference for Highly Methylated Loci. PLoS One 2014 Jun 13;9(6):e99603.

Christensen LL,  Holm A,  Rantala J,  Kallioniemi O,  Rasmussen MH, Ostenfeld MS,  Dagnaes-Hansen F,  Øster B,  Schepeler T,  Tobiasen H,  Thorsen K,  Sieber OM,  Gibbs P,  Lamy P, Hansen TF, Jakobsen A,  Riising EM,  Helin K,  Lubinski J,  Hagemann-Madsen R, Laurberg S,  Ørntoft TF,  Andersen CL. Functional Screening Identifies miRNAs Influencing Apoptosis and Proliferation in Colorectal Cancer. PLoS One 2014 Jun 3;9(6):e96767.

Haber DA and Velculescu VE. Blood-Based Analyses of Cancer: Circulating Tumor Cells and Circulating Tumor DNA. Cancer Discov 2014 May 6. [Epub ahead of print]

Lopez-Serra P, Marcilla M, Villanueva A, Ramos-Fernandez A, Palau A, Leal L, Wahi JE, Fernando Setien-Baranda F, Karolina Szczesna K, Catia Moutinho C, Martinez-Cardus A, Heyn H, Sandoval J, Puertas S, Vidal A, Sanjuan X, Martinez-Balibrea E, Vinals F, Perales JC, Bramsem JB, Ørntoft TF, Andersen CL, Tabernero J, McDermott U, Boxer MB, Vander Heiden MG, Pablo Albar J, Esteller M.  A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect. Nature Comm 2014 Apr 3;5:3608.

Whiffin N, Hosking FJ, Farrington SM, Palles C, Dobbins SE, Zgaga L, Lloyd A, Kinnersley B, Gorman M, Tenesa A, Broderick P, Wang Y, Barclay E, Hayward C, Martin L, Buchanan DD, Ko Win A, Hopper J, Jenkins M, Lindor NM, Newcomb PA, Gallinger S, Conti D, Schumacher F, Casey G, Liu T, The Swedish Low-Risk Colorectal Cancer Study Group, Campbell H, Lindblom A, Houlston RS, Tomlinson IP, Dunlop MG.  Identification of susceptibility loci for colorectal cancer in a genome-wide meta-analysis. Hum Mol Genet. 2014 Apr 29. [Epub ahead of print]

Pitkänen E, Cajuso T, Katainen R, Kaasinen E, Välimäki N, Palin K, Taipale J, Aaltonen LA, and Kilpivaara O. Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer. Oncotarget 2014 Feb 15;5(3):853-9.

Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014 Feb 19;6(224):224ra24.

Shi Y, Nikulenkov F, Zawacka-Pankau J, Li H, Gabdoulline R, Xu J, Eriksson S, Hedström E, Issaeva N, Kel A, Arnér ESJ and Selivanova G. ROS-dependent activation of JNK converts p53 into an efficient inhibitor of oncogenes leading to robust apoptosis. Cell Death Differ.2014 Jan 10. doi: 10.1038/cdd.2013.186.

Cajuso T, Hänninen UA, Kondelin J, Gylfe AE,  Tanskanen T,  Katainen R, Pitkänen E,  Ristolainen H, Kaasinen E,  Taipale M,  Taipale J, Böhm J, Renkonen-Sinisal L, Mecklin JP, Järvinen H, Tuupanen S,  Kilpivaara O and  Vahteristo P. Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer. Int. J. Cancer. doi: 10.1002/ijc.28705

Moutinho C,  Martinez-Cardús A,  Santos C,  Navarro-Pérez V,  Martínez-Balibrea E,  Musulen E,  Carmona FJ,  Sartore-Bianchi A,  Cassingena A,  Siena S,  Elez E,  Tabernero J,  Salazar R, Abad A,  Esteller M. Epigenetic Inactivation of the BRCA1 Interactor SRBC and Resistance to Oxaliplatin in Colorectal Cancer. J Natl Cancer Inst 2014 106(1): djt322

Gylfe AE, Katainen R, Kondelin J, Tanskanen T, Cajuso T, Hänninen U, Taipale J, Taipale M, Renkonen-Sinisalo L, Järvinen H, Mecklin JP, Kilpivaara O, Pitkänen E, Vahteristo P, Tuupanen S, Karhu A, Aaltonen LA. Eleven Candidate Susceptibility Genes for Common Familial Colorectal Cancer. PLoS Genet 2013 9(10): e1003876.

Diaz LA Jr, Sausen M, Fisher GA, Velculescu VE. Insights into therapeutic resistance from whole-genome analyses of circulating tumor DNA. Oncotarget 2013 Oct;4(10):1856-7.

Manor O, Segal E. Predicting Disease Risk Using Bootstrap Ranking and Classification Algorithms. PLoS Comput Biol. 2013 Aug;9(8):e1003200.

Deyneko IV, Kel AE Kel-Margolis OV, Deineko EV, Wingender E, Weiss S. MatrixCatch–a novel tool for the recognition of composite regulatory elements in promoters. BMC Bioinformatics 2013 Aug 8;14:241

Church DN, Briggs SEW, Palles C, Domingo E, Kearsey SJ, Jonathon M. Grimes JM, Gorman M, Martin L,  Howarth KM, Hodgson SV, The NSECG Collaborators, Kaur K, Taylor J and Tomlinson IPM. DNA polymerase 1 and d exonuclease domain
mutations in endometrial cancer. Hum. Mol. Genet.2013 22(14):2820-2828.

Whiffin N, Dobbins SE, Hosking FJ, Palles C, Tenesa A, Wang Y, Farrington SM, Jones AM, Broderick P, Campbell H, Newcomb PA, Casey G, Conti DV, Schumacher F, Gallinger S, Lindor NM, Hopper J, Jenkins M, Dunlop MG, Tomlinson IP, Houlston RS. Deciphering the genetic architecture of low-penetrance susceptibility to colorectal cancer. Hum. Mol. Genet. 2013 22(24): 5075-5082.

Sur I, Tuupanen S, Whitington T, Aaltonen LA, Taipale J. Lessons from Functional Analysis of Genome-Wide Association Studies. Cancer Res 2013 73:4180-4184.

Yan J, Enge M, Whitington T, Dave K, Liu J, Sur I, Schmierer B, Jolma A, Kivioja T, Taipale M, Taipale J. Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites. Cell  2013 154, 801–813.

Bardelli A, Corso S, Bertotti A, Hobor S, Valtorta E, Siravegna G, Sartore-Bianchi A, Scala E, Cassingena A, Zecchin D, Apicella M, Migliardi G, Galimi F, Lauricella C  Zanon C, Perera T, Veronese S, Corti G, Amatu A, Gambacorta M, Diaz LA Jr, Sausen M, Velculescu VE, Comoglio P, Trusolino L, Di Nicolantonio F, Giordano S, Siena S. Amplification of the MET Receptor Drives Resistance to Anti-EGFR Therapies in Colorectal Cancer. Cancer discovery 2013 3:658-73.

Stegmaier P, Kel A, Wingender E, Borlak J. A discriminative approach for unsupervised clustering of DNA sequence motifs. PLoS Comput Biol 2013 9(3) e1002958.

Kilpivaara O and Aaltonen LA. Diagnostic Cancer Genome Sequencing and the Contribution of Germline Variants. Science 2013: Vol 339 no. 6127 pp 1559-62.

Manor O and Segal E. Robust Prediction of Expression Differences among Human Individuals Using Only Genotype Information.PLoS Genet. 2013 Mar;9(3):e1003396.

Wingender, E. Criteria for an updated classification of human transcription factor DNA-binding domains. J. Bioinform. Comput. Biol. 2013 11, 1340007.

Wingender E, Schoeps T, Dönitz J. TFClass:an expandable hierarchical classification of human transcription factors. Nucleic Acids Res. 2013 41, D165-D170.

Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lamarie P, Ukkonen E, Kivioja T, Taipale J. DNA-Binding Specificities of Human Transcription Factors. Cell 152: 327-339, 17 January 2013.

Øster B, Linnet L, Christensen LL, Thorsen K, Ongen H, Dermitzakis ET, Sandoval J, Moran S, Esteller M, Hansen TF, Lamy P, Laurberg S, Ørntoft TF, Andersen CL. Non-CpG island promoter hypomethylation and miR-149 regulate the expression of SRPX2 in colorectal cancer. Int J Cancer. 2013 132: 2303–2315.

2012

Christensen LL, Tobiasen H, Holm A, Schepeler T, Ostenfeld MS, Thorsen K, Rasmussen MH, Birkenkamp-Demtroeder K, Sieber OM, Gibbs P, Lubinski J, Lamy P, Laurberg S, Øster B, Hansen KQ, Hagemann-Madsen R, Byskov K, Ørntoft TF, Andersen CL. MiRNA-362-3p induces cell cycle arrest through targeting of E2F1, USF2 and PTPN1 and is associated with recurrence of colorectal cancer. Int J Cancer. 2012 Dec 30

Palles C, Cazier JB, Howarth KM, Domingo E, Jones AM, Broderick P, et al. Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat Genet. 2012 Dec 23. 

Sur IK, Hallikas O, Vaharautio A, Yan J, Turunen M, Enge M, Taipale M, Karhu A, Aaltonen LA, Taipale J. Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors. Science. 2012 Dec 7;338(6112):1360-3.

Nikulenkov F, Spinnler C, Li H, Tonelli C, Shi Y, Turunen M, Kivioja T, Ignatiev I, Kel A, Taipale J, Selivanova G. Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis. Cell Death Differ. 2012 Dec;19:1992-2002.

Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D, O’Shaughnessy J, Kinzler KW, Parmigiani G, Vogelstein B, Diaz LA Jr, Velculescu VE. Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing. Sci Transl Med 2012 133; p133ra58

Lubbe SJ, Pittman AM, Olver B, Lloyd A, Vijayakrishnan J, Naranjo S, Dobbins S, Broderick P, Gomez-Skarmeta JL, Houlston RS. The 14q22.2 colorectal cancer variant rs4444235 shows cis-acting regulation of BMP4. Oncogene 31, 3777–3784 2012.

Dunlop MG, Dobbins SE, Farrington SM, Jones AM, Palles C, Whiffin N, et al. Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nat Genet. 2012 May 27;44(7):770-6.

Roberts NJ, Vogelstein JT, Parmigiani G, Kinzler KW,Vogelstein B, Velculescu VE. The Predictive Capacity of Personal Genome Sequencing. Sci. Transl. Med. 4: 133ra58, 2012

Dallosso AR, Øster, B, Greenhough A, Thorsen K, Curry TJ, Owen C, Hancock AL, Szemes M, Paraskeva C, Frank M, Andersen CL, Malik K. Long-range epigenetic silencing of chromosome 5q31 protocadherins is involved in early and late stages of colorectal tumorigenesis through modulation of oncogenic pathways. Oncogene 31, 4409-4419, 2012

Alhopuro P, Sammalkorpi H, Niittymäki I, Biström M, Raitila A, Saharinen J, Nousiainen K, Lehtonen HJ, Heliövaara E, Puhakka J, Tuupanen S, Sousa S, Seruca R, Ferreira AM, Hofstra RMW, Mecklin JP, Järvinen H, Ristimäki A, Ørntoft TF, Hautaniemi S, Arango D, Karhu A, Aaltonen LA. Candidate driver genes in microsatellite-unstable colorectal cancer. Int. J. Cancer: 130, 1558–1566, 2012

Lopez-Serra P and Esteller M. DNA-methylation-associated silencing of tumor-suppressor microRNAs in cancer. Oncogene. 2012 Mar 29;31(13):1609-22.

2011

Mäkinen N, Mehine M, Tolvanen J, Kaasinen E, Li Y, Lehtonen HJ, Gentile M, Yan J, Enge M, Taipale M, Aavikko M, Katainen R, Virolainen E, Böhling T, Koski TA, Launonen V, Sjöberg J, Taipale J, Vahteristo P, Aaltonen LA. MED12, the Mediator Complex Subunit 12 Gene, Is Mutated at High Frequency in Uterine Leiomyomas. Science. 2011 Oct 14;334(6053):252-5.

Stegmaier P, Voss N, Meier T, Kel A, Wingender E, Borlak J.Advanced Computational Biology Methods Identify Molecular Switches for Malignancy in an EGF Mouse Model of Liver Cancer. PLoS One 2011 6(3):e17738