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Items: 42

1.

The evolutionary landscape of colorectal tumorigenesis.

Cross W, Kovac M, Mustonen V, Temko D, Davis H, Baker AM, Biswas S, Arnold R, Chegwidden L, Gatenbee C, Anderson AR, Koelzer VH, Martinez P, Jiang X, Domingo E, Woodcock DJ, Feng Y, Kovacova M, Maughan T; S:CORT Consortium, Jansen M, Rodriguez-Justo M, Ashraf S, Guy R, Cunningham C, East JE, Wedge DC, Wang LM, Palles C, Heinimann K, Sottoriva A, Leedham SJ, Graham TA, Tomlinson IPM.

Nat Ecol Evol. 2018 Oct;2(10):1661-1672. doi: 10.1038/s41559-018-0642-z. Epub 2018 Aug 31.

PMID:
30177804
2.

Fibroblasts from bank voles inhabiting Chernobyl have increased resistance against oxidative and DNA stresses.

Mustonen V, Kesäniemi J, Lavrinienko A, Tukalenko E, Mappes T, Watts PC, Jurvansuu J.

BMC Cell Biol. 2018 Aug 29;19(1):17. doi: 10.1186/s12860-018-0169-9.

3.

Uncovering Natural Longevity Alleles from Intercrossed Pools of Aging Fission Yeast Cells.

Ellis DA, Mustonen V, Rodríguez-López M, Rallis C, Malecki M, Jeffares DC, Bähler J.

Genetics. 2018 Oct;210(2):733-744. doi: 10.1534/genetics.118.301262. Epub 2018 Aug 2.

4.

Clonal Heterogeneity Influences the Fate of New Adaptive Mutations.

Vázquez-García I, Salinas F, Li J, Fischer A, Barré B, Hallin J, Bergström A, Alonso-Perez E, Warringer J, Mustonen V, Liti G.

Cell Rep. 2017 Oct 17;21(3):732-744. doi: 10.1016/j.celrep.2017.09.046.

5.

Evaluating genetic drift in time-series evolutionary analysis.

R Nené N, Mustonen V, J R Illingworth C.

J Theor Biol. 2018 Jan 21;437:51-57. doi: 10.1016/j.jtbi.2017.09.021. Epub 2017 Sep 25.

6.

Predicting evolution.

Lässig M, Mustonen V, Walczak AM.

Nat Ecol Evol. 2017 Feb 21;1(3):77. doi: 10.1038/s41559-017-0077.

PMID:
28812721
7.

Rapid identification of genes controlling virulence and immunity in malaria parasites.

Abkallo HM, Martinelli A, Inoue M, Ramaprasad A, Xangsayarath P, Gitaka J, Tang J, Yahata K, Zoungrana A, Mitaka H, Acharjee A, Datta PP, Hunt P, Carter R, Kaneko O, Mustonen V, Illingworth CJR, Pain A, Culleton R.

PLoS Pathog. 2017 Jul 12;13(7):e1006447. doi: 10.1371/journal.ppat.1006447. eCollection 2017 Jul.

8.

Social rhythms of the heart.

Pantzar M, Ruckenstein M, Mustonen V.

Health Sociol Rev. 2017 Jan 2;26(1):22-37. doi: 10.1080/14461242.2016.1184580. Epub 2016 Jun 2.

9.

Landscape of somatic mutations in 560 breast cancer whole-genome sequences.

Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjærde OC, Langerød A, Ringnér M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O'Meara S, Pauporté I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodríguez-González FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van't Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg Å, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Børresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR.

Nature. 2016 Jun 2;534(7605):47-54. doi: 10.1038/nature17676. Epub 2016 May 2.

10.

Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies.

McKerrell T, Moreno T, Ponstingl H, Bolli N, Dias JM, Tischler G, Colonna V, Manasse B, Bench A, Bloxham D, Herman B, Fletcher D, Park N, Quail MA, Manes N, Hodkinson C, Baxter J, Sierra J, Foukaneli T, Warren AJ, Chi J, Costeas P, Rad R, Huntly B, Grove C, Ning Z, Tyler-Smith C, Varela I, Scott M, Nomdedeu J, Mustonen V, Vassiliou GS.

Blood. 2016 Jul 7;128(1):e1-9. doi: 10.1182/blood-2015-11-683334. Epub 2016 Apr 27.

11.

Adenoma development in familial adenomatous polyposis and MUTYH-associated polyposis: somatic landscape and driver genes.

Rashid M, Fischer A, Wilson CH, Tiffen J, Rust AG, Stevens P, Idziaszczyk S, Maynard J, Williams GT, Mustonen V, Sampson JR, Adams DJ.

J Pathol. 2016 Jan;238(1):98-108. doi: 10.1002/path.4643. Epub 2015 Nov 2.

12.

Discrepancies in expert decision-making in forensic fingerprint examination.

Mustonen V, Hakkarainen K, Tuunainen J, Pohjola P.

Forensic Sci Int. 2015 Sep;254:215-26. doi: 10.1016/j.forsciint.2015.07.031. Epub 2015 Jul 29.

PMID:
26254629
13.

Pathway and network analysis of cancer genomes.

Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, Boutros PC, Stuart JM, Linding R, Lopez-Bigas N, Stein LD; Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consortium.

Nat Methods. 2015 Jul;12(7):615-621. doi: 10.1038/nmeth.3440.

14.

The value of monitoring to control evolving populations.

Fischer A, Vázquez-García I, Mustonen V.

Proc Natl Acad Sci U S A. 2015 Jan 27;112(4):1007-12. doi: 10.1073/pnas.1409403112. Epub 2015 Jan 13.

15.

Identifying selection in the within-host evolution of influenza using viral sequence data.

Illingworth CJ, Fischer A, Mustonen V.

PLoS Comput Biol. 2014 Jul 31;10(7):e1003755. doi: 10.1371/journal.pcbi.1003755. eCollection 2014 Jul.

16.

High-definition reconstruction of clonal composition in cancer.

Fischer A, Vázquez-García I, Illingworth CJR, Mustonen V.

Cell Rep. 2014 Jun 12;7(5):1740-1752. doi: 10.1016/j.celrep.2014.04.055. Epub 2014 May 29.

17.

A high-definition view of functional genetic variation from natural yeast genomes.

Bergström A, Simpson JT, Salinas F, Barré B, Parts L, Zia A, Nguyen Ba AN, Moses AM, Louis EJ, Mustonen V, Warringer J, Durbin R, Liti G.

Mol Biol Evol. 2014 Apr;31(4):872-88. doi: 10.1093/molbev/msu037. Epub 2014 Jan 14.

18.

High-resolution mapping of complex traits with a four-parent advanced intercross yeast population.

Cubillos FA, Parts L, Salinas F, Bergström A, Scovacricchi E, Zia A, Illingworth CJ, Mustonen V, Ibstedt S, Warringer J, Louis EJ, Durbin R, Liti G.

Genetics. 2013 Nov;195(3):1141-55. doi: 10.1534/genetics.113.155515. Epub 2013 Sep 13.

19.

Computational approaches to identify functional genetic variants in cancer genomes.

Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group.

Nat Methods. 2013 Aug;10(8):723-9. doi: 10.1038/nmeth.2562.

20.

Inferring genome-wide recombination landscapes from advanced intercross lines: application to yeast crosses.

Illingworth CJ, Parts L, Bergström A, Liti G, Mustonen V.

PLoS One. 2013 May 2;8(5):e62266. doi: 10.1371/journal.pone.0062266. Print 2013.

21.

EMu: probabilistic inference of mutational processes and their localization in the cancer genome.

Fischer A, Illingworth CJ, Campbell PJ, Mustonen V.

Genome Biol. 2013 Apr 29;14(4):R39. doi: 10.1186/gb-2013-14-4-r39.

22.

Components of selection in the evolution of the influenza virus: linkage effects beat inherent selection.

Illingworth CJ, Mustonen V.

PLoS Pathog. 2012 Dec;8(12):e1003091. doi: 10.1371/journal.ppat.1003091. Epub 2012 Dec 27.

23.

GraphAlignment: Bayesian pairwise alignment of biological networks.

Kolář M, Meier J, Mustonen V, Lässig M, Berg J.

BMC Syst Biol. 2012 Nov 21;6:144. doi: 10.1186/1752-0509-6-144.

24.

A method to infer positive selection from marker dynamics in an asexual population.

Illingworth CJ, Mustonen V.

Bioinformatics. 2012 Mar 15;28(6):831-7. doi: 10.1093/bioinformatics/btr722. Epub 2012 Jan 5.

25.

Quantifying selection acting on a complex trait using allele frequency time series data.

Illingworth CJ, Parts L, Schiffels S, Liti G, Mustonen V.

Mol Biol Evol. 2012 Apr;29(4):1187-97. doi: 10.1093/molbev/msr289. Epub 2011 Nov 23.

26.

Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts.

Papaemmanuil E, Cazzola M, Boultwood J, Malcovati L, Vyas P, Bowen D, Pellagatti A, Wainscoat JS, Hellstrom-Lindberg E, Gambacorti-Passerini C, Godfrey AL, Rapado I, Cvejic A, Rance R, McGee C, Ellis P, Mudie LJ, Stephens PJ, McLaren S, Massie CE, Tarpey PS, Varela I, Nik-Zainal S, Davies HR, Shlien A, Jones D, Raine K, Hinton J, Butler AP, Teague JW, Baxter EJ, Score J, Galli A, Della Porta MG, Travaglino E, Groves M, Tauro S, Munshi NC, Anderson KC, El-Naggar A, Fischer A, Mustonen V, Warren AJ, Cross NC, Green AR, Futreal PA, Stratton MR, Campbell PJ; Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium.

N Engl J Med. 2011 Oct 13;365(15):1384-95. doi: 10.1056/NEJMoa1103283. Epub 2011 Sep 26.

27.

Emergent neutrality in adaptive asexual evolution.

Schiffels S, Szöllosi GJ, Mustonen V, Lässig M.

Genetics. 2011 Dec;189(4):1361-75. doi: 10.1534/genetics.111.132027. Epub 2011 Sep 16.

28.

Distinguishing driver and passenger mutations in an evolutionary history categorized by interference.

Illingworth CJ, Mustonen V.

Genetics. 2011 Nov;189(3):989-1000. doi: 10.1534/genetics.111.133975. Epub 2011 Sep 6.

29.

Germline fitness-based scoring of cancer mutations.

Fischer A, Greenman C, Mustonen V.

Genetics. 2011 Jun;188(2):383-93. doi: 10.1534/genetics.111.127480. Epub 2011 Mar 24.

30.

Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma.

Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J, Bignell G, Butler A, Cho J, Dalgliesh GL, Galappaththige D, Greenman C, Hardy C, Jia M, Latimer C, Lau KW, Marshall J, McLaren S, Menzies A, Mudie L, Stebbings L, Largaespada DA, Wessels LF, Richard S, Kahnoski RJ, Anema J, Tuveson DA, Perez-Mancera PA, Mustonen V, Fischer A, Adams DJ, Rust A, Chan-on W, Subimerb C, Dykema K, Furge K, Campbell PJ, Teh BT, Stratton MR, Futreal PA.

Nature. 2011 Jan 27;469(7331):539-42. doi: 10.1038/nature09639. Epub 2011 Jan 19. Erratum in: Nature. 2012 Apr 5;484(7392):130.

31.

Fitness flux and ubiquity of adaptive evolution.

Mustonen V, Lässig M.

Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4248-53. doi: 10.1073/pnas.0907953107. Epub 2010 Feb 9.

32.

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation.

Mustonen V, Lässig M.

Trends Genet. 2009 Mar;25(3):111-9. doi: 10.1016/j.tig.2009.01.002. Epub 2009 Feb 18.

PMID:
19232770
33.

Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites.

Mustonen V, Kinney J, Callan CG Jr, Lässig M.

Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12376-81. doi: 10.1073/pnas.0805909105. Epub 2008 Aug 22.

34.

Molecular evolution under fitness fluctuations.

Mustonen V, Lässig M.

Phys Rev Lett. 2008 Mar 14;100(10):108101. Epub 2008 Mar 10.

PMID:
18352233
35.

Adaptations to fluctuating selection in Drosophila.

Mustonen V, Lässig M.

Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2277-82. Epub 2007 Feb 7.

36.

Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies.

Mustonen V, Lässig M.

Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15936-41. Epub 2005 Oct 19.

37.

Equilibrium statistical mechanics of a grain boundary.

Abraham DB, Mustonen V, Wood AJ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Mar;71(3 Pt 2A):036106. Epub 2005 Mar 8.

PMID:
15903492
38.

Relaxation dynamics of a system with a grain boundary.

Abraham DB, Mustonen V, Wood AJ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Dec;70(6 Pt 2):066138. Epub 2004 Dec 27.

PMID:
15697465
39.

Wetting effects at a grain boundary.

Abraham DB, Mustonen V, Wood AJ.

Phys Rev Lett. 2004 Aug 13;93(7):076101. Epub 2004 Aug 10.

PMID:
15324251
40.

Serum calcium and phosphorus homeostasis in man studied by means of the sodium-EDTA test.

KALLIOMAKI JL, MARKKANEN TK, MUSTONEN VA.

Acta Med Scand. 1961 Aug;170:211-4. No abstract available.

PMID:
13750965
41.

Sexual behavior after cerebral vascular accident. A study on patients below the age of 60 years.

KALLIOMAKI JL, MARKKANEN TK, MUSTONEN VA.

Fertil Steril. 1961 Mar-Apr;12:156-8. No abstract available.

PMID:
13750966
42.

Standard electrocardiogram in artificial hypocalcemia.

KALLIOMAKI JL, MARKKANEN TK, MUSTONEN VA.

Ann Med Intern Fenn. 1961;50:163-6. No abstract available.

PMID:
14453336

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