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Items: 50

1.

Off the street phasing (OTSP): no hassle haplotype phasing for molecular PGD applications.

Zeevi DA, Zahdeh F, Kling Y, Carmi S, Altarescu G.

J Assist Reprod Genet. 2019 Jan 8. doi: 10.1007/s10815-018-1392-1. [Epub ahead of print]

PMID:
30617673
2.

Haploseek: a 24-hour all-in-one method for preimplantation genetic diagnosis (PGD) of monogenic disease and aneuploidy.

Backenroth D, Zahdeh F, Kling Y, Peretz A, Rosen T, Kort D, Zeligson S, Dror T, Kirshberg S, Burak E, Segel R, Levy-Lahad E, Zangen D, Altarescu G, Carmi S, Zeevi DA.

Genet Med. 2018 Nov 19. doi: 10.1038/s41436-018-0351-7. [Epub ahead of print]

PMID:
30449887
3.

FactorialHMM: Fast and exact inference in factorial hidden Markov models.

Schweiger R, Erlich Y, Carmi S.

Bioinformatics. 2018 Nov 15. doi: 10.1093/bioinformatics/bty944. [Epub ahead of print]

PMID:
30445428
4.

Identity inference of genomic data using long-range familial searches.

Erlich Y, Shor T, Pe'er I, Carmi S.

Science. 2018 Nov 9;362(6415):690-694. doi: 10.1126/science.aau4832. Epub 2018 Oct 11.

PMID:
30309907
5.

A study of Kibbutzim in Israel reveals risk factors for cardiometabolic traits and subtle population structure.

Granot-Hershkovitz E, Karasik D, Friedlander Y, Rodriguez-Murillo L, Dorajoo R, Liu J, Sewda A, Peter I, Carmi S, Hochner H.

Eur J Hum Genet. 2018 Dec;26(12):1848-1858. doi: 10.1038/s41431-018-0230-3. Epub 2018 Aug 14.

PMID:
30108283
6.

POLD1 and POLE Gene Mutations in Jewish Cohorts of Early-Onset Colorectal Cancer and of Multiple Colorectal Adenomas.

Rosner G, Gluck N, Carmi S, Bercovich D, Fliss-Issakov N, Ben-Yehoyada M, Aharon-Caspi S, Kellerman E, Strul H, Shibolet O, Kariv R.

Dis Colon Rectum. 2018 Sep;61(9):1073-1079. doi: 10.1097/DCR.0000000000001150.

PMID:
30086056
7.

Germline DNA replication timing shapes mammalian genome composition.

Yehuda Y, Blumenfeld B, Mayorek N, Makedonski K, Vardi O, Cohen-Daniel L, Mansour Y, Baror-Sebban S, Masika H, Farago M, Berger M, Carmi S, Buganim Y, Koren A, Simon I.

Nucleic Acids Res. 2018 Sep 19;46(16):8299-8310. doi: 10.1093/nar/gky610.

8.

High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation.

Lencz T, Yu J, Palmer C, Carmi S, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Joseph V, Klein R, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Atzmon G, Pe'er I.

Hum Genet. 2018 Apr;137(4):343-355. doi: 10.1007/s00439-018-1886-z. Epub 2018 Apr 28.

PMID:
29705978
9.

Environment dominates over host genetics in shaping human gut microbiota.

Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, Costea PI, Godneva A, Kalka IN, Bar N, Shilo S, Lador D, Vila AV, Zmora N, Pevsner-Fischer M, Israeli D, Kosower N, Malka G, Wolf BC, Avnit-Sagi T, Lotan-Pompan M, Weinberger A, Halpern Z, Carmi S, Fu J, Wijmenga C, Zhernakova A, Elinav E, Segal E.

Nature. 2018 Mar 8;555(7695):210-215. doi: 10.1038/nature25973. Epub 2018 Feb 28.

PMID:
29489753
10.

Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease.

Hui KY, Fernandez-Hernandez H, Hu J, Schaffner A, Pankratz N, Hsu NY, Chuang LS, Carmi S, Villaverde N, Li X, Rivas M, Levine AP, Bao X, Labrias PR, Haritunians T, Ruane D, Gettler K, Chen E, Li D, Schiff ER, Pontikos N, Barzilai N, Brant SR, Bressman S, Cheifetz AS, Clark LN, Daly MJ, Desnick RJ, Duerr RH, Katz S, Lencz T, Myers RH, Ostrer H, Ozelius L, Payami H, Peter Y, Rioux JD, Segal AW, Scott WK, Silverberg MS, Vance JM, Ubarretxena-Belandia I, Foroud T, Atzmon G, Pe'er I, Ioannou Y, McGovern DPB, Yue Z, Schadt EE, Cho JH, Peter I.

Sci Transl Med. 2018 Jan 10;10(423). pii: eaai7795. doi: 10.1126/scitranslmed.aai7795.

11.

The genetic variation in the R1a clade among the Ashkenazi Levites' Y chromosome.

Behar DM, Saag L, Karmin M, Gover MG, Wexler JD, Sanchez LF, Greenspan E, Kushniarevich A, Davydenko O, Sahakyan H, Yepiskoposyan L, Boattini A, Sarno S, Pagani L, Carmi S, Tzur S, Metspalu E, Bormans C, Skorecki K, Metspalu M, Rootsi S, Villems R.

Sci Rep. 2017 Nov 2;7(1):14969. doi: 10.1038/s41598-017-14761-7.

12.

Differential analysis of mutations in the Jewish population and their implications for diseases.

Einhorn Y, Weissglas-Volkov D, Carmi S, Ostrer H, Friedman E, Shomron N.

Genet Res (Camb). 2017 May 15;99:e3. doi: 10.1017/S0016672317000015.

PMID:
28502252
13.

The time and place of European admixture in Ashkenazi Jewish history.

Xue J, Lencz T, Darvasi A, Pe'er I, Carmi S.

PLoS Genet. 2017 Apr 4;13(4):e1006644. doi: 10.1371/journal.pgen.1006644. eCollection 2017 Apr.

14.

A non-zero variance of Tajima's estimator for two sequences even for infinitely many unlinked loci.

King L, Wakeley J, Carmi S.

Theor Popul Biol. 2018 Jul;122:22-29. doi: 10.1016/j.tpb.2017.03.002. Epub 2017 Mar 21.

PMID:
28341209
15.

Genomic insights into the population structure and history of the Irish Travellers.

Gilbert E, Carmi S, Ennis S, Wilson JF, Cavalleri GL.

Sci Rep. 2017 Feb 9;7:42187. doi: 10.1038/srep42187.

16.

A Recurrent ERCC3 Truncating Mutation Confers Moderate Risk for Breast Cancer.

Vijai J, Topka S, Villano D, Ravichandran V, Maxwell KN, Maria A, Thomas T, Gaddam P, Lincoln A, Kazzaz S, Wenz B, Carmi S, Schrader KA, Hart SN, Lipkin SM, Neuhausen SL, Walsh MF, Zhang L, Lejbkowicz F, Rennert H, Stadler ZK, Robson M, Weitzel JN, Domchek S, Daly MJ, Couch FJ, Nathanson KL, Norton L, Rennert G, Offit K.

Cancer Discov. 2016 Nov;6(11):1267-1275. Epub 2016 Sep 21.

17.

Transcriptome and proteome analyses and the role of atypical calpain protein and autophagy in the spliced leader silencing pathway in Trypanosoma brucei.

Hope R, Egarmina K, Voloshin K, Waldman Ben-Asher H, Carmi S, Eliaz D, Drori Y, Michaeli S.

Mol Microbiol. 2016 Oct;102(1):1-21. doi: 10.1111/mmi.13417. Epub 2016 Aug 31.

18.

Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs.

Yang S, Carmi S, Pe'er I.

J Comput Biol. 2016 Jun;23(6):495-507. doi: 10.1089/cmb.2016.0016. Epub 2016 Apr 22.

19.

Expanding the phenotype of CRB2 mutations - A new ciliopathy syndrome?

Jaron R, Rosenfeld N, Zahdeh F, Carmi S, Beni-Adani L, Doviner V, Picard E, Segel R, Zeligson S, Carmel L, Renbaum P, Levy-Lahad E.

Clin Genet. 2016 Dec;90(6):540-544. doi: 10.1111/cge.12764. Epub 2016 May 2.

PMID:
26925547
20.

An Ashkenazi founder mutation in the PKHD1 gene.

Quint A, Sagi M, Carmi S, Daum H, Macarov M, Ben Neriah Z, Meiner V, Elpeleg O, Lerer I.

Eur J Med Genet. 2016 Feb;59(2):86-90. doi: 10.1016/j.ejmg.2015.12.013. Epub 2015 Dec 23.

PMID:
26721323
21.

Expanded genetic screening panel for the Ashkenazi Jewish population.

Baskovich B, Hiraki S, Upadhyay K, Meyer P, Carmi S, Barzilai N, Darvasi A, Ozelius L, Peter I, Cho JH, Atzmon G, Clark L, Yu J, Lencz T, Pe'er I, Ostrer H, Oddoux C.

Genet Med. 2016 May;18(5):522-8. doi: 10.1038/gim.2015.123. Epub 2015 Sep 3.

22.

The SMC' is a highly accurate approximation to the ancestral recombination graph.

Wilton PR, Carmi S, Hobolth A.

Genetics. 2015 May;200(1):343-55. doi: 10.1534/genetics.114.173898. Epub 2015 Mar 17.

23.

Genotyping of geographically diverse Druze trios reveals substructure and a recent bottleneck.

Zidan J, Ben-Avraham D, Carmi S, Maray T, Friedman E, Atzmon G.

Eur J Hum Genet. 2015 Aug;23(8):1093-9. doi: 10.1038/ejhg.2014.218. Epub 2014 Nov 5.

24.

Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins.

Carmi S, Hui KY, Kochav E, Liu X, Xue J, Grady F, Guha S, Upadhyay K, Ben-Avraham D, Mukherjee S, Bowen BM, Thomas T, Vijai J, Cruts M, Froyen G, Lambrechts D, Plaisance S, Van Broeckhoven C, Van Damme P, Van Marck H, Barzilai N, Darvasi A, Offit K, Bressman S, Ozelius LJ, Peter I, Cho JH, Ostrer H, Atzmon G, Clark LN, Lencz T, Pe'er I.

Nat Commun. 2014 Sep 9;5:4835. doi: 10.1038/ncomms5835.

25.

A genome-wide map of hyper-edited RNA reveals numerous new sites.

Porath HT, Carmi S, Levanon EY.

Nat Commun. 2014 Aug 27;5:4726. doi: 10.1038/ncomms5726.

26.

A renewal theory approach to IBD sharing.

Carmi S, Wilton PR, Wakeley J, Pe'er I.

Theor Popul Biol. 2014 Nov;97:35-48. doi: 10.1016/j.tpb.2014.08.002. Epub 2014 Aug 18.

27.

Two splicing factors carrying serine-arginine motifs, TSR1 and TSR1IP, regulate splicing, mRNA stability, and rRNA processing in Trypanosoma brucei.

Gupta SK, Chikne V, Eliaz D, Tkacz ID, Naboishchikov I, Carmi S, Waldman Ben-Asher H, Michaeli S.

RNA Biol. 2014;11(6):715-31. Epub 2014 May 13.

28.

Characterization of ovarian cancer cell metabolism and response to chemotherapy by (31)p magnetic resonance spectroscopy.

Abramov Y, Carmi S, Anteby SO, Ringel I.

Oncol Res. 2013;20(11):529-36. doi: 10.3727/096504013X13747716581372.

PMID:
24063283
29.

Random walk with priorities in communicationlike networks.

Bastas N, Maragakis M, Argyrakis P, ben-Avraham D, Havlin S, Carmi S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Aug;88(2):022803. Epub 2013 Aug 5.

PMID:
24032879
30.

The hnRNP F/H homologue of Trypanosoma brucei is differentially expressed in the two life cycle stages of the parasite and regulates splicing and mRNA stability.

Gupta SK, Kosti I, Plaut G, Pivko A, Tkacz ID, Cohen-Chalamish S, Biswas DK, Wachtel C, Waldman Ben-Asher H, Carmi S, Glaser F, Mandel-Gutfreund Y, Michaeli S.

Nucleic Acids Res. 2013 Jul;41(13):6577-94. doi: 10.1093/nar/gkt369. Epub 2013 May 10.

31.

Basal splicing factors regulate the stability of mature mRNAs in trypanosomes.

Gupta SK, Carmi S, Waldman Ben-Asher H, Tkacz ID, Naboishchikov I, Michaeli S.

J Biol Chem. 2013 Feb 15;288(7):4991-5006. doi: 10.1074/jbc.M112.416578. Epub 2013 Jan 2.

32.

The variance of identity-by-descent sharing in the Wright-Fisher model.

Carmi S, Palamara PF, Vacic V, Lencz T, Darvasi A, Pe'er I.

Genetics. 2013 Mar;193(3):911-28. doi: 10.1534/genetics.112.147215. Epub 2012 Dec 24.

33.

Ex vivo 1H and 31P magnetic resonance spectroscopy as a means for tumor characterization in ovarian cancer patients.

Abramov Y, Carmi S, Anteby SO, Ringel I.

Oncol Rep. 2013 Jan;29(1):321-8. doi: 10.3892/or.2012.2071. Epub 2012 Oct 5.

PMID:
23042519
34.

31P-magnetic resonance spectra of ovarian cancer cells exposed to chemotherapy within a three-dimensional Matrigel construct.

Abramov Y, Carmi S, Cohen JS, Anteby SO, Ringel I.

Oncol Rep. 2012 Aug;28(2):735-41. doi: 10.3892/or.2012.1810. Epub 2012 May 10.

PMID:
22581188
35.

Fractional Feynman-Kac equation for weak ergodicity breaking.

Carmi S, Barkai E.

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Dec;84(6 Pt 1):061104. Epub 2011 Dec 5.

PMID:
22304037
36.

Large-scale DNA editing of retrotransposons accelerates mammalian genome evolution.

Carmi S, Church GM, Levanon EY.

Nat Commun. 2011 Nov 1;2:519. doi: 10.1038/ncomms1525.

PMID:
22044998
37.

Identification of widespread ultra-edited human RNAs.

Carmi S, Borukhov I, Levanon EY.

PLoS Genet. 2011 Oct;7(10):e1002317. doi: 10.1371/journal.pgen.1002317. Epub 2011 Oct 20.

38.

Epidemic threshold for the susceptible-infectious-susceptible model on random networks.

Parshani R, Carmi S, Havlin S.

Phys Rev Lett. 2010 Jun 25;104(25):258701. Epub 2010 Jun 22.

PMID:
20867419
39.

The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution.

Kolev NG, Franklin JB, Carmi S, Shi H, Michaeli S, Tschudi C.

PLoS Pathog. 2010 Sep 9;6(9):e1001090. doi: 10.1371/journal.ppat.1001090.

40.

Fractional Feynman-Kac equation for non-brownian functionals.

Turgeman L, Carmi S, Barkai E.

Phys Rev Lett. 2009 Nov 6;103(19):190201. Epub 2009 Nov 6.

PMID:
20365911
41.

Persistent ER stress induces the spliced leader RNA silencing pathway (SLS), leading to programmed cell death in Trypanosoma brucei.

Goldshmidt H, Matas D, Kabi A, Carmi S, Hope R, Michaeli S.

PLoS Pathog. 2010 Jan 22;6(1):e1000731. doi: 10.1371/journal.ppat.1000731.

42.

Asymptotic behavior of the Kleinberg model.

Carmi S, Carter S, Sun J, Ben-Avraham D.

Phys Rev Lett. 2009 Jun 12;102(23):238702. Epub 2009 Jun 11.

PMID:
19658979
43.

Partition of networks into basins of attraction.

Carmi S, Krapivsky PL, Ben-Avraham D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Dec;78(6 Pt 2):066111. Epub 2008 Dec 22.

PMID:
19256909
44.

Efficiency of complex production in changing environment.

Carmi S, Levanon EY, Eisenberg E.

BMC Syst Biol. 2009 Jan 7;3:3. doi: 10.1186/1752-0509-3-3.

45.

Priority diffusion model in lattices and complex networks.

Maragakis M, Carmi S, ben-Avraham D, Havlin S, Argyrakis P.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Feb;77(2 Pt 1):020103. Epub 2008 Feb 7.

PMID:
18351969
46.

Limited path percolation in complex networks.

López E, Parshani R, Cohen R, Carmi S, Havlin S.

Phys Rev Lett. 2007 Nov 2;99(18):188701. Epub 2007 Oct 29.

PMID:
17995444
47.

A model of Internet topology using k-shell decomposition.

Carmi S, Havlin S, Kirkpatrick S, Shavitt Y, Shir E.

Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11150-4. Epub 2007 Jun 22.

48.

Connectivity and expression in protein networks: proteins in a complex are uniformly expressed.

Carmi S, Levanon EY, Havlin S, Eisenberg E.

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Mar;73(3 Pt 1):031909. Epub 2006 Mar 14.

PMID:
16605560
49.

Determination of intracellular pH and compartmentation using diffusion-weighted NMR spectroscopy with pH-sensitive indicators.

Cohen JS, Motiei M, Carmi S, Shiperto D, Yefet O, Ringel I.

Magn Reson Med. 2004 May;51(5):900-3.

50.

How painting can be used as a clinical tool.

Rosin AJ, Matz E, Carmi S.

Geriatrics. 1977 Jan;32(1):41-6. No abstract available.

PMID:
830601

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