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Items: 47

1.

Small RNA sequences derived from pre-microRNAs in the supraspliceosome.

Mahlab-Aviv S, Boulos A, Peretz AR, Eliyahu T, Carmel L, Sperling R, Linial M.

Nucleic Acids Res. 2018 Sep 8. doi: 10.1093/nar/gky791. [Epub ahead of print]

PMID:
30203035
2.

Alu exaptation enriches the human transcriptome by introducing new gene ends.

Lavi E, Carmel L.

RNA Biol. 2018;15(6):715-725. doi: 10.1080/15476286.2018.1429880. Epub 2018 Mar 26.

PMID:
29493382
3.

Evidence for convergent evolution of SINE-directed Staufen-mediated mRNA decay.

Lucas BA, Lavi E, Shiue L, Cho H, Katzman S, Miyoshi K, Siomi MC, Carmel L, Ares M Jr, Maquat LE.

Proc Natl Acad Sci U S A. 2018 Jan 30;115(5):968-973. doi: 10.1073/pnas.1715531115. Epub 2018 Jan 16.

4.

Inferring Past Environments from Ancient Epigenomes.

Gokhman D, Malul A, Carmel L.

Mol Biol Evol. 2017 Oct 1;34(10):2429-2438. doi: 10.1093/molbev/msx211.

5.

Identification of introns harboring functional sequence elements through positional conservation.

Chorev M, Joseph Bekker A, Goldberger J, Carmel L.

Sci Rep. 2017 Jun 23;7(1):4201. doi: 10.1038/s41598-017-04476-0.

6.

Gene ORGANizer: linking genes to the organs they affect.

Gokhman D, Kelman G, Amartely A, Gershon G, Tsur S, Carmel L.

Nucleic Acids Res. 2017 Jul 3;45(W1):W138-W145. doi: 10.1093/nar/gkx302.

7.

Archaic Adaptive Introgression in TBX15/WARS2.

Racimo F, Gokhman D, Fumagalli M, Ko A, Hansen T, Moltke I, Albrechtsen A, Carmel L, Huerta-Sánchez E, Nielsen R.

Mol Biol Evol. 2017 Mar 1;34(3):509-524. doi: 10.1093/molbev/msw283.

8.

The role of nucleotide composition in premature termination codon recognition.

Zahdeh F, Carmel L.

BMC Bioinformatics. 2016 Dec 7;17(1):519.

9.

System-wide Analysis of the T Cell Response.

Covacu R, Philip H, Jaronen M, Almeida J, Kenison JE, Darko S, Chao CC, Yaari G, Louzoun Y, Carmel L, Douek DC, Efroni S, Quintana FJ.

Cell Rep. 2016 Mar 22;14(11):2733-44. doi: 10.1016/j.celrep.2016.02.056. Epub 2016 Mar 10.

10.

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
11.

Epigenetics: It's Getting Old. Past Meets Future in Paleoepigenetics.

Gokhman D, Meshorer E, Carmel L.

Trends Ecol Evol. 2016 Apr;31(4):290-300. doi: 10.1016/j.tree.2016.01.010. Epub 2016 Feb 15. Review.

PMID:
26898827
12.

LEMONS - A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms Lacking Reference Genomes.

Levin L, Bar-Yaacov D, Bouskila A, Chorev M, Carmel L, Mishmar D.

PLoS One. 2015 Nov 25;10(11):e0143329. doi: 10.1371/journal.pone.0143329. eCollection 2015.

13.

JuncDB: an exon-exon junction database.

Chorev M, Guy L, Carmel L.

Nucleic Acids Res. 2016 Jan 4;44(D1):D101-9. doi: 10.1093/nar/gkv1142. Epub 2015 Oct 30.

14.

Combined mineralocorticoid and glucocorticoid deficiency is caused by a novel founder nicotinamide nucleotide transhydrogenase mutation that alters mitochondrial morphology and increases oxidative stress.

Weinberg-Shukron A, Abu-Libdeh A, Zhadeh F, Carmel L, Kogot-Levin A, Kamal L, Kanaan M, Zeligson S, Renbaum P, Levy-Lahad E, Zangen D.

J Med Genet. 2015 Sep;52(9):636-41. doi: 10.1136/jmedgenet-2015-103078. Epub 2015 Jun 12.

PMID:
26070314
15.

Reconstructing the DNA methylation maps of the Neandertal and the Denisovan.

Gokhman D, Lavi E, Prüfer K, Fraga MF, Riancho JA, Kelso J, Pääbo S, Meshorer E, Carmel L.

Science. 2014 May 2;344(6183):523-7. doi: 10.1126/science.1250368. Epub 2014 Apr 17.

16.

Computational identification of functional introns: high positional conservation of introns that harbor RNA genes.

Chorev M, Carmel L.

Nucleic Acids Res. 2013 Jun;41(11):5604-13. doi: 10.1093/nar/gkt244. Epub 2013 Apr 19.

17.

Dependencies among editing sites in serotonin 2C receptor mRNA.

Carmel L, Koonin EV, Dracheva S.

PLoS Comput Biol. 2012;8(9):e1002663. doi: 10.1371/journal.pcbi.1002663. Epub 2012 Sep 6.

18.

ApoB-containing lipoproteins regulate angiogenesis by modulating expression of VEGF receptor 1.

Avraham-Davidi I, Ely Y, Pham VN, Castranova D, Grunspan M, Malkinson G, Gibbs-Bar L, Mayseless O, Allmog G, Lo B, Warren CM, Chen TT, Ungos J, Kidd K, Shaw K, Rogachev I, Wan W, Murphy PM, Farber SA, Carmel L, Shelness GS, Iruela-Arispe ML, Weinstein BM, Yaniv K.

Nat Med. 2012 Jun;18(6):967-73. doi: 10.1038/nm.2759.

19.

The function of introns.

Chorev M, Carmel L.

Front Genet. 2012 Apr 13;3:55. doi: 10.3389/fgene.2012.00055. eCollection 2012.

20.

Origin and evolution of spliceosomal introns.

Rogozin IB, Carmel L, Csuros M, Koonin EV.

Biol Direct. 2012 Apr 16;7:11. doi: 10.1186/1745-6150-7-11. Review.

21.

XX ovarian dysgenesis is caused by a PSMC3IP/HOP2 mutation that abolishes coactivation of estrogen-driven transcription.

Zangen D, Kaufman Y, Zeligson S, Perlberg S, Fridman H, Kanaan M, Abdulhadi-Atwan M, Abu Libdeh A, Gussow A, Kisslov I, Carmel L, Renbaum P, Levy-Lahad E.

Am J Hum Genet. 2011 Oct 7;89(4):572-9. doi: 10.1016/j.ajhg.2011.09.006. Epub 2011 Sep 29.

22.

The role of reverse transcriptase in intron gain and loss mechanisms.

Cohen NE, Shen R, Carmel L.

Mol Biol Evol. 2012 Jan;29(1):179-86. doi: 10.1093/molbev/msr192. Epub 2011 Jul 29.

PMID:
21804076
23.

The ecoresponsive genome of Daphnia pulex.

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL.

Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761.

24.

EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution.

Carmel L, Wolf YI, Rogozin IB, Koonin EV.

Adv Bioinformatics. 2010:167408. doi: 10.1155/2010/167408. Epub 2010 May 6.

25.

A maximum likelihood method for reconstruction of the evolution of eukaryotic gene structure.

Carmel L, Rogozin IB, Wolf YI, Koonin EV.

Methods Mol Biol. 2009;541:357-71. doi: 10.1007/978-1-59745-243-4_16. Review.

26.

Endothelial cells promote migration and proliferation of enteric neural crest cells via beta1 integrin signaling.

Nagy N, Mwizerwa O, Yaniv K, Carmel L, Pieretti-Vanmarcke R, Weinstein BM, Goldstein AM.

Dev Biol. 2009 Jun 15;330(2):263-72. doi: 10.1016/j.ydbio.2009.03.025. Epub 2009 Apr 1.

27.

A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes.

Carmel L, Koonin EV.

Genome Biol Evol. 2009 Sep 22;1:382-90. doi: 10.1093/gbe/evp038.

28.

Potency and fate specification in CNS stem cell populations in vitro.

Ravin R, Hoeppner DJ, Munno DM, Carmel L, Sullivan J, Levitt DL, Miller JL, Athaide C, Panchision DM, McKay RD.

Cell Stem Cell. 2008 Dec 4;3(6):670-80. doi: 10.1016/j.stem.2008.09.012.

29.

Superposition of transcriptional behaviors determines gene state.

Efroni S, Carmel L, Schaefer CG, Buetow KH.

PLoS One. 2008 Aug 6;3(8):e2901. doi: 10.1371/journal.pone.0002901.

30.

Robust linear dimensionality reduction.

Koren Y, Carmel L.

IEEE Trans Vis Comput Graph. 2004 Jul-Aug;10(4):459-70. doi: 10.1109/TVCG.2004.17.

PMID:
18579973
31.

Homoplasy in genome-wide analysis of rare amino acid replacements: the molecular-evolutionary basis for Vavilov's law of homologous series.

Rogozin IB, Thomson K, Csürös M, Carmel L, Koonin EV.

Biol Direct. 2008 Mar 17;3:7. doi: 10.1186/1745-6150-3-7.

32.

Predicting the receptive range of olfactory receptors.

Haddad R, Carmel L, Sobel N, Harel D.

PLoS Comput Biol. 2008 Feb;4(2):e18. doi: 10.1371/journal.pcbi.0040018.

33.

Evolution of protein domain promiscuity in eukaryotes.

Basu MK, Carmel L, Rogozin IB, Koonin EV.

Genome Res. 2008 Mar;18(3):449-61. doi: 10.1101/gr.6943508. Epub 2008 Jan 29.

34.

Patterns of intron gain and conservation in eukaryotic genes.

Carmel L, Rogozin IB, Wolf YI, Koonin EV.

BMC Evol Biol. 2007 Oct 12;7:192.

35.

Analysis of rare amino acid replacements supports the Coelomata clade.

Rogozin IB, Wolf YI, Carmel L, Koonin EV.

Mol Biol Evol. 2007 Dec;24(12):2594-7. Epub 2007 Oct 5.

PMID:
17921482
36.

Widespread positive selection in synonymous sites of mammalian genes.

Resch AM, Carmel L, Mariño-Ramírez L, Ogurtsov AY, Shabalina SA, Rogozin IB, Koonin EV.

Mol Biol Evol. 2007 Aug;24(8):1821-31. Epub 2007 May 23.

37.

Evolutionarily conserved genes preferentially accumulate introns.

Carmel L, Rogozin IB, Wolf YI, Koonin EV.

Genome Res. 2007 Jul;17(7):1045-50. Epub 2007 May 10.

38.

Three distinct modes of intron dynamics in the evolution of eukaryotes.

Carmel L, Wolf YI, Rogozin IB, Koonin EV.

Genome Res. 2007 Jul;17(7):1034-44. Epub 2007 May 10.

39.

Ecdysozoan clade rejected by genome-wide analysis of rare amino acid replacements.

Rogozin IB, Wolf YI, Carmel L, Koonin EV.

Mol Biol Evol. 2007 Apr;24(4):1080-90. Epub 2007 Feb 13.

PMID:
17299026
40.

Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family.

Kuznetsova E, Proudfoot M, Gonzalez CF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, Yakunin AF.

J Biol Chem. 2006 Nov 24;281(47):36149-61. Epub 2006 Sep 21.

41.

Unifying measures of gene function and evolution.

Wolf YI, Carmel L, Koonin EV.

Proc Biol Sci. 2006 Jun 22;273(1593):1507-15.

42.

Gene expression profile of empirically delineated classes of unexplained chronic fatigue.

Carmel L, Efroni S, White PD, Aslakson E, Vollmer-Conna U, Rajeevan MS.

Pharmacogenomics. 2006 Apr;7(3):375-86.

PMID:
16610948
43.

Combining hierarchy and energy for drawing directed graphs.

Carmel L, Harel D, Koren Y.

IEEE Trans Vis Comput Graph. 2004 Jan-Feb;10(1):46-57.

PMID:
15382697
44.

Towards an odor communication system.

Harel D, Carmel L, Lancet D.

Comput Biol Chem. 2003 May;27(2):121-33.

PMID:
12821309
45.

Estimating the size of the olfactory repertoire.

Carmel L, Harel D, Lancet D.

Bull Math Biol. 2001 Nov;63(6):1063-78.

PMID:
11732176
46.

Healing bone using recombinant human bone morphogenetic protein 2 and copolymer.

Kirker-Head CA, Gerhart TN, Armstrong R, Schelling SH, Carmel LA.

Clin Orthop Relat Res. 1998 Apr;(349):205-17.

PMID:
9584385
47.

Birth order, suicidal preoccupation, and scores suggesting manic-depressive tendencies.

Bergman KJ, Carmel LH, Lester D.

Psychol Rep. 1997 Apr;80(2):442.

PMID:
9129363

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