Liran Carmel

Liran Carmel

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Liran Carmel

Publications by authors named "Liran Carmel"

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Reconstructing Denisovan Anatomy Using DNA Methylation Maps.

Cell 2019 Sep;179(1):180-192.e10

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.08.035DOI Listing
September 2019

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

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

a Department of Genetics , The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem , Jerusalem , Israel.

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http://dx.doi.org/10.1080/15476286.2018.1429880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6152444PMC
November 2018

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

Nucleic Acids Res 2018 11;46(20):11014-11029

Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.

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http://dx.doi.org/10.1093/nar/gky791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237757PMC
November 2018

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

Proc Natl Acad Sci U S A 2018 01 16;115(5):968-973. Epub 2018 Jan 16.

Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642;

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http://dx.doi.org/10.1073/pnas.1715531115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798355PMC
January 2018

Inferring Past Environments from Ancient Epigenomes.

Mol Biol Evol 2017 10;34(10):2429-2438

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel.

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https://academic.oup.com/mbe/article/34/10/2429/4010936
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http://dx.doi.org/10.1093/molbev/msx211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850778PMC
October 2017

Gene ORGANizer: linking genes to the organs they affect.

Nucleic Acids Res 2017 07;45(W1):W138-W145

Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkx302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570240PMC
July 2017

Identification of introns harboring functional sequence elements through positional conservation.

Sci Rep 2017 06 23;7(1):4201. Epub 2017 Jun 23.

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.

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http://dx.doi.org/10.1038/s41598-017-04476-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5482813PMC
June 2017

Archaic Adaptive Introgression in TBX15/WARS2.

Mol Biol Evol 2017 03;34(3):509-524

Department of Integrative Biology, University of California Berkeley, Berkeley, CA.

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http://dx.doi.org/10.1093/molbev/msw283DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5430617PMC
March 2017

The role of nucleotide composition in premature termination codon recognition.

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

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel.

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http://dx.doi.org/10.1186/s12859-016-1384-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142417PMC
December 2016

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

Trends Ecol Evol 2016 Apr 15;31(4):290-300. Epub 2016 Feb 15.

Department of Genetics, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.tree.2016.01.010DOI Listing
April 2016

System-wide Analysis of the T Cell Response.

Cell Rep 2016 Mar 10;14(11):2733-44. Epub 2016 Mar 10.

Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.02.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4805488PMC
March 2016

JuncDB: an exon-exon junction database.

Nucleic Acids Res 2016 Jan 30;44(D1):D101-9. Epub 2015 Oct 30.

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel

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http://dx.doi.org/10.1093/nar/gkv1142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702826PMC
January 2016

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

Science 2014 May 17;344(6183):523-7. Epub 2014 Apr 17.

Department of Genetics, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel.

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http://dx.doi.org/10.1126/science.1250368DOI Listing
May 2014

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

Nucleic Acids Res 2013 Jun 19;41(11):5604-13. Epub 2013 Apr 19.

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.

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http://dx.doi.org/10.1093/nar/gkt244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3675471PMC
June 2013

Dependencies among editing sites in serotonin 2C receptor mRNA.

PLoS Comput Biol 2012 6;8(9):e1002663. Epub 2012 Sep 6.

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel.

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http://dx.plos.org/10.1371/journal.pcbi.1002663
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http://dx.doi.org/10.1371/journal.pcbi.1002663DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435259PMC
January 2013

The function of introns.

Front Genet 2012 13;3:55. Epub 2012 Apr 13.

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Jerusalem, Israel.

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http://dx.doi.org/10.3389/fgene.2012.00055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3325483PMC
October 2012

Origin and evolution of spliceosomal introns.

Biol Direct 2012 Apr 16;7:11. Epub 2012 Apr 16.

National Center for Biotechnology Information NLM/NIH, 8600 Rockville Pike, Bldg, 38A, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1186/1745-6150-7-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488318PMC
April 2012

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

Mol Biol Evol 2012 Jan 29;29(1):179-86. Epub 2011 Jul 29.

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msr192DOI Listing
January 2012

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

Adv Bioinformatics 2010 6:167408. Epub 2010 May 6.

Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel.

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http://dx.doi.org/10.1155/2010/167408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866244PMC
July 2011

The ecoresponsive genome of Daphnia pulex.

Science 2011 Feb;331(6017):555-61

Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA.

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http://www3.nd.edu/~mpfrende/PDFs/Science-2011-Colbourne-555
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http://www.sciencemag.org/cgi/doi/10.1126/science.1197761
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http://dx.doi.org/10.1126/science.1197761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3529199PMC
February 2011

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

Genome Biol Evol 2009 Sep 22;1:382-90. Epub 2009 Sep 22.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1093/gbe/evp038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817431PMC
September 2009

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

Methods Mol Biol 2009 ;541:357-71

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1007/978-1-59745-243-4_16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3410445PMC
June 2009

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

Cell Stem Cell 2008 Dec;3(6):670-80

Laboratory of Molecular Biology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1016/j.stem.2008.09.012DOI Listing
December 2008

Robust linear dimensionality reduction.

IEEE Trans Vis Comput Graph 2004 Jul-Aug;10(4):459-70

AT&T Labs--Research, Florham Park, NJ 07932-0971, USA.

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http://dx.doi.org/10.1109/TVCG.2004.17DOI Listing
August 2008

Superposition of transcriptional behaviors determines gene state.

PLoS One 2008 Aug 6;3(8):e2901. Epub 2008 Aug 6.

Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002901PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2488367PMC
August 2008

Evolution of protein domain promiscuity in eukaryotes.

Genome Res 2008 Mar 29;18(3):449-61. Epub 2008 Jan 29.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

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http://www.genome.org/cgi/doi/10.1101/gr.6943508
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http://dx.doi.org/10.1101/gr.6943508DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2259109PMC
March 2008

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

Biol Direct 2008 Mar 17;3. Epub 2008 Mar 17.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1186/1745-6150-3-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2292158PMC
March 2008

Predicting the receptive range of olfactory receptors.

PLoS Comput Biol 2008 Feb;4(2):e18

Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel.

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https://dx.plos.org/10.1371/journal.pcbi.0040018
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http://dx.doi.org/10.1371/journal.pcbi.0040018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2222922PMC
February 2008

Analysis of rare amino acid replacements supports the Coelomata clade.

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

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http://dx.doi.org/10.1093/molbev/msm218DOI Listing
December 2007

Patterns of intron gain and conservation in eukaryotic genes.

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

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

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http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2148-7-192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2151770PMC
October 2007

Widespread positive selection in synonymous sites of mammalian genes.

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

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1093/molbev/msm100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632937PMC
August 2007

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

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

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

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http://dx.doi.org/10.1101/gr.6438607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899114PMC
July 2007

Evolutionarily conserved genes preferentially accumulate introns.

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

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.

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http://dx.doi.org/10.1101/gr.5978207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899115PMC
July 2007

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

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

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.1093/molbev/msm029DOI Listing
April 2007

Unifying measures of gene function and evolution.

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

National Institutes of Health, National Center for Biotechnology Information, National Library of Medicine Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1098/rspb.2006.3472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1560323PMC
June 2006

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

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

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.

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http://dx.doi.org/10.2217/14622416.7.3.375DOI Listing
April 2006

Combining hierarchy and energy for drawing directed graphs.

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

Department of Computer Science and Applied Mathematics, the Weizmann Institute of Science, Rehovot 76100, Israel.

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http://dx.doi.org/10.1109/TVCG.2004.1260757DOI Listing
October 2004