Publications by authors named "Arif Harmanci"

24Publications

Identification of novel fusion transcripts in meningioma.

J Neurooncol 2020 Sep 19;149(2):219-230. Epub 2020 Sep 19.

Department of Neurosurgery, Baylor College of Medicine, 7200 Cambridge 9th Floor, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1007/s11060-020-03599-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7553203PMC
September 2020

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.

Cell 2020 03 20;180(5):915-927.e16. Epub 2020 Feb 20.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06511, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.01.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7210002PMC
March 2020

CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data.

Nat Commun 2020 01 3;11(1):89. Epub 2020 Jan 3.

Center for Computational Systems Medicine, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.

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http://dx.doi.org/10.1038/s41467-019-13779-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6941987PMC
January 2020

When Biology Gets Personal: Hidden Challenges of Privacy and Ethics in Biological Big Data.

Pac Symp Biocomput 2019 ;24:386-390

Computational Biology and Bioinformatics Program, Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, 06511, USA*This work is partially supported by NIH grant U01EB023686.,

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February 2020

Analysis of sensitive information leakage in functional genomics signal profiles through genomic deletions.

Nat Commun 2018 06 22;9(1):2453. Epub 2018 Jun 22.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA.

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http://dx.doi.org/10.1038/s41467-018-04875-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015012PMC
June 2018

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals.

Nat Commun 2016 Apr 18;7:11101. Epub 2016 Apr 18.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1038/ncomms11101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837449PMC
April 2016

Quantification of private information leakage from phenotype-genotype data: linking attacks.

Nat Methods 2016 Mar 1;13(3):251-6. Epub 2016 Feb 1.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.

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http://www.nature.com/articles/nmeth.3746
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http://dx.doi.org/10.1038/nmeth.3746DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834871PMC
March 2016

MUSIC: identification of enriched regions in ChIP-Seq experiments using a mappability-corrected multiscale signal processing framework.

Genome Biol 2014 ;15(10):474

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/s13059-014-0474-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234855PMC
October 2015

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

Stochastic sampling of the RNA structural alignment space.

Nucleic Acids Res 2009 Jul 8;37(12):4063-75. Epub 2009 May 8.

Department of Electrical and Computer Engineering, University of Rochester, Hopeman 204, RC Box 270126, Rochester, NY 14627, USA.

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https://nar.oxfordjournals.org/content/37/12/4063.full-text-
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gkp276
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http://dx.doi.org/10.1093/nar/gkp276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709569PMC
July 2009

PARTS: probabilistic alignment for RNA joinT secondary structure prediction.

Nucleic Acids Res 2008 Apr 26;36(7):2406-17. Epub 2008 Feb 26.

Department of Electrical and Computer Engineering, University of Rochester, Hopeman 204, RC Box 270126, Rochester, NY 14627, USA.

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http://dx.doi.org/10.1093/nar/gkn043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367733PMC
April 2008

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign.

BMC Bioinformatics 2007 Apr 19;8:130. Epub 2007 Apr 19.

Department of Electrical and Computer Engineering, University of Rochester, Hopeman 204, Rochester, NY 14627, USA.

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http://dx.doi.org/10.1186/1471-2105-8-130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1868766PMC
April 2007