Peter Calabrese

Peter Calabrese

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Peter Calabrese

Peter Calabrese

Publications by authors named "Peter Calabrese"

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34Publications

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AID-RNA polymerase II transcription-dependent deamination of IgV DNA.

Nucleic Acids Res 2019 Nov;47(20):10815-10829

Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1093/nar/gkz821DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6846656PMC
November 2019

Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments.

J Comput Biol 2019 Nov 15. Epub 2019 Nov 15.

Quantitative and Computational Biology, University of Southern California, Los Angeles, California.

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http://dx.doi.org/10.1089/cmb.2019.0264DOI Listing
November 2019

Estimating Exceptionally Rare Germline and Somatic Mutation Frequencies via Next Generation Sequencing.

PLoS One 2016 24;11(6):e0158340. Epub 2016 Jun 24.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158340PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920415PMC
July 2017

Single cell lineage tracing reveals a role for TgfβR2 in intestinal stem cell dynamics and differentiation.

Proc Natl Acad Sci U S A 2016 10 10;113(43):12192-12197. Epub 2016 Oct 10.

Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR 97239.

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http://dx.doi.org/10.1073/pnas.1611980113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5087053PMC
October 2016

Germline Stem Cell Competition, Mutation Hot Spots, Genetic Disorders, and Older Fathers.

Annu Rev Genomics Hum Genet 2016 08 8;17:219-43. Epub 2016 Apr 8.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089-2910; email: ,

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http://dx.doi.org/10.1146/annurev-genom-083115-022656DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5007215PMC
August 2016

New evidence for positive selection helps explain the paternal age effect observed in achondroplasia.

Hum Mol Genet 2013 Oct 4;22(20):4117-26. Epub 2013 Jun 4.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

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http://dx.doi.org/10.1093/hmg/ddt260DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3781639PMC
October 2013

Age-dependent germline mosaicism of the most common noonan syndrome mutation shows the signature of germline selection.

Am J Hum Genet 2013 Jun 30;92(6):917-26. Epub 2013 May 30.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1016/j.ajhg.2013.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682763PMC
June 2013

Positive selection for new disease mutations in the human germline: evidence from the heritable cancer syndrome multiple endocrine neoplasia type 2B.

PLoS Genet 2012 16;8(2):e1002420. Epub 2012 Feb 16.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA.

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http://dx.doi.org/10.1371/journal.pgen.1002420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280958PMC
February 2013

Analysis of a single-stranded DNA-scanning process in which activation-induced deoxycytidine deaminase (AID) deaminates C to U haphazardly and inefficiently to ensure mutational diversity.

J Biol Chem 2011 Jul 12;286(28):24931-42. Epub 2011 May 12.

Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-2910, USA.

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http://dx.doi.org/10.1074/jbc.M111.241208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137067PMC
July 2011

A simple algebraic cancer equation: calculating how cancers may arise with normal mutation rates.

BMC Cancer 2010 Jan 5;10. Epub 2010 Jan 5.

Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1186/1471-2407-10-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829925PMC
January 2010

Allele-specific expression assays using Solexa.

BMC Genomics 2009 Sep 9;10:422. Epub 2009 Sep 9.

Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA.

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http://dx.doi.org/10.1186/1471-2164-10-422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2749874PMC
September 2009

Understanding what determines the frequency and pattern of human germline mutations.

Nat Rev Genet 2009 Jul;10(7):478-88

Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, California 90089-2910, USA.

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http://dx.doi.org/10.1038/nrg2529DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744436PMC
July 2009

The ups and downs of mutation frequencies during aging can account for the Apert syndrome paternal age effect.

PLoS Genet 2009 Jul 10;5(7):e1000558. Epub 2009 Jul 10.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700275PMC
July 2009

A germ-line-selective advantage rather than an increased mutation rate can explain some unexpectedly common human disease mutations.

Proc Natl Acad Sci U S A 2008 Jul 16;105(29):10143-8. Epub 2008 Jul 16.

Molecular and Computational Biology Program, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1073/pnas.0801267105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2474563PMC
July 2008

Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase.

J Biol Chem 2008 Jun 16;283(25):17428-39. Epub 2008 Apr 16.

Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-2910, USA.

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http://dx.doi.org/10.1074/jbc.M802121200DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2427360PMC
June 2008

Mammalian meiotic recombination hot spots.

Annu Rev Genet 2007 ;41:369-99

Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1146/annurev.genet.41.110306.130301DOI Listing
May 2008

The molecular anatomy of spontaneous germline mutations in human testes.

PLoS Biol 2007 Sep;5(9):e224

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.0050224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1951783PMC
September 2007

A population genetics model with recombination hotspots that are heterogeneous across the population.

Authors:
Peter Calabrese

Proc Natl Acad Sci U S A 2007 Mar 5;104(11):4748-52. Epub 2007 Mar 5.

Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1073/pnas.0610195104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1838671PMC
March 2007

APOBEC3G DNA deaminase acts processively 3' --> 5' on single-stranded DNA.

Nat Struct Mol Biol 2006 May 23;13(5):392-9. Epub 2006 Apr 23.

Department of Biological Sciences Molecular and Computational Section, University of Southern California, Los Angeles, California 90089-2910, USA.

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http://dx.doi.org/10.1038/nsmb1086DOI Listing
May 2006

A nonparametric test reveals selection for rapid flowering in the Arabidopsis genome.

PLoS Biol 2006 May 25;4(5):e137. Epub 2006 Apr 25.

Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.

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http://dx.doi.org/10.1371/journal.pbio.0040137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440937PMC
May 2006

High-resolution recombination patterns in a region of human chromosome 21 measured by sperm typing.

PLoS Genet 2006 May 5;2(5):e70. Epub 2006 May 5.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, USA.

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http://dx.doi.org/10.1371/journal.pgen.0020070DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1456319PMC
May 2006

Numbers of mutations to different types of colorectal cancer.

BMC Cancer 2005 Oct 3;5:126. Epub 2005 Oct 3.

Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1186/1471-2407-5-126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1266026PMC
October 2005

Biochemical analysis of hypermutational targeting by wild type and mutant activation-induced cytidine deaminase.

J Biol Chem 2004 Dec 14;279(49):51612-21. Epub 2004 Sep 14.

Department of Biological Sciences, Hedco Molecular Biology Laboratories, University of Southern California, Los Angeles, California 90089-1340, USA.

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http://dx.doi.org/10.1074/jbc.M408135200DOI Listing
December 2004

Polyploid and multilocus extensions of the Wahlund inequality.

Theor Popul Biol 2004 Dec;66(4):381-91

Program in Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 1042 West 36th Place--DRB 289, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1016/j.tpb.2004.07.001DOI Listing
December 2004

Fast identification and statistical evaluation of segmental homologies in comparative maps.

Bioinformatics 2003 ;19 Suppl 1:i74-80

Department of Mathematics, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1093/bioinformatics/btg1008DOI Listing
October 2004

Ectopic pregnancy diagnosis and the pseudo-sac.

Fertil Steril 2004 May;81(5):1225-8

Medical Research Council, Biostatistics Unit, Institute of Public Health, University Forvite Site, Cambridge, United Kingdom.

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http://dx.doi.org/10.1016/j.fertnstert.2003.09.068DOI Listing
May 2004

Pretumor progression: clonal evolution of human stem cell populations.

Am J Pathol 2004 Apr;164(4):1337-46

Department of Biological Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1615336PMC
http://dx.doi.org/10.1016/S0002-9440(10)63220-8DOI Listing
April 2004

Enhanced stem cell survival in familial adenomatous polyposis.

Am J Pathol 2004 Apr;164(4):1369-77

Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S000294401063223
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1615334PMC
http://dx.doi.org/10.1016/S0002-9440(10)63223-3DOI Listing
April 2004

Colorectal pretumor progression before and after loss of DNA mismatch repair.

Am J Pathol 2004 Apr;164(4):1447-53

Department of Biological Sciences, Program in Molecular and Computational Biology, University of Southern California, Los Angeles, California 90033, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1615342PMC
http://dx.doi.org/10.1016/S0002-9440(10)63231-2DOI Listing
April 2004

Hot and cold spots of recombination in the human genome: the reason we should find them and how this can be achieved.

Am J Hum Genet 2003 Jul 22;73(1):5-16. Epub 2003 May 22.

Molecular and Computational Biology Program, University of Southern California, 835 West 37th Street, SHS 172, Los Angeles, CA 90089-1340, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1180590PMC
http://dx.doi.org/10.1086/376419DOI Listing
July 2003

Dinucleotide repeats in the Drosophila and human genomes have complex, length-dependent mutation processes.

Mol Biol Evol 2003 May 2;20(5):715-25. Epub 2003 Apr 2.

University of Southern California, USA.

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http://dx.doi.org/10.1093/molbev/msg084DOI Listing
May 2003

Haplotype block structure and its applications to association studies: power and study designs.

Am J Hum Genet 2002 Dec 18;71(6):1386-94. Epub 2002 Nov 18.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles 90089, USA.

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http://dx.doi.org/10.1086/344780DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC378580PMC
December 2002