Franziska Michor

Franziska Michor

UNVERIFIED PROFILE

Are you Franziska Michor?   Register this Author

Register author
Franziska Michor

Franziska Michor

Publications by authors named "Franziska Michor"

Are you Franziska Michor?   Register this Author

100Publications

2557Reads

20Profile Views

Ascl2-Dependent Cell Dedifferentiation Drives Regeneration of Ablated Intestinal Stem Cells.

Cell Stem Cell 2020 Mar 20;26(3):377-390.e6. Epub 2020 Feb 20.

Department of Medical Oncology and Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02215, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2019.12.011DOI Listing
March 2020

DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding.

Bioinformatics 2019 Oct;35(19):3849-3851

Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btz074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6761956PMC
October 2019

Stochastic Evolution of Pancreatic Cancer Metastases During Logistic Clonal Expansion.

JCO Clin Cancer Inform 2019 03;3:1-11

Dana-Farber Cancer Institute, Boston, MA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1200/CCI.18.00079DOI Listing
March 2019

Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution.

Nat Genet 2018 12;50(12):1620-1623

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41588-018-0217-6
Publisher Site
http://dx.doi.org/10.1038/s41588-018-0217-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467055PMC
December 2018

KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.

Cancer Cell 2018 12 21;34(6):939-953.e9. Epub 2018 Nov 21.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA 02215, USA; The Eli and Edythe L Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Ludwig Center at Harvard, Boston, MA 02215, USA. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S15356108183048
Publisher Site
http://dx.doi.org/10.1016/j.ccell.2018.10.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310147PMC
December 2018

Hidden heterogeneity and circadian-controlled cell fate inferred from single cell lineages.

Nat Commun 2018 12 18;9(1):5372. Epub 2018 Dec 18.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, 02215, MA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41467-018-07788-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299096PMC
December 2018

Computational Model of Progression to Multiple Myeloma Identifies Optimum Screening Strategies.

JCO Clin Cancer Inform 2018 12;2:1-12

Philipp M. Altrock, Moffitt Cancer Center and Research Institute; Morsani College of Medicine, University of South Florida, Tampa, FL; Jeremy Ferlic and Franziska Michor, Dana-Farber Cancer Institute and Harvard University; Harvard T.H. Chan School of Public Health, Boston; Franziska Michor, Center for Cancer Evolution, Dana-Farber Cancer Institute, and The Ludwig Center at Harvard, Boston; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA; Tobias Galla, University of Manchester, Manchester, United Kingdom; and Michael H. Tomasson, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1200/CCI.17.00131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6873949PMC
December 2018

Fitness variation in isogenic populations leads to a novel evolutionary mechanism for crossing fitness valleys.

Commun Biol 2018 26;1:151. Epub 2018 Sep 26.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s42003-018-0160-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158234PMC
September 2018

Mathematical modeling identifies optimum lapatinib dosing schedules for the treatment of glioblastoma patients.

PLoS Comput Biol 2018 01 2;14(1):e1005924. Epub 2018 Jan 2.

Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massasschusetts, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1005924DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766249PMC
January 2018

Nuclear topology modulates the mutational landscapes of cancer genomes.

Nat Struct Mol Biol 2017 Nov 2;24(11):1000-1006. Epub 2017 Oct 2.

Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.3474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5744871PMC
November 2017

Stochastic Tunneling of Two Mutations in a Population of Cancer Cells.

PLoS One 2013 26;8(6):e65724. Epub 2013 Jun 26.

Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0065724PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694076PMC
October 2017

Estimating mono- and bi-phasic regression parameters using a mixture piecewise linear Bayesian hierarchical model.

PLoS One 2017 19;12(7):e0180756. Epub 2017 Jul 19.

Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180756PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516991PMC
September 2017

Distance in cancer gene expression from stem cells predicts patient survival.

PLoS One 2017 23;12(3):e0173589. Epub 2017 Mar 23.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0173589PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363813PMC
August 2017

SIApopr: a computational method to simulate evolutionary branching trees for analysis of tumor clonal evolution.

Bioinformatics 2017 Jul;33(14):2221-2223

Department of Biostatistics and Computational Biology, Center for Cancer Evolution, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btx146DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870718PMC
July 2017

Pharmacokinetics and Drug Interactions Determine Optimum Combination Strategies in Computational Models of Cancer Evolution.

Cancer Res 2017 07 31;77(14):3908-3921. Epub 2017 May 31.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/0008-5472.CAN-16-2871DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5553595PMC
July 2017

Mathematical Modeling Links Pregnancy-Associated Changes and Breast Cancer Risk.

Cancer Res 2017 06 30;77(11):2800-2809. Epub 2017 Mar 30.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/0008-5472.CAN-16-2504DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5477484PMC
June 2017

Clonal Hematopoiesis Associated With Adverse Outcomes After Autologous Stem-Cell Transplantation for Lymphoma.

J Clin Oncol 2017 May 9;35(14):1598-1605. Epub 2017 Jan 9.

Christopher J. Gibson, R. Coleman Lindsley, Brenton G. Mar, Jiantao Shi, Ann S. Lacasce, Arnold S. Freedman, David C. Fisher, Eric Jacobsen, Philippe Armand, Edwin P. Alyea, John Koreth, Vincent Ho, Robert J. Soiffer, Joseph H. Antin, Jerome Ritz, Sarah Nikiforow, Franziska Michor, and Donna Neuberg, Dana-Farber Cancer Institute; Jiantao Shi and Franziska Michor, Harvard T.H. Chan School of Public Health; Siddhartha Jaiswal, Elizabeth A. Morgan, and Benjamin L. Ebert, Brigham and Women's Hospital, Boston; Benjamin L. Ebert, Broad Institute, Cambridge, MA; Vatche Tchekmedyian, Memorial Sloan Kettering Cancer Center, New York, NY; Alysia Bosworth, Anita Bansal, and Stephen J. Forman, City of Hope National Medical Center, Duarte, CA; and Liton Francisco, Jianbo He, Ravi Bhatia, and Smita Bhatia, University of Alabama at Birmingham, Birmingham, AL.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1200/JCO.2016.71.6712DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5455707PMC
May 2017

A computational strategy to adjust for copy number in tumor Hi-C data.

Bioinformatics 2016 12 16;32(24):3695-3701. Epub 2016 Aug 16.

Department of Computational Biology and Biostatistics, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btw540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078171PMC
December 2016

Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells.

Cell Rep 2016 12;17(12):3395-3406

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2016.11.080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5467646PMC
December 2016

Mathematical modeling of erythrocyte chimerism informs genetic intervention strategies for sickle cell disease.

Am J Hematol 2016 09 14;91(9):931-7. Epub 2016 Jul 14.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/ajh.24449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5093908PMC
September 2016

Myeloma Cell Dynamics in Response to Treatment Supports a Model of Hierarchical Differentiation and Clonal Evolution.

Clin Cancer Res 2016 Aug 22;22(16):4206-4214. Epub 2016 Mar 22.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1078-0432.CCR-15-2793DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987182PMC
August 2016

The mathematics of cancer: integrating quantitative models.

Nat Rev Cancer 2015 Dec;15(12):730-45

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard T.H. Chan School of Public Health, 450 Brookline Avenue, Boston, Massachusetts 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrc4029DOI Listing
December 2015

On the validity of using increases in 5-year survival rates to measure success in the fight against cancer.

PLoS One 2014 23;9(7):e83100. Epub 2014 Jul 23.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0083100PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108307PMC
November 2015

Improving Cancer Treatment via Mathematical Modeling: Surmounting the Challenges Is Worth the Effort.

Cell 2015 Nov;163(5):1059-1063

Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2015.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676401PMC
November 2015

An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer.

PLoS Comput Biol 2015 Sep 17;11(9):e1004350. Epub 2015 Sep 17.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1004350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4575033PMC
September 2015

The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells.

Cancer Inform 2015 15;14(Suppl 4):19-31. Epub 2015 Jul 15.

Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University, Palo Alto, CA, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.4137/CIN.S19338DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4504404PMC
August 2015

Stochastic tunneling and metastable states during the somatic evolution of cancer.

Genetics 2015 Apr 26;199(4):1213-28. Epub 2015 Jan 26.

Theoretical Physics, School of Physics and Astronomy, The University of Manchester, Manchester M13 9PL, United Kingdom

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.114.171553DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4391561PMC
April 2015

Polyploidy can drive rapid adaptation in yeast.

Nature 2015 Mar 2;519(7543):349-52. Epub 2015 Mar 2.

1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts 02215, USA [3] Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland 20815, USA [4] Department of Pediatric Hematology/Oncology, Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature14187DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497379PMC
March 2015

Epigenetic diversity in hematopoietic neoplasms.

Biochim Biophys Acta 2014 Dec 18;1846(2):477-84. Epub 2014 Sep 18.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bbcan.2014.09.003DOI Listing
December 2014

Dynamics of chronic myeloid leukemia response to dasatinib, nilotinib, and high-dose imatinib.

Haematologica 2014 Nov 12;99(11):1701-9. Epub 2014 Sep 12.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.3324/haematol.2013.085977DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4222479PMC
November 2014

Non-cell-autonomous driving of tumour growth supports sub-clonal heterogeneity.

Nature 2014 Oct 30;514(7520):54-8. Epub 2014 Jul 30.

1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA [3] Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA [4] BBS Program, Harvard Medical School, Boston, Massachusetts 02115, USA [5] Harvard Stem Cell Institute and the Broad Institute, Cambridge, Massachusetts 02138, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature13556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184961PMC
October 2014

Evolution of acquired resistance to anti-cancer therapy.

J Theor Biol 2014 Aug 25;355:10-20. Epub 2014 Mar 25.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jtbi.2014.02.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058397PMC
August 2014

Clonal evolution in breast cancer revealed by single nucleus genome sequencing.

Nature 2014 Aug 30;512(7513):155-60. Epub 2014 Jul 30.

1] The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA [2] The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA [3] The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computational Biology, Houston, Texas 77030, USA.

View Article

Download full-text PDF

Source
https://dash.harvard.edu/bitstream/handle/1/14065379/4158312
Web Search
http://michorlab.dfci.harvard.edu/publications/Nature2014a.p
Web Search
http://www.nature.com/doifinder/10.1038/nature13600
Publisher Site
http://dx.doi.org/10.1038/nature13600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4158312PMC
August 2014

Most human non-GCIMP glioblastoma subtypes evolve from a common proneural-like precursor glioma.

Cancer Cell 2014 Aug;26(2):288-300

Division of Human Biology and Solid Tumor Translational Research, Fred Hutchinson Cancer Research Center, Department of Neurosurgery and Alvord Brain Tumor Center, University of Washington, Seattle, WA 98109, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ccr.2014.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4143139PMC
August 2014

Histone modifications are associated with transcript isoform diversity in normal and cancer cells.

PLoS Comput Biol 2014 Jun 5;10(6):e1003611. Epub 2014 Jun 5.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1003611DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4046914PMC
June 2014

Integrative analysis of 1q23.3 copy-number gain in metastatic urothelial carcinoma.

Clin Cancer Res 2014 Apr 31;20(7):1873-83. Epub 2014 Jan 31.

Authors' Affiliations: Departments of Biostatistics and Computational Biology, and Medical Oncology; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute; Department of Biostatistics, Harvard School of Public Health; Department of Pathology; Translational Medicine Division, Brigham and Women's Hospital, Boston; Broad Institute of Harvard and MIT, Cambridge, Massachusetts; Sidney Kimmel Cancer Center; Department of Pathology, Johns Hopkins University, Baltimore, Maryland; Department of Urology, Memorial Sloan-Kettering Cancer Center, New York, New York; and Hospital del Mar Research Institute-IMIM, Barcelona; and Hospital Parc Tauli, Sabadell, Spain.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1078-0432.CCR-13-0759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975677PMC
April 2014

Understanding tissue context influences on intratumour heterogeneity.

Nat Cell Biol 2014 Apr;16(4):301-2

Center for Bioengineering and Tissue Regeneration and Departments of Surgery, Anatomy, Bioengineering and Therapeutics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Helen Diller Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94143, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncb2942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180082PMC
April 2014

Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.

J Natl Cancer Inst 2014 Apr 3;106(5). Epub 2014 Apr 3.

Affiliations of authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (MR, ACC, LT, FM, CH, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (MR, ACC, LT, FM, CH, GP); Center for Cancer Research (WW, S-hK, MB) and Department of Pathology (EO), Massachusetts General Hospital, Boston, MA; City University of New York School of Public Health, Hunter College, New York, NY (LW); Sung-hoon Kim, Yonsei University College of Medicine, Seoul, Korea (S-HK).

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/jnci/dju048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580556PMC
April 2014

Genetic and phenotypic diversity in breast tumor metastases.

Cancer Res 2014 Mar 21;74(5):1338-48. Epub 2014 Jan 21.

Authors' Affiliations: Departments of Medical Oncology and Biostatistics and Computational Biology, Dana-Farber Cancer Institute; Department of Medicine, Brigham and Women's Hospital; Department of Medicine, Harvard Medical School; Department of Biostatistics, Harvard School of Public Health, Boston; Departments of Physics and Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Harvard Stem Cell Institute, Cambridge, Massachusetts; Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York; Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medical Oncology, Hospital Clinic, Institut d'Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain; Department of Pathology, MizMedi Hospital, Seoul, South Korea; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; and Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/0008-5472.CAN-13-2357-TDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963810PMC
March 2014

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity.

Cell Rep 2014 Feb 23;6(3):514-27. Epub 2014 Jan 23.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2013.12.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928845PMC
February 2014

Patterns of proliferative activity in the colonic crypt determine crypt stability and rates of somatic evolution.

PLoS Comput Biol 2013 13;9(6):e1003082. Epub 2013 Jun 13.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
https://dx.plos.org/10.1371/journal.pcbi.1003082
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1003082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3681728PMC
January 2014

Mathematical modeling of PDGF-driven glioblastoma reveals optimized radiation dosing schedules.

Cell 2014 Jan;156(3):603-616

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2013.12.029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923371PMC
January 2014

A physical sciences network characterization of non-tumorigenic and metastatic cells.

Authors:
David B Agus Jenolyn F Alexander Wadih Arap Shashanka Ashili Joseph E Aslan Robert H Austin Vadim Backman Kelly J Bethel Richard Bonneau Wei-Chiang Chen Chira Chen-Tanyolac Nathan C Choi Steven A Curley Matthew Dallas Dhwanil Damania Paul C W Davies Paolo Decuzzi Laura Dickinson Luis Estevez-Salmeron Veronica Estrella Mauro Ferrari Claudia Fischbach Jasmine Foo Stephanie I Fraley Christian Frantz Alexander Fuhrmann Philippe Gascard Robert A Gatenby Yue Geng Sharon Gerecht Robert J Gillies Biana Godin William M Grady Alex Greenfield Courtney Hemphill Barbara L Hempstead Abigail Hielscher W Daniel Hillis Eric C Holland Arig Ibrahim-Hashim Tyler Jacks Roger H Johnson Ahyoung Joo Jonathan E Katz Laimonas Kelbauskas Carl Kesselman Michael R King Konstantinos Konstantopoulos Casey M Kraning-Rush Peter Kuhn Kevin Kung Brian Kwee Johnathon N Lakins Guillaume Lambert David Liao Jonathan D Licht Jan T Liphardt Liyu Liu Mark C Lloyd Anna Lyubimova Parag Mallick John Marko Owen J T McCarty Deirdre R Meldrum Franziska Michor Shannon M Mumenthaler Vivek Nandakumar Thomas V O'Halloran Steve Oh Renata Pasqualini Matthew J Paszek Kevin G Philips Christopher S Poultney Kuldeepsinh Rana Cynthia A Reinhart-King Robert Ros Gregg L Semenza Patti Senechal Michael L Shuler Srimeenakshi Srinivasan Jack R Staunton Yolanda Stypula Hariharan Subramanian Thea D Tlsty Garth W Tormoen Yiider Tseng Alexander van Oudenaarden Scott S Verbridge Jenny C Wan Valerie M Weaver Jonathan Widom Christine Will Denis Wirtz Jonathan Wojtkowiak Pei-Hsun Wu

Sci Rep 2013 ;3:1449

Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep01449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636513PMC
October 2013

DNA replication timing and higher-order nuclear organization determine single-nucleotide substitution patterns in cancer genomes.

Nat Commun 2013 ;4:1502

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Instituteh, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms2502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633418PMC
June 2013

Epidermal growth factor receptor tyrosine kinase inhibitor-resistant disease.

J Clin Oncol 2013 Mar 11;31(8):1070-80. Epub 2013 Feb 11.

University School of Medicine, Nashville,TN, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1200/JCO.2012.43.3912DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589701PMC
March 2013

Selection pressure exerted by imatinib therapy leads to disparate outcomes of imatinib discontinuation trials.

Haematologica 2012 Oct 14;97(10):1553-61. Epub 2012 Mar 14.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://www.haematologica.org/cgi/doi/10.3324/haematol.2012.0
Publisher Site
http://dx.doi.org/10.3324/haematol.2012.062844DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3487556PMC
October 2012

The probable cell of origin of NF1- and PDGF-driven glioblastomas.

PLoS One 2011 9;6(9):e24454. Epub 2011 Sep 9.

Department of Regenerative Medicine, Cleveland Clinic, Cleveland, Ohio, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024454PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170338PMC
June 2012

A race between tumor immunoescape and genome maintenance selects for optimum levels of (epi)genetic instability.

PLoS Comput Biol 2012 16;8(2):e1002370. Epub 2012 Feb 16.

PRESTO, Japan Science and Technology Agency, Graduate School of Mathematical Sciences, The University of Tokyo, Institute for Virus Research, Kyoto University, Kyoto, Japan.

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1002370
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1002370DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280962PMC
June 2012

Fitness conferred by BCR-ABL kinase domain mutations determines the risk of pre-existing resistance in chronic myeloid leukemia.

PLoS One 2011 28;6(11):e27682. Epub 2011 Nov 28.

Program for Industrial and Systems Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027682PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225363PMC
April 2012

Evolution of the cancer genome.

Trends Genet 2012 Apr 16;28(4):155-63. Epub 2012 Feb 16.

Department of Biostatistics and Computational Biology, Harvard School of Public Health, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.tig.2012.01.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711268PMC
April 2012

Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer.

Clin Cancer Res 2012 Mar 6;18(5):1323-33. Epub 2012 Jan 6.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts 02215, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1078-0432.CCR-11-2271DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3569085PMC
March 2012

A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis.

PLoS Comput Biol 2012 Jan 5;8(1):e1002337. Epub 2012 Jan 5.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.plos.org/10.1371/journal.pcbi.1002337
Publisher Site
http://dx.doi.org/10.1371/journal.pcbi.1002337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3252265PMC
January 2012

Computational modeling of pancreatic cancer reveals kinetics of metastasis suggesting optimum treatment strategies.

Cell 2012 Jan;148(1-2):362-75

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Harvard School of Public Health, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://linkinghub.elsevier.com/retrieve/pii/S009286741101514
Publisher Site
http://dx.doi.org/10.1016/j.cell.2011.11.060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289413PMC
January 2012

Evolutionary modeling of combination treatment strategies to overcome resistance to tyrosine kinase inhibitors in non-small cell lung cancer.

Mol Pharm 2011 Dec 25;8(6):2069-79. Epub 2011 Oct 25.

Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1021/mp200270vDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3230244PMC
December 2011

DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes.

Nat Biotechnol 2011 Nov 20;29(12):1103-8. Epub 2011 Nov 20.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nbt.2030
Publisher Site
http://dx.doi.org/10.1038/nbt.2030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923360PMC
November 2011

Dynamics of chronic myeloid leukemia response to long-term targeted therapy reveal treatment effects on leukemic stem cells.

Blood 2011 Aug 8;118(6):1622-31. Epub 2011 Jun 8.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.

View Article

Download full-text PDF

Source
http://www.bloodjournal.org/cgi/doi/10.1182/blood-2011-02-33
Publisher Site
http://dx.doi.org/10.1182/blood-2011-02-339267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156048PMC
August 2011

What does physics have to do with cancer?

Nat Rev Cancer 2011 Aug 18;11(9):657-70. Epub 2011 Aug 18.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA. harvard.edu

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nrc3092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711102PMC
August 2011

DNA secondary structures and epigenetic determinants of cancer genome evolution.

Nat Struct Mol Biol 2011 Jul 3;18(8):950-5. Epub 2011 Jul 3.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.2089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963273PMC
July 2011

Intratumor heterogeneity in evolutionary models of tumor progression.

Genetics 2011 Jun 15;188(2):461-77. Epub 2011 Mar 15.

Department of Mathematics, Duke University, Durham, North Carolina 27708, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1534/genetics.110.125724DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122322PMC
June 2011

Evolutionary dynamics of BRCA1 alterations in breast tumorigenesis.

J Theor Biol 2011 Mar 29;273(1):207-15. Epub 2010 Dec 29.

Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jtbi.2010.12.033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3713469PMC
March 2011

Evolutionary dynamics of intratumor heterogeneity.

PLoS One 2011 Mar 30;6(3):e17866. Epub 2011 Mar 30.

Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0017866PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068148PMC
March 2011

Stochastic dynamics of cancer initiation.

Phys Biol 2011 Feb 7;8(1):015002. Epub 2011 Feb 7.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1088/1478-3975/8/1/015002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3569097PMC
February 2011

The therapeutic implications of plasticity of the cancer stem cell phenotype.

PLoS One 2010 Dec 17;5(12):e14366. Epub 2010 Dec 17.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, Massachusetts, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0014366PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3003707PMC
December 2010

The origins and implications of intratumor heterogeneity.

Cancer Prev Res (Phila) 2010 Nov 19;3(11):1361-4. Epub 2010 Oct 19.

Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/1940-6207.CAPR-10-0234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633425PMC
November 2010

A mathematical framework to determine the temporal sequence of somatic genetic events in cancer.

Proc Natl Acad Sci U S A 2010 Oct 23;107(41):17604-9. Epub 2010 Sep 23.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

View Article

Download full-text PDF

Source
http://www.pnas.org/lookup/doi/10.1073/pnas.1009117107
Publisher Site
http://dx.doi.org/10.1073/pnas.1009117107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955151PMC
October 2010