Publications Authored by Alexander Krasnitz

The Immune Landscape of Cancer.

Authors:

Vésteinn Thorsson David L Gibbs Scott D Brown Denise Wolf Dante S Bortone Tai-Hsien Ou Yang Eduard Porta-Pardo Galen F Gao Christopher L Plaisier James A Eddy Elad Ziv Aedin C Culhane Evan O Paull I K Ashok Sivakumar Andrew J Gentles Raunaq Malhotra Farshad Farshidfar Antonio Colaprico Joel S Parker Lisle E Mose Nam Sy Vo Jianfang Liu Yuexin Liu Janet Rader Varsha Dhankani Sheila M Reynolds Reanne Bowlby Andrea Califano Andrew D Cherniack Dimitris Anastassiou Davide Bedognetti Younes Mokrab Aaron M Newman Arvind Rao Ken Chen Alexander Krasnitz Hai Hu Tathiane M Malta Houtan Noushmehr Chandra Sekhar Pedamallu Susan Bullman Akinyemi I Ojesina Andrew Lamb Wanding Zhou Hui Shen Toni K Choueiri John N Weinstein Justin Guinney Joel Saltz Robert A Holt Charles S Rabkin Alexander J Lazar Jonathan S Serody Elizabeth G Demicco Mary L Disis Benjamin G Vincent Ilya Shmulevich

Immunity 2019 Aug;51(2):411-412

Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2019.08.004	DOI Listing

August 2019

CORE: A Software Tool for Delineating Regions of Recurrent DNA Copy Number Alteration in Cancer.

Authors:

Guoli Sun Alexander Krasnitz

Methods Mol Biol 2019 ;1878:85-93

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

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http://dx.doi.org/10.1007/978-1-4939-8868-6_4	DOI Listing

May 2019

Statistically Supported Identification of Tumor Subtypes.

Authors:

Guoli Sun Alexander Krasnitz

Methods Mol Biol 2019 ;1878:209-216

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.

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http://dx.doi.org/10.1007/978-1-4939-8868-6_12	DOI Listing

May 2019

Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer.

Authors:

Hervé Tiriac Pascal Belleau Dannielle D Engle Dennis Plenker Astrid Deschênes Tim D D Somerville Fieke E M Froeling Richard A Burkhart Robert E Denroche Gun-Ho Jang Koji Miyabayashi C Megan Young Hardik Patel Michelle Ma Joseph F LaComb Randze Lerie D Palmaira Ammar A Javed Jasmine C Huynh Molly Johnson Kanika Arora Nicolas Robine Minita Shah Rashesh Sanghvi Austin B Goetz Cinthya Y Lowder Laura Martello Else Driehuis Nicolas LeComte Gokce Askan Christine A Iacobuzio-Donahue Hans Clevers Laura D Wood Ralph H Hruban Elizabeth Thompson Andrew J Aguirre Brian M Wolpin Aaron Sasson Joseph Kim Maoxin Wu Juan Carlos Bucobo Peter Allen Divyesh V Sejpal William Nealon James D Sullivan Jordan M Winter Phyllis A Gimotty Jean L Grem Dominick J DiMaio Jonathan M Buscaglia Paul M Grandgenett Jonathan R Brody Michael A Hollingsworth Grainne M O'Kane Faiyaz Notta Edward Kim James M Crawford Craig Devoe Allyson Ocean Christopher L Wolfgang Kenneth H Yu Ellen Li Christopher R Vakoc Benjamin Hubert Sandra E Fischer Julie M Wilson Richard Moffitt Jennifer Knox Alexander Krasnitz Steven Gallinger David A Tuveson

Cancer Discov 2018 09 31;8(9):1112-1129. Epub 2018 May 31.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

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http://dx.doi.org/10.1158/2159-8290.CD-18-0349	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6125219	PMC

September 2018

The Immune Landscape of Cancer.

Authors:

Vésteinn Thorsson David L Gibbs Scott D Brown Denise Wolf Dante S Bortone Tai-Hsien Ou Yang Eduard Porta-Pardo Galen F Gao Christopher L Plaisier James A Eddy Elad Ziv Aedin C Culhane Evan O Paull I K Ashok Sivakumar Andrew J Gentles Raunaq Malhotra Farshad Farshidfar Antonio Colaprico Joel S Parker Lisle E Mose Nam Sy Vo Jianfang Liu Yuexin Liu Janet Rader Varsha Dhankani Sheila M Reynolds Reanne Bowlby Andrea Califano Andrew D Cherniack Dimitris Anastassiou Davide Bedognetti Younes Mokrab Aaron M Newman Arvind Rao Ken Chen Alexander Krasnitz Hai Hu Tathiane M Malta Houtan Noushmehr Chandra Sekhar Pedamallu Susan Bullman Akinyemi I Ojesina Andrew Lamb Wanding Zhou Hui Shen Toni K Choueiri John N Weinstein Justin Guinney Joel Saltz Robert A Holt Charles S Rabkin Alexander J Lazar Jonathan S Serody Elizabeth G Demicco Mary L Disis Benjamin G Vincent Ilya Shmulevich

Immunity 2018 04 5;48(4):812-830.e14. Epub 2018 Apr 5.

Institute for Systems Biology, 401 Terry Ave N, Seattle, WA 98109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2018.03.023	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5982584	PMC

April 2018

Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer.

Cancer Res 2018 01 27;78(2):348-358. Epub 2017 Nov 27.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-1138	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5771881	PMC

January 2018

Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer.

Authors:

Mamoru Kato Daniel A Vasco Ryuichi Sugino Daichi Narushima Alexander Krasnitz

R Soc Open Sci 2017 Sep 27;4(9):171060. Epub 2017 Sep 27.

Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1098/rsos.171060	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627131	PMC

September 2017

Early Detection of Cancer in Blood Using Single-Cell Analysis: A Proposal.

Authors:

Alexander Krasnitz Jude Kendall Joan Alexander Dan Levy Michael Wigler

Trends Mol Med 2017 07 3;23(7):594-603. Epub 2017 Jun 3.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molmed.2017.05.005	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5502711	PMC

July 2017

Mammary Tumor-Associated RNAs Impact Tumor Cell Proliferation, Invasion, and Migration.

Authors:

Sarah D Diermeier Kung-Chi Chang Susan M Freier Junyan Song Osama El Demerdash Alexander Krasnitz Frank Rigo C Frank Bennett David L Spector

Cell Rep 2016 09;17(1):261-274

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079290	PMC
http://dx.doi.org/10.1016/j.celrep.2016.08.081	DOI Listing

September 2016

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling.

Authors:

Timour Baslan Jude Kendall Brian Ward Hilary Cox Anthony Leotta Linda Rodgers Michael Riggs Sean D'Italia Guoli Sun Mao Yong Kristy Miskimen Hannah Gilmore Michael Saborowski Nevenka Dimitrova Alexander Krasnitz Lyndsay Harris Michael Wigler James Hicks

Genome Res 2015 May 9;25(5):714-24. Epub 2015 Apr 9.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA;

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http://dx.doi.org/10.1101/gr.188060.114	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417119	PMC

May 2015

Computational methods for DNA copy-number analysis of tumors.

Authors:

Jude Kendall Alexander Krasnitz

Methods Mol Biol 2014 ;1176:243-59

Cold Spring Harbor Laboratory, 1 Bungtown Road, 11724, Cold Spring Harbor, NY, USA.

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http://dx.doi.org/10.1007/978-1-4939-0992-6_20	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5136461	PMC

March 2015

Significant distinct branches of hierarchical trees: a framework for statistical analysis and applications to biological data.

Authors:

Guoli Sun Alexander Krasnitz

BMC Genomics 2014 Nov 19;15:1000. Epub 2014 Nov 19.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1186/1471-2164-15-1000	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253613	PMC

November 2014

Target inference from collections of genomic intervals.

Authors:

Alexander Krasnitz Guoli Sun Peter Andrews Michael Wigler

Proc Natl Acad Sci U S A 2013 Jun 6;110(25):E2271-8. Epub 2013 Jun 6.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1073/pnas.1306909110	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690846	PMC

June 2013

DDX5 regulates DNA replication and is required for cell proliferation in a subset of breast cancer cells.

Authors:

Anthony Mazurek Weijun Luo Alexander Krasnitz James Hicks R Scott Powers Bruce Stillman

Cancer Discov 2012 Sep 29;2(9):812-25. Epub 2012 Jun 29.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://dx.doi.org/10.1158/2159-8290.CD-12-0116	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440546	PMC

September 2012

A tumour suppressor network relying on the polyamine-hypusine axis.

Authors:

Claudio Scuoppo Cornelius Miething Lisa Lindqvist José Reyes Cristian Ruse Iris Appelmann Seungtai Yoon Alexander Krasnitz Julie Teruya-Feldstein Darryl Pappin Jerry Pelletier Scott W Lowe

Nature 2012 Jul;487(7406):244-8

Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York 11724, USA.

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http://www.nature.com/articles/nature11126	Publisher Site
http://dx.doi.org/10.1038/nature11126	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530829	PMC

July 2012

A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions.

Authors:

Wen Xue Thomas Kitzing Stephanie Roessler Johannes Zuber Alexander Krasnitz Nikolaus Schultz Kate Revill Susann Weissmueller Amy R Rappaport Janelle Simon Jack Zhang Weijun Luo James Hicks Lars Zender Xin Wei Wang Scott Powers Michael Wigler Scott W Lowe

Proc Natl Acad Sci U S A 2012 May 7;109(21):8212-7. Epub 2012 May 7.

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

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http://dx.doi.org/10.1073/pnas.1206062109	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361457	PMC

May 2012

Genomic architecture characterizes tumor progression paths and fate in breast cancer patients.

Sci Transl Med 2010 Jun;2(38):38ra47

Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway.

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http://dx.doi.org/10.1126/scitranslmed.3000611	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3972440	PMC

June 2010

A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding.

Authors:

Monique Floer Xin Wang Vidya Prabhu Georgina Berrozpe Santosh Narayan Dan Spagna David Alvarez Jude Kendall Alexander Krasnitz Asya Stepansky James Hicks Gene O Bryant Mark Ptashne

Cell 2010 Apr;141(3):407-18

Molecular Biology Program, Sloan Kettering Institute, 1275 York Avenue, New York, NY 10021, USA.

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http://dx.doi.org/10.1016/j.cell.2010.03.048	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032599	PMC

April 2010

Inferring tumor progression from genomic heterogeneity.

Authors:

Nicholas Navin Alexander Krasnitz Linda Rodgers Kerry Cook Jennifer Meth Jude Kendall Michael Riggs Yvonne Eberling Jennifer Troge Vladimir Grubor Dan Levy Pär Lundin Susanne Månér Anders Zetterberg James Hicks Michael Wigler

Genome Res 2010 Jan 10;20(1):68-80. Epub 2009 Nov 10.

Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.099622.109	Publisher Site
http://dx.doi.org/10.1101/gr.099622.109	DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2798832	PMC