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Items: 1 to 50 of 65

1.

Statistically Supported Identification of Tumor Subtypes.

Sun G, Krasnitz A.

Methods Mol Biol. 2019;1878:209-216. doi: 10.1007/978-1-4939-8868-6_12.

PMID:
30378078
2.

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

Sun G, Krasnitz A.

Methods Mol Biol. 2019;1878:85-93. doi: 10.1007/978-1-4939-8868-6_4.

PMID:
30378070
3.

Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer.

Tiriac H, Belleau P, Engle DD, Plenker D, Deschênes A, Somerville TDD, Froeling FEM, Burkhart RA, Denroche RE, Jang GH, Miyabayashi K, Young CM, Patel H, Ma M, LaComb JF, Palmaira RLD, Javed AA, Huynh JC, Johnson M, Arora K, Robine N, Shah M, Sanghvi R, Goetz AB, Lowder CY, Martello L, Driehuis E, LeComte N, Askan G, Iacobuzio-Donahue CA, Clevers H, Wood LD, Hruban RH, Thompson E, Aguirre AJ, Wolpin BM, Sasson A, Kim J, Wu M, Bucobo JC, Allen P, Sejpal DV, Nealon W, Sullivan JD, Winter JM, Gimotty PA, Grem JL, DiMaio DJ, Buscaglia JM, Grandgenett PM, Brody JR, Hollingsworth MA, O'Kane GM, Notta F, Kim E, Crawford JM, Devoe C, Ocean A, Wolfgang CL, Yu KH, Li E, Vakoc CR, Hubert B, Fischer SE, Wilson JM, Moffitt R, Knox J, Krasnitz A, Gallinger S, Tuveson DA.

Cancer Discov. 2018 Sep;8(9):1112-1129. doi: 10.1158/2159-8290.CD-18-0349. Epub 2018 May 31.

PMID:
29853643
4.

The Immune Landscape of Cancer.

Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L.

Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5.

5.

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation.

Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ; Cancer Genome Atlas Research Network, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M.

Cell. 2018 Apr 5;173(2):338-354.e15. doi: 10.1016/j.cell.2018.03.034.

6.

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

Alexander J, Kendall J, McIndoo J, Rodgers L, Aboukhalil R, Levy D, Stepansky A, Sun G, Chobardjiev L, Riggs M, Cox H, Hakker I, Nowak DG, Laze J, Llukani E, Srivastava A, Gruschow S, Yadav SS, Robinson B, Atwal G, Trotman LC, Lepor H, Hicks J, Wigler M, Krasnitz A.

Cancer Res. 2018 Jan 15;78(2):348-358. doi: 10.1158/0008-5472.CAN-17-1138. Epub 2017 Nov 27.

PMID:
29180472
7.

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

Kato M, Vasco DA, Sugino R, Narushima D, Krasnitz A.

R Soc Open Sci. 2017 Sep 27;4(9):171060. doi: 10.1098/rsos.171060. eCollection 2017 Sep.

8.

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

Krasnitz A, Kendall J, Alexander J, Levy D, Wigler M.

Trends Mol Med. 2017 Jul;23(7):594-603. doi: 10.1016/j.molmed.2017.05.005. Epub 2017 Jun 3. Review.

9.

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

Diermeier SD, Chang KC, Freier SM, Song J, El Demerdash O, Krasnitz A, Rigo F, Bennett CF, Spector DL.

Cell Rep. 2016 Sep 27;17(1):261-274. doi: 10.1016/j.celrep.2016.08.081.

10.

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

Baslan T, Kendall J, Ward B, Cox H, Leotta A, Rodgers L, Riggs M, D'Italia S, Sun G, Yong M, Miskimen K, Gilmore H, Saborowski M, Dimitrova N, Krasnitz A, Harris L, Wigler M, Hicks J.

Genome Res. 2015 May;25(5):714-24. doi: 10.1101/gr.188060.114. Epub 2015 Apr 9.

11.
12.

Computational methods for DNA copy-number analysis of tumors.

Kendall J, Krasnitz A.

Methods Mol Biol. 2014;1176:243-59. doi: 10.1007/978-1-4939-0992-6_20.

13.

Two Distinct Categories of Focal Deletions in Cancer Genomes.

Rajaram M, Zhang J, Wang T, Li J, Kuscu C, Qi H, Kato M, Grubor V, Weil RJ, Helland A, Borrenson-Dale AL, Cho KR, Levine DA, Houghton AN, Wolchok JD, Myeroff L, Markowitz SD, Lowe SW, Zhang M, Krasnitz A, Lucito R, Mu D, Powers RS.

PLoS One. 2013 Jun 21;8(6):e66264. doi: 10.1371/journal.pone.0066264. Print 2013.

14.

Target inference from collections of genomic intervals.

Krasnitz A, Sun G, Andrews P, Wigler M.

Proc Natl Acad Sci U S A. 2013 Jun 18;110(25):E2271-8. doi: 10.1073/pnas.1306909110. Epub 2013 Jun 6.

15.

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

Mazurek A, Luo W, Krasnitz A, Hicks J, Powers RS, Stillman B.

Cancer Discov. 2012 Sep;2(9):812-25. doi: 10.1158/2159-8290.CD-12-0116. Epub 2012 Jun 29.

16.

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

Scuoppo C, Miething C, Lindqvist L, Reyes J, Ruse C, Appelmann I, Yoon S, Krasnitz A, Teruya-Feldstein J, Pappin D, Pelletier J, Lowe SW.

Nature. 2012 Jul 12;487(7406):244-8. doi: 10.1038/nature11126.

17.

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

Xue W, Kitzing T, Roessler S, Zuber J, Krasnitz A, Schultz N, Revill K, Weissmueller S, Rappaport AR, Simon J, Zhang J, Luo W, Hicks J, Zender L, Wang XW, Powers S, Wigler M, Lowe SW.

Proc Natl Acad Sci U S A. 2012 May 22;109(21):8212-7. doi: 10.1073/pnas.1206062109. Epub 2012 May 7.

18.

Tumour evolution inferred by single-cell sequencing.

Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, Wigler M.

Nature. 2011 Apr 7;472(7341):90-4. doi: 10.1038/nature09807. Epub 2011 Mar 13.

19.

Towards patient-based cancer therapeutics.

Cancer Target Discovery and Development Network, Schreiber SL, Shamji AF, Clemons PA, Hon C, Koehler AN, Munoz B, Palmer M, Stern AM, Wagner BK, Powers S, Lowe SW, Guo X, Krasnitz A, Sawey ET, Sordella R, Stein L, Trotman LC, Califano A, Dalla-Favera R, Ferrando A, Iavarone A, Pasqualucci L, Silva J, Stockwell BR, Hahn WC, Chin L, DePinho RA, Boehm JS, Gopal S, Huang A, Root DE, Weir BA, Gerhard DS, Zenklusen JC, Roth MG, White MA, Minna JD, MacMillan JB, Posner BA.

Nat Biotechnol. 2010 Sep;28(9):904-6. doi: 10.1038/nbt0910-904. No abstract available.

20.

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

Russnes HG, Vollan HKM, Lingjærde OC, Krasnitz A, Lundin P, Naume B, Sørlie T, Borgen E, Rye IH, Langerød A, Chin SF, Teschendorff AE, Stephens PJ, Månér S, Schlichting E, Baumbusch LO, Kåresen R, Stratton MP, Wigler M, Caldas C, Zetterberg A, Hicks J, Børresen-Dale AL.

Sci Transl Med. 2010 Jun 30;2(38):38ra47. doi: 10.1126/scitranslmed.3000611.

21.

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

Floer M, Wang X, Prabhu V, Berrozpe G, Narayan S, Spagna D, Alvarez D, Kendall J, Krasnitz A, Stepansky A, Hicks J, Bryant GO, Ptashne M.

Cell. 2010 Apr 30;141(3):407-18. doi: 10.1016/j.cell.2010.03.048.

22.

Inferring tumor progression from genomic heterogeneity.

Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J, Wigler M.

Genome Res. 2010 Jan;20(1):68-80. doi: 10.1101/gr.099622.109. Epub 2009 Nov 10.

23.

Functional identification of tumor-suppressor genes through an in vivo RNA interference screen in a mouse lymphoma model.

Bric A, Miething C, Bialucha CU, Scuoppo C, Zender L, Krasnitz A, Xuan Z, Zuber J, Wigler M, Hicks J, McCombie RW, Hemann MT, Hannon GJ, Powers S, Lowe SW.

Cancer Cell. 2009 Oct 6;16(4):324-35. doi: 10.1016/j.ccr.2009.08.015.

24.

An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer.

Zender L, Xue W, Zuber J, Semighini CP, Krasnitz A, Ma B, Zender P, Kubicka S, Luk JM, Schirmacher P, McCombie WR, Wigler M, Hicks J, Hannon GJ, Powers S, Lowe SW.

Cell. 2008 Nov 28;135(5):852-64. doi: 10.1016/j.cell.2008.09.061. Epub 2008 Nov 13.

25.

Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA).

Grubor V, Krasnitz A, Troge JE, Meth JL, Lakshmi B, Kendall JT, Yamrom B, Alex G, Pai D, Navin N, Hufnagel LA, Lee YH, Cook K, Allen SL, Rai KR, Damle RN, Calissano C, Chiorazzi N, Wigler M, Esposito D.

Blood. 2009 Feb 5;113(6):1294-303. doi: 10.1182/blood-2008-05-158865. Epub 2008 Oct 15.

26.

Brk is coamplified with ErbB2 to promote proliferation in breast cancer.

Xiang B, Chatti K, Qiu H, Lakshmi B, Krasnitz A, Hicks J, Yu M, Miller WT, Muthuswamy SK.

Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12463-8. doi: 10.1073/pnas.0805009105. Epub 2008 Aug 21.

27.

DLC1 is a chromosome 8p tumor suppressor whose loss promotes hepatocellular carcinoma.

Xue W, Krasnitz A, Lucito R, Sordella R, Vanaelst L, Cordon-Cardo C, Singer S, Kuehnel F, Wigler M, Powers S, Zender L, Lowe SW.

Genes Dev. 2008 Jun 1;22(11):1439-44. doi: 10.1101/gad.1672608.

28.

Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer.

Kendall J, Liu Q, Bakleh A, Krasnitz A, Nguyen KC, Lakshmi B, Gerald WL, Powers S, Mu D.

Proc Natl Acad Sci U S A. 2007 Oct 16;104(42):16663-8. Epub 2007 Oct 9.

29.

Copy-number variants in patients with a strong family history of pancreatic cancer.

Lucito R, Suresh S, Walter K, Pandey A, Lakshmi B, Krasnitz A, Sebat J, Wigler M, Klein AP, Brune K, Palmisano E, Maitra A, Goggins M, Hruban RH.

Cancer Biol Ther. 2007 Oct;6(10):1592-9. Epub 2007 Jul 12.

PMID:
17912030
30.

Strong association of de novo copy number mutations with autism.

Sebat J, Lakshmi B, Malhotra D, Troge J, Lese-Martin C, Walsh T, Yamrom B, Yoon S, Krasnitz A, Kendall J, Leotta A, Pai D, Zhang R, Lee YH, Hicks J, Spence SJ, Lee AT, Puura K, Lehtimäki T, Ledbetter D, Gregersen PK, Bregman J, Sutcliffe JS, Jobanputra V, Chung W, Warburton D, King MC, Skuse D, Geschwind DH, Gilliam TC, Ye K, Wigler M.

Science. 2007 Apr 20;316(5823):445-9. Epub 2007 Mar 15.

31.

Novel patterns of genome rearrangement and their association with survival in breast cancer.

Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E, Esposito D, Alexander J, Troge J, Grubor V, Yoon S, Wigler M, Ye K, Børresen-Dale AL, Naume B, Schlicting E, Norton L, Hägerström T, Skoog L, Auer G, Månér S, Lundin P, Zetterberg A.

Genome Res. 2006 Dec;16(12):1465-79.

32.

High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors.

Hicks J, Muthuswamy L, Krasnitz A, Navin N, Riggs M, Grubor V, Esposito D, Alexander J, Troge J, Wigler M, Maner S, Lundin P, Zetterberg A.

Cold Spring Harb Symp Quant Biol. 2005;70:51-63.

PMID:
16869738
33.

Coherent gluon production in very-high-energy heavy-ion collisions.

Krasnitz A, Nara Y, Venugopalan R.

Phys Rev Lett. 2001 Nov 5;87(19):192302. Epub 2001 Oct 23.

PMID:
11690405
34.

Initial gluon multiplicity in heavy-ion collisions.

Krasnitz A, Venugopalan R.

Phys Rev Lett. 2001 Feb 26;86(9):1717-20.

PMID:
11290231
35.

Initial energy density of gluons produced in very-high-energy nuclear collisions

Krasnitz A, Venugopalan R.

Phys Rev Lett. 2000 May 8;84(19):4309-12.

PMID:
10990673
36.

Chern-Simons number diffusion in (1+1)-dimensional Higgs theory.

Forcrand Pd, Krasnitz A, Potting R.

Phys Rev D Part Fields. 1994 Nov 15;50(10):R6054-R6057. No abstract available.

PMID:
10017646
37.

Baryon density correlations in high temperature hadronic matter.

Bernard C, DeGrand TA, DeTar C, Gottlieb S, Krasnitz A, Sugar RL, Toussaint D.

Phys Rev D Part Fields. 1994 Jun 1;49(11):6051-6062. No abstract available.

PMID:
10016931
38.

Effects of spatial size, lattice doubling, and source operators on the hadron spectrum with dynamical staggered quarks at 6/g2=5.6.

Bitar KM, Edwards R, Heller UM, Kennedy AD, Gottlieb S, Kogut JB, Krasnitz A, Liu W, Ogilvie MC, Renken RL, Sinclair DK, Sugar RL, Toussaint D, Wang KC.

Phys Rev D Part Fields. 1994 Jun 1;49(11):6026-6038. No abstract available.

PMID:
10016929
39.

Hadron spectrum and matrix elements in QCD with dynamical Wilson fermions at 6/g2=5.3.

Bitar KM, DeGrand T, Edwards R, Gottlieb S, Heller UM, Kennedy AD, Kogut JB, Krasnitz A, Liu W, Ogilvie MC, Renken RL, Rossi P, Sinclair DK, Sugar RL, Toussaint D, Wang KC.

Phys Rev D Part Fields. 1994 Apr 1;49(7):3546-3562. No abstract available.

PMID:
10017350
40.

Finite-size and quark mass effects on the QCD spectrum with two flavors.

Bernard C, Blum T, DeGrand TA, DeTar C, Gottlieb S, Krasnitz A, Sugar RL, Toussaint D.

Phys Rev D Part Fields. 1993 Nov 1;48(9):4419-4434. No abstract available.

PMID:
10016722
41.

Simple hadronic matrix elements with Wilson valence quarks and dynamical staggered fermions at 6/g2=5.6.

Bitar KM, DeGrand T, Edwards R, Gottlieb S, Heller UM, Kennedy AD, Kogut JB, Krasnitz A, Liu W, Ogilvie MC, Renken RL, Rossi P, Sinclair DK, Sugar RL, Toussaint D, Wang KC.

Phys Rev D Part Fields. 1993 Jul 1;48(1):370-387. No abstract available.

PMID:
10016090
42.

Thermodynamics of lattice QCD with two light quarks on a 16(3) x 8 lattice.

Gottlieb S, Krasnitz A, Heller UM, Kennedy AD, Kogut JB, Renken RL, Sinclair DK, Sugar RL, Toussaint D, Wang KC.

Phys Rev D Part Fields. 1993 Apr 15;47(8):3619-3632. No abstract available.

PMID:
10015982
43.

QCD thermodynamics with two flavors of Wilson quarks at Nt=6.

Bernard C, Ogilvie MC, DeGrand TA, DeTar C, Gottlieb S, Krasnitz A, Sugar RL, Toussaint D.

Phys Rev D Part Fields. 1992 Nov 15;46(10):4741-4748. No abstract available.

PMID:
10014846
44.

Hadron spectrum in QCD with valence Wilson fermions and dynamical staggered fermions at 6/g2=5.6.

Bitar KM, DeGrand T, Edwards R, Gottlieb S, Heller UM, Kennedy AD, Kogut JB, Krasnitz A, Liu W, Ogilvie MC, Renken RL, Rossi P, Sinclair DK, Sugar RL, Toussaint D, Wang KC.

Phys Rev D Part Fields. 1992 Sep 1;46(5):2169-2178. No abstract available.

PMID:
10015133
45.

QCD thermodynamics with two flavors at Nt=6.

Bernard C, Ogilvie MC, DeGrand TA, DeTar C, Gottlieb S, Krasnitz A, Sugar RL, Toussaint D.

Phys Rev D Part Fields. 1992 May 15;45(10):3854-3861. No abstract available.

PMID:
10014278
46.

Spatial structure of screening propagators in hot QCD.

Bernard C, DeGrand TA, DeTar C, Gottlieb S, Krasnitz A, Ogilvie MC, Sugar RL, Toussaint D.

Phys Rev Lett. 1992 Apr 6;68(14):2125-2128. No abstract available.

PMID:
10045315
47.

Glueballs and topology in lattice QCD with two light flavors.

Bitar KM, Edwards R, Heller UM, Kennedy AD, DeGrand TA, Gottlieb S, Krasnitz A, Kogut JB, Renken RL, Liu W, Rossi P, Ogilvie MC, Sinclair DK, Wang KC, Sugar RL, Teper M, Toussaint D.

Phys Rev D Part Fields. 1991 Oct 1;44(7):2090-2109. No abstract available.

PMID:
10014090
48.

Spectroscopy with multiple field configurations.

Krasnitz A.

Phys Rev D Part Fields. 1991 Apr 15;43(8):2694-2700. No abstract available.

PMID:
10013659
49.

Hadron thermodynamics with Wilson quarks.

Bitar KM, DeGrand T, Edwards R, Gottlieb S, Heller UM, Kennedy AD, Kogut JB, Krasnitz A, Liu W, Ogilvie MC, Renken RL, Rossi P, Sinclair DK, Sugar RL, Teper M, Toussaint D, Wang KC.

Phys Rev D Part Fields. 1991 Apr 1;43(7):2396-2400. No abstract available.

PMID:
10013622
50.

Hadron spectrum in QCD at 6/g2=5.6.

Bitar KM, Edwards R, Heller UM, Kennedy AD, Liu W, DeGrand TA, Gottlieb S, Krasnitz A, Kogut JB, Renken RL, Ogilvie MC, Rossi P, Sinclair DK, Wang KC, Sugar RL, Teper M, Toussaint D.

Phys Rev D Part Fields. 1990 Dec 1;42(11):3794-3818. No abstract available.

PMID:
10012790

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