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1.

Boosting signal-to-noise in complex biology: prior knowledge is power.

Ideker, Trey; Dutkowski, Janusz; Hood, Leroy.

Cell ; 144(6): 860-3, 2011 Mar 18.

Article in English | MEDLINE | ID: mdl-21414478

2.

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate.

Lin, Yin C; Jhunjhunwala, Suchit; Benner, Christopher; Heinz, Sven; Welinder, Eva; Mansson, Robert; Sigvardsson, Mikael; Hagman, James; Espinoza, Celso A; Dutkowski, Janusz; Ideker, Trey; Glass, Christopher K; Murre, Cornelis.

Nat Immunol ; 11(7): 635-43, 2010 Jul.

Article in English | MEDLINE | ID: mdl-20543837

3.

Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors.

Mercer, Elinore M; Lin, Yin C; Benner, Christopher; Jhunjhunwala, Suchit; Dutkowski, Janusz; Flores, Martha; Sigvardsson, Mikael; Ideker, Trey; Glass, Christopher K; Murre, Cornelis.

Immunity ; 35(3): 413-25, 2011 Sep 23.

Article in English | MEDLINE | ID: mdl-21903424

4.

A Distributed Network for Intensive Longitudinal Monitoring in Metastatic Triple-Negative Breast Cancer.

Blau, C Anthony; Ramirez, Arturo B; Blau, Sibel; Pritchard, Colin C; Dorschner, Michael O; Schmechel, Stephen C; Martins, Timothy J; Mahen, Elisabeth M; Burton, Kimberly A; Komashko, Vitalina M; Radenbaugh, Amie J; Dougherty, Katy; Thomas, Anju; Miller, Christopher P; Annis, James; Fromm, Jonathan R; Song, Chaozhong; Chang, Elizabeth; Howard, Kellie; Austin, Sharon; Schmidt, Rodney A; Linenberger, Michael L; Becker, Pamela S; Senecal, Francis M; Mecham, Brigham H; Lee, Su-In; Madan, Anup; Ronen, Roy; Dutkowski, Janusz; Heimfeld, Shelly; Wood, Brent L; Stilwell, Jackie L; Kaldjian, Eric P; Haussler, David; Zhu, Jingchun.

J Natl Compr Canc Netw ; 14(1): 8-17, 2016 01.

Article in English | MEDLINE | ID: mdl-26733551

5.

NeXO Web: the NeXO ontology database and visualization platform.

Dutkowski, Janusz; Ono, Keiichiro; Kramer, Michael; Yu, Michael; Pratt, Dexter; Demchak, Barry; Ideker, Trey.

Nucleic Acids Res ; 42(Database issue): D1269-74, 2014 Jan.

Article in English | MEDLINE | ID: mdl-24271398

6.

Inferring gene ontologies from pairwise similarity data.

Kramer, Michael; Dutkowski, Janusz; Yu, Michael; Bafna, Vineet; Ideker, Trey.

Bioinformatics ; 30(12): i34-42, 2014 Jun 15.

Article in English | MEDLINE | ID: mdl-24932003

7.

Novel data-mining approach identifies biomarkers for diagnosis of Kawasaki disease.

Tremoulet, Adriana H; Dutkowski, Janusz; Sato, Yuichiro; Kanegaye, John T; Ling, Xuefeng B; Burns, Jane C.

Pediatr Res ; 78(5): 547-53, 2015 Nov.

Article in English | MEDLINE | ID: mdl-26237629

8.

Improving breast cancer survival analysis through competition-based multidimensional modeling.

Bilal, Erhan; Dutkowski, Janusz; Guinney, Justin; Jang, In Sock; Logsdon, Benjamin A; Pandey, Gaurav; Sauerwine, Benjamin A; Shimoni, Yishai; Moen Vollan, Hans Kristian; Mecham, Brigham H; Rueda, Oscar M; Tost, Jorg; Curtis, Christina; Alvarez, Mariano J; Kristensen, Vessela N; Aparicio, Samuel; Børresen-Dale, Anne-Lise; Caldas, Carlos; Califano, Andrea; Friend, Stephen H; Ideker, Trey; Schadt, Eric E; Stolovitzky, Gustavo A; Margolin, Adam A.

PLoS Comput Biol ; 9(5): e1003047, 2013.

Article in English | MEDLINE | ID: mdl-23671412

9.

Protein networks as logic functions in development and cancer.

Dutkowski, Janusz; Ideker, Trey.

PLoS Comput Biol ; 7(9): e1002180, 2011 Sep.

Article in English | MEDLINE | ID: mdl-21980275

10.

Systematic Analysis of Genetic and Pathway Determinants of Eribulin Sensitivity across 100 Human Cancer Cell Lines from the Cancer Cell Line Encyclopedia (CCLE).

Sachdev, Pallavi; Ronen, Roy; Dutkowski, Janusz; Littlefield, Bruce A.

Cancers (Basel) ; 14(18)2022 Sep 19.

Article in English | MEDLINE | ID: mdl-36139690

11.

Pathway-level mutation analysis in primary high-grade serous ovarian cancer and matched brain metastases.

Duchnowska, Renata; Supernat, Anna Maria; Peksa, Rafal; Lukasiewicz, Marta; Stokowy, Tomasz; Ronen, Roy; Dutkowski, Janusz; Uminska, Monika; Izycka-Swieszewska, Ewa; Kowalczyk, Anna; Och, Waldemar; Rucinska, Monika; Olszewski, Wojciech P; Mandat, Tomasz; Jarosz, Bozena; Bienkowski, Michal; Biernat, Wojciech; Jassem, Jacek.

Sci Rep ; 12(1): 20537, 2022 11 29.

Article in English | MEDLINE | ID: mdl-36446793

12.

Safety, Feasibility, and Merits of Longitudinal Molecular Testing of Multiple Metastatic Sites to Inform mTNBC Patient Treatment in the Intensive Trial of Omics in Cancer.

Burton, Kimberly A; Mahen, Elisabeth; Konnick, Eric Quentin; Blau, Sibel; Dorschner, Michael O; Ramirez, Arturo B; Schmechel, Stephen C; Song, Chaozhong; Parulkar, Rahul; Parker, Stephanie; Senecal, Francis Mark; Pritchard, Colin C; Mecham, Brigham H; Szeto, Christopher; Spilman, Patricia; Zhu, Jingchun; Gadi, Vijayakrishna K; Ronen, Roy; Stilwell, Jackie; Kaldjian, Eric; Dutkowski, Janusz; Benz, Stephen Charles; Rabizadeh, Shahrooz; Soon-Shiong, Patrick; Blau, C Anthony.

JCO Precis Oncol ; 6: e2100280, 2022 03.

Article in English | MEDLINE | ID: mdl-35294224

13.

MODEVO: exploring modularity and evolution of protein interaction networks.

Wozniak, Michal; Tiuryn, Jerzy; Dutkowski, Janusz.

Bioinformatics ; 26(14): 1790-1, 2010 Jul 15.

Article in English | MEDLINE | ID: mdl-20507893

14.

Phylogeny-guided interaction mapping in seven eukaryotes.

Dutkowski, Janusz; Tiuryn, Jerzy.

BMC Bioinformatics ; 10: 393, 2009 Nov 30.

Article in English | MEDLINE | ID: mdl-19948065

15.

Identification of functional modules from conserved ancestral protein-protein interactions.

Dutkowski, Janusz; Tiuryn, Jerzy.

Bioinformatics ; 23(13): i149-58, 2007 Jul 01.

Article in English | MEDLINE | ID: mdl-17646291

16.

On consensus biomarker selection.

Dutkowski, Janusz; Gambin, Anna.

BMC Bioinformatics ; 8 Suppl 5: S5, 2007 May 24.

Article in English | MEDLINE | ID: mdl-17570864

17.

Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.

Yu, Michael Ku; Kramer, Michael; Dutkowski, Janusz; Srivas, Rohith; Licon, Katherine; Kreisberg, Jason; Ng, Cherie T; Krogan, Nevan; Sharan, Roded; Ideker, Trey.

Cell Syst ; 2(2): 77-88, 2016 Feb 24.

Article in English | MEDLINE | ID: mdl-26949740

18.

Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo.

Joshi, Shweta; Singh, Alok R; Zulcic, Muamera; Bao, Lei; Messer, Karen; Ideker, Trey; Dutkowski, Janusz; Durden, Donald L.

PLoS One ; 9(4): e95893, 2014.

Article in English | MEDLINE | ID: mdl-24770346

19.

A probabilistic model of neutral and selective dynamics of protein network evolution.

Dutkowski, Janusz; Tiuryn, Jerzy.

J Comput Biol ; 20(9): 631-42, 2013 Sep.

Article in English | MEDLINE | ID: mdl-23931333

20.

A gene ontology inferred from molecular networks.

Dutkowski, Janusz; Kramer, Michael; Surma, Michal A; Balakrishnan, Rama; Cherry, J Michael; Krogan, Nevan J; Ideker, Trey.

Nat Biotechnol ; 31(1): 38-45, 2013 Jan.

Article in English | MEDLINE | ID: mdl-23242164

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Boosting signal-to-noise in complex biology: prior knowledge is power.

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate.

Multilineage priming of enhancer repertoires precedes commitment to the B and myeloid cell lineages in hematopoietic progenitors.

A Distributed Network for Intensive Longitudinal Monitoring in Metastatic Triple-Negative Breast Cancer.

NeXO Web: the NeXO ontology database and visualization platform.

Inferring gene ontologies from pairwise similarity data.

Novel data-mining approach identifies biomarkers for diagnosis of Kawasaki disease.

Improving breast cancer survival analysis through competition-based multidimensional modeling.

Protein networks as logic functions in development and cancer.

Systematic Analysis of Genetic and Pathway Determinants of Eribulin Sensitivity across 100 Human Cancer Cell Lines from the Cancer Cell Line Encyclopedia (CCLE).

Pathway-level mutation analysis in primary high-grade serous ovarian cancer and matched brain metastases.

Safety, Feasibility, and Merits of Longitudinal Molecular Testing of Multiple Metastatic Sites to Inform mTNBC Patient Treatment in the Intensive Trial of Omics in Cancer.

MODEVO: exploring modularity and evolution of protein interaction networks.

Phylogeny-guided interaction mapping in seven eukaryotes.

Identification of functional modules from conserved ancestral protein-protein interactions.

On consensus biomarker selection.

Translation of Genotype to Phenotype by a Hierarchy of Cell Subsystems.

Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo.

A probabilistic model of neutral and selective dynamics of protein network evolution.

A gene ontology inferred from molecular networks.