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The role of synthetic biology in climate change mitigation.

DeLisi C.

Biol Direct. 2019 Aug 20;14(1):14. doi: 10.1186/s13062-019-0247-8.


A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer.

Chen HR, Sherr DH, Hu Z, DeLisi C.

BMC Med Genomics. 2016 Jul 30;9(1):51. doi: 10.1186/s12920-016-0212-7.


Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

Granger BR, Chang YC, Wang Y, DeLisi C, Segrè D, Hu Z.

PLoS Comput Biol. 2016 Apr 15;12(4):e1004875. doi: 10.1371/journal.pcbi.1004875. eCollection 2016 Apr.


Mutated Pathways as a Guide to Adjuvant Therapy Treatments for Breast Cancer.

Liu Y, Hu Z, DeLisi C.

Mol Cancer Ther. 2016 Jan;15(1):184-9. doi: 10.1158/1535-7163.MCT-15-0601. Epub 2015 Dec 1.


Evaluation and integration of cancer gene classifiers: identification and ranking of plausible drivers.

Liu Y, Tian F, Hu Z, DeLisi C.

Sci Rep. 2015 May 11;5:10204. doi: 10.1038/srep10204.


Igf1 and Pacap rescue cerebellar granule neurons from apoptosis via a common transcriptional program.

Maino B, D'Agata V, Severini C, Ciotti MT, Calissano P, Copani A, Chang YC, DeLisi C, Cavallaro S.

Cell Death Discov. 2015;1. pii: 15029. Epub 2015 Sep 7.


The COMBREX project: design, methodology, and initial results.

Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, DeLisi C, Roberts RJ, Steffen M, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.


VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies.

Hu Z, Chang YC, Wang Y, Huang CL, Liu Y, Tian F, Granger B, Delisi C.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W225-31. doi: 10.1093/nar/gkt401. Epub 2013 May 28.


Genome-wide association studies.

Yang TH, Kon M, DeLisi C.

Methods Mol Biol. 2013;939:233-51. doi: 10.1007/978-1-62703-107-3_15.


TATA binding proteins can recognize nontraditional DNA sequences.

Ahn S, Huang CL, Ozkumur E, Zhang X, Chinnala J, Yalcin A, Bandyopadhyay S, Russek S, Unlü MS, DeLisi C, Irani RJ.

Biophys J. 2012 Oct 3;103(7):1510-7. doi: 10.1016/j.bpj.2012.08.030. Epub 2012 Oct 2.


Pathway-based classification of cancer subtypes.

Kim S, Kon M, DeLisi C.

Biol Direct. 2012 Jul 3;7:21. doi: 10.1186/1745-6150-7-21.


Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge.

Huang CL, Lamb J, Chindelevitch L, Kostrowicki J, Guinney J, Delisi C, Ziemek D.

BMC Bioinformatics. 2012 Mar 23;13:46. doi: 10.1186/1471-2105-13-46.


Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer.

Shigemizu D, Hu Z, Hung JH, Huang CL, Wang Y, DeLisi C.

PLoS Comput Biol. 2012 Feb;8(2):e1002347. doi: 10.1371/journal.pcbi.1002347. Epub 2012 Feb 9.


The NIH National Center for Integrative Biomedical Informatics (NCIBI).

Athey BD, Cavalcoli JD, Jagadish HV, Omenn GS, Mirel B, Kretzler M, Burant C, Isokpehi RD, DeLisi C; NCIBI faculty, trainees, and staff.

J Am Med Inform Assoc. 2012 Mar-Apr;19(2):166-70. doi: 10.1136/amiajnl-2011-000552. Epub 2011 Nov 19.


Gene set enrichment analysis: performance evaluation and usage guidelines.

Hung JH, Yang TH, Hu Z, Weng Z, DeLisi C.

Brief Bioinform. 2012 May;13(3):281-91. doi: 10.1093/bib/bbr049. Epub 2011 Sep 7. Review.


Combinations of newly confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to increased disease risk.

Yang TH, Kon M, Hung JH, Delisi C.

BMC Med Genomics. 2011 Aug 9;4:63. doi: 10.1186/1755-8794-4-63.


COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.

Roberts RJ, Chang YC, Hu Z, Rachlin JN, Anton BP, Pokrzywa RM, Choi HP, Faller LL, Guleria J, Housman G, Klitgord N, Mazumdar V, McGettrick MG, Osmani L, Swaminathan R, Tao KR, Letovsky S, Vitkup D, Segrè D, Salzberg SL, Delisi C, Steffen M, Kasif S.

Nucleic Acids Res. 2011 Jan;39(Database issue):D11-4. doi: 10.1093/nar/gkq1168. Epub 2010 Nov 21.


Robust gene network analysis reveals alteration of the STAT5a network as a hallmark of prostate cancer.

Reddy A, Huang CC, Liu H, Delisi C, Nevalainen MT, Szalma S, Bhanot G.

Genome Inform. 2010;24:139-53.


Phenotypic connections in surprising places.

Linghu B, DeLisi C.

Genome Biol. 2010;11(4):116. doi: 10.1186/gb-2010-11-4-116. Epub 2010 Apr 28.


Identification of functional modules that correlate with phenotypic difference: the influence of network topology.

Hung JH, Whitfield TW, Yang TH, Hu Z, Weng Z, DeLisi C.

Genome Biol. 2010;11(2):R23. doi: 10.1186/gb-2010-11-2-r23. Epub 2010 Feb 26.


Label-free microarray imaging for direct detection of DNA hybridization and single-nucleotide mismatches.

Ozkumur E, Ahn S, Yalçin A, Lopez CA, Cevik E, Irani RJ, DeLisi C, Chiari M, Unlü MS.

Biosens Bioelectron. 2010 Mar 15;25(7):1789-95. doi: 10.1016/j.bios.2009.12.032. Epub 2010 Jan 4.


Identification of a microRNA panel for clear-cell kidney cancer.

Juan D, Alexe G, Antes T, Liu H, Madabhushi A, Delisi C, Ganesan S, Bhanot G, Liou LS.

Urology. 2010 Apr;75(4):835-41. doi: 10.1016/j.urology.2009.10.033. Epub 2009 Dec 29.


Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

Linghu B, Snitkin ES, Hu Z, Xia Y, Delisi C.

Genome Biol. 2009;10(9):R91. doi: 10.1186/gb-2009-10-9-r91. Epub 2009 Sep 3.


VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology.

Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, DeLisi C.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W115-21. doi: 10.1093/nar/gkp406. Epub 2009 May 21.


Applications of optical resonance to biological imaging and label-free protein microarrays.

Unlü MS, Ozkumur IE, Needham J, Bergstein DA, Goldberg BB, Yalcin A, Spuhler P, Irani R, DeLisi C.

Conf Proc IEEE Eng Med Biol Soc. 2008;2008:2643. doi: 10.1109/IEMBS.2008.4649744.


Machine learning for regulatory analysis and transcription factor target prediction in yeast.

Holloway DT, Kon M, Delisi C.

Syst Synth Biol. 2007 Mar;1(1):25-46. doi: 10.1007/s11693-006-9003-3.


Meetings that changed the world: Santa Fe 1986: Human genome baby-steps.

DeLisi C.

Nature. 2008 Oct 16;455(7215):876-7. doi: 10.1038/455876a. No abstract available.


Identification of novel epigenetic markers for clear cell renal cell carcinoma.

Dalgin GS, Drever M, Williams T, King T, DeLisi C, Liou LS.

J Urol. 2008 Sep;180(3):1126-30. doi: 10.1016/j.juro.2008.04.137. Epub 2008 Jul 18.


In silico regulatory analysis for exploring human disease progression.

Holloway DT, Kon M, DeLisi C.

Biol Direct. 2008 Jun 18;3:24. doi: 10.1186/1745-6150-3-24.


Breast cancer stratification from analysis of micro-array data of micro-dissected specimens.

Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, Delisi C, Bhanot G.

Genome Inform. 2007;18:130-40.


Classifying transcription factor targets and discovering relevant biological features.

Holloway DT, Kon M, DeLisi C.

Biol Direct. 2008 May 30;3:22. doi: 10.1186/1745-6150-3-22.


VisANT: an integrative framework for networks in systems biology.

Hu Z, Snitkin ES, DeLisi C.

Brief Bioinform. 2008 Jul;9(4):317-25. doi: 10.1093/bib/bbn020. Epub 2008 May 7.


Analyzing networks with VisANT.

Hu Z, Mellor J, DeLisi C.

Curr Protoc Bioinformatics. 2004 Dec;Chapter 8:Unit 8.8. doi: 10.1002/0471250953.bi0808s08.


High-precision high-coverage functional inference from integrated data sources.

Linghu B, Snitkin ES, Holloway DT, Gustafson AM, Xia Y, DeLisi C.

BMC Bioinformatics. 2008 Feb 25;9:119. doi: 10.1186/1471-2105-9-119.


Resonant Cavity Imaging: A Means Toward High-Throughput Label-Free Protein Detection.

Bergstein DA, Ozkumur E, Wu AC, Yalçin A, Colson JR, Needham JW, Irani RJ, Gershoni JM, Goldberg BB, Delisi C, Ruane MF, Unlü MS.

IEEE J Sel Top Quantum Electron. 2008;14(1):131-139.


High expression of lymphocyte-associated genes in node-negative HER2+ breast cancers correlates with lower recurrence rates.

Alexe G, Dalgin GS, Scanfeld D, Tamayo P, Mesirov JP, DeLisi C, Harris L, Barnard N, Martel M, Levine AJ, Ganesan S, Bhanot G.

Cancer Res. 2007 Nov 15;67(22):10669-76.


Analysis of breast cancer progression using principal component analysis and clustering.

Alexe G, Dalgin GS, Ganesan S, Delisi C, Bhanot G.

J Biosci. 2007 Aug;32(5):1027-39.


Portraits of breast cancer progression.

Dalgin GS, Alexe G, Scanfeld D, Tamayo P, Mesirov JP, Ganesan S, DeLisi C, Bhanot G.

BMC Bioinformatics. 2007 Aug 6;8:291.


VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.

Hu Z, Ng DM, Yamada T, Chen C, Kawashima S, Mellor J, Linghu B, Kanehisa M, Stuart JM, DeLisi C.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W625-32. Epub 2007 Jun 22.


Binding site graphs: a new graph theoretical framework for prediction of transcription factor binding sites.

Reddy TE, DeLisi C, Shakhnovich BE.

PLoS Comput Biol. 2007 May;3(5):e90. Epub 2007 Apr 10.


Towards zoomable multidimensional maps of the cell.

Hu Z, Mellor J, Wu J, Kanehisa M, Stuart JM, DeLisi C.

Nat Biotechnol. 2007 May;25(5):547-54. Review.


Positional clustering improves computational binding site detection and identifies novel cis-regulatory sites in mammalian GABAA receptor subunit genes.

Reddy TE, Shakhnovich BE, Roberts DS, Russek SJ, DeLisi C.

Nucleic Acids Res. 2007;35(3):e20. Epub 2007 Jan 3.


Data perturbation independent diagnosis and validation of breast cancer subtypes using clustering and patterns.

Alexe G, Dalgin GS, Ramaswamy R, Delisi C, Bhanot G.

Cancer Inform. 2007 Feb 19;2:243-74.


Identification and characterization of renal cell carcinoma gene markers.

Dalgin GS, Holloway DT, Liou LS, DeLisi C.

Cancer Inform. 2007 Feb 9;3:65-92.


Towards the identification of essential genes using targeted genome sequencing and comparative analysis.

Gustafson AM, Snitkin ES, Parker SC, DeLisi C, Kasif S.

BMC Genomics. 2006 Oct 19;7:265.


Comparative assessment of performance and genome dependence among phylogenetic profiling methods.

Snitkin ES, Gustafson AM, Mellor J, Wu J, DeLisi C.

BMC Bioinformatics. 2006 Sep 27;7:420.


An equilibrium partitioning model connecting gene expression and cis-motif content.

Mellor J, DeLisi C.

Bioinformatics. 2006 Jul 15;22(14):e368-74.


The interaction map of yeast: terra incognita?

Mellor J, DeLisi C.

J Biol. 2006;5(4):10. Epub 2006 Jun 8.


Gene annotation and network inference by phylogenetic profiling.

Wu J, Hu Z, DeLisi C.

BMC Bioinformatics. 2006 Feb 17;7:80.

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