Publications by authors named "Gyan Bhanot"

59Publications

A Quasi Birth-and-Death model for tumor recurrence.

J Theor Biol 2019 11 30;480:175-191. Epub 2019 Jul 30.

Department of Physics & Astronomy, Rutgers University, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1016/j.jtbi.2019.07.017DOI Listing
November 2019

TuBA: Tunable biclustering algorithm reveals clinically relevant tumor transcriptional profiles in breast cancer.

Gigascience 2019 06;8(6)

Department of Physics and Astronomy, Rutgers University, 136 Frelinghuysen Rd, Piscataway, NJ 08854.

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http://dx.doi.org/10.1093/gigascience/giz064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6582332PMC
June 2019

On statistical modeling of sequencing noise in high depth data to assess tumor evolution.

J Stat Phys 2018 Jul 21;172(1):143-155. Epub 2017 Dec 21.

Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ.

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http://dx.doi.org/10.1007/s10955-017-1945-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6051708PMC
July 2018

Using Cluster Analysis to Group Countries for Cost-effectiveness Analysis: An Application to Sub-Saharan Africa.

Med Decis Making 2018 02 19;38(2):139-149. Epub 2017 Aug 19.

Department of Preventive Medicine and Community Health, New Jersey Medical School, Rutgers University, Newark NJ, USA (AS).

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http://dx.doi.org/10.1177/0272989X17724773DOI Listing
February 2018

The Modular Adaptive Ribosome.

PLoS One 2016 3;11(11):e0166021. Epub 2016 Nov 3.

Department of Physics, Rutgers University, Piscataway, New Jersey 08854, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0166021PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5094737PMC
June 2017

Glutaminase 2 is a novel negative regulator of small GTPase Rac1 and mediates p53 function in suppressing metastasis.

Elife 2016 Jan 11;5:e10727. Epub 2016 Jan 11.

Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, United States.

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http://dx.doi.org/10.7554/eLife.10727DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749555PMC
January 2016

Differential regulation of antagonistic pleiotropy in synthetic and natural populations suggests its role in adaptation.

G3 (Bethesda) 2015 Feb 23;5(5):699-709. Epub 2015 Feb 23.

Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, 400005, India

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http://dx.doi.org/10.1534/g3.115.017020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426359PMC
February 2015

IRF5 is a novel regulator of CXCL13 expression in breast cancer that regulates CXCR5(+) B- and T-cell trafficking to tumor-conditioned media.

Immunol Cell Biol 2015 May-Jun;93(5):486-99. Epub 2014 Dec 23.

1] Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers Biomedical and Health Sciences, Newark, NJ, USA [2] Rutgers Biomedical and Health Sciences, New Jersey Medical School-Cancer Center, UMDNJ, Newark, NJ, USA.

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http://dx.doi.org/10.1038/icb.2014.110DOI Listing
February 2016

Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets.

Bioinformatics 2015 Feb 24;31(4):492-500. Epub 2014 Aug 24.

Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, USA, Department of Physics, Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands and IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10003, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu569DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325538PMC
February 2015

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge.

Bioinformatics 2015 Feb 23;31(4):462-70. Epub 2014 Jul 23.

Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA Kavli Institute for Theoretical Physics, Kohn Hall, University of California, Santa Barbara, CA 93106, Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, and Detroit, MI 48201, USA, College of Plant Protection and College of Science, Hunan Agricultural University, Changsha, 410128, China, School of Computing, Clemson University, Clemson, SC 29634, USA, Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, IBM T.J. Watson Research Center, Computational Biology Center, Yorktown Heights, NY 10003, Department of Molecular Biology and Biochemistry, Department of Physics and BioMaPS Institute, Rutgers University, Piscataway, NJ 08854 and Department of Computer Science, Wayne State University, Detroit, MI 48202, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu490DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325537PMC
February 2015

Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge.

Bioinformatics 2015 Feb 3;31(4):453-61. Epub 2014 Jul 3.

Johann Bernoulli Institute for Mathematics and Computer Science, University of Groningen, 9700 AK Groningen, The Netherlands, University of California, Irvine, CA 92617, Department of Physics and Department of Molecular Biology and Biochemistry, Busch Campus, Rutgers University, Piscataway, NJ 08854, IBM T.J. Watson Research Center, Computational Biology, Yorktown Heights, NY 10598, Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4325536PMC
February 2015

Bird to human transmission biases and vaccine escape mutants in H5N1 infections.

PLoS One 2014 2;9(7):e100754. Epub 2014 Jul 2.

Department of Physics, Rutgers the State University of New Jersey, Piscataway, New Jersey, United States of America; The Cancer Institute of New Jersey, New Brunswick, New Jersey, United States of America; The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America; Department of Molecular Biology & Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America; BioMaPS Institute, Rutgers University, Piscataway, New Jersey, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0100754PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079711PMC
February 2015

ERBB2 overexpression suppresses stress-induced autophagy and renders ERBB2-induced mammary tumorigenesis independent of monoallelic Becn1 loss.

Autophagy 2014 Apr 30;10(4):662-76. Epub 2014 Jan 30.

Rutgers University; State University of New Jersey; New Brunswick, NJ USA; Rutgers Cancer Institute of New Jersey; New Brunswick, NJ USA; Division of Medical Oncology; Department of Internal Medicine; Rutgers Robert Wood Johnson Medical School; Piscataway, NJ USA.

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http://dx.doi.org/10.4161/auto.27867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091153PMC
April 2014

Yeast growth plasticity is regulated by environment-specific multi-QTL interactions.

G3 (Bethesda) 2014 Jan 28;4(5):769-77. Epub 2014 Jan 28.

Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India

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http://dx.doi.org/10.1534/g3.113.009142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4025475PMC
January 2014

Sporulation genes associated with sporulation efficiency in natural isolates of yeast.

PLoS One 2013 17;8(7):e69765. Epub 2013 Jul 17.

Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069765PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3714247PMC
March 2014

Identifying microRNA/mRNA dysregulations in ovarian cancer.

BMC Res Notes 2012 Mar 27;5:164. Epub 2012 Mar 27.

The Cancer Institute of New Jersey, New Brunswick, NJ, USA.

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http://dx.doi.org/10.1186/1756-0500-5-164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342161PMC
March 2012

Robust multi-tissue gene panel for cancer detection.

BMC Cancer 2010 Jun 22;10:319. Epub 2010 Jun 22.

Centocor R&D, Inc, 145 King of Prussia Rd, Radnor, PA 19087, USA.

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http://dx.doi.org/10.1186/1471-2407-10-319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906482PMC
June 2010

Expectation-maximization-driven geodesic active contour with overlap resolution (EMaGACOR): application to lymphocyte segmentation on breast cancer histopathology.

IEEE Trans Biomed Eng 2010 Jul 17;57(7):1676-89. Epub 2010 Feb 17.

Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1109/TBME.2010.2041232DOI Listing
July 2010

ConsensusCluster: a software tool for unsupervised cluster discovery in numerical data.

OMICS 2010 Feb;14(1):109-13

BioMaPS Institute, Rutgers University, Piscataway, New Jersey 08854, USA.

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http://dx.doi.org/10.1089/omi.2009.0083DOI Listing
February 2010

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

Urology 2010 Apr 29;75(4):835-41. Epub 2009 Dec 29.

Department of Pathology, Boston University, Boston, Massachusetts 02118, USA.

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http://dx.doi.org/10.1016/j.urology.2009.10.033DOI Listing
April 2010

A 2D mechanistic model of breast ductal carcinoma in situ (DCIS) morphology and progression.

J Theor Biol 2010 Apr 16;263(4):393-406. Epub 2009 Dec 16.

BioMaPS Institute, Rutgers University, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1016/j.jtbi.2009.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2839055PMC
April 2010

Computerized image-based detection and grading of lymphocytic infiltration in HER2+ breast cancer histopathology.

IEEE Trans Biomed Eng 2010 Mar 30;57(3):642-53. Epub 2009 Oct 30.

Department of Biomedical Engineering, Rutgers University, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.1109/TBME.2009.2035305DOI Listing
March 2010

Towards improved cancer diagnosis and prognosis using analysis of gene expression data and computer aided imaging.

Exp Biol Med (Maywood) 2009 Aug 2;234(8):860-79. Epub 2009 Jun 2.

Department of Biology and Biochemistry and Department of Physics, Rutgers University, Piscataway, NJ 08854, USA.

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http://dx.doi.org/10.3181/0902-MR-89DOI Listing
August 2009

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

Genome Inform 2007 ;18:130-40

The Broad Institute of MIT and Harvard, Cambridge MA 02142, USA.

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August 2008

Patterns of evolution and host gene mimicry in influenza and other RNA viruses.

PLoS Pathog 2008 Jun 6;4(6):e1000079. Epub 2008 Jun 6.

BioMaPS Institute, Rutgers University, Piscataway, New Jersey, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1000079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390760PMC
June 2008

Portraits of breast cancer progression.

BMC Bioinformatics 2007 Aug 6;8:291. Epub 2007 Aug 6.

Boston University, Boston, MA 02215, USA.

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http://dx.doi.org/10.1186/1471-2105-8-291DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1978212PMC
August 2007

Constructing near-perfect phylogenies with multiple homoplasy events.

Bioinformatics 2006 Jul;22(14):e514-22

School of EECS, University of Central Florida, Orlando, FL 32816-2362, USA.

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http://dx.doi.org/10.1093/bioinformatics/btl262DOI Listing
July 2006

A robust meta-classification strategy for cancer diagnosis from gene expression data.

Proc IEEE Comput Syst Bioinform Conf 2005 :322-5

IBM Computational Biology Center, IBM T.J. Watson Research Center, Yorktown Heights, NY 10598, USA.

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http://conferences.computer.org/bioinformatics/CSB2005/PDF3/
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http://dx.doi.org/10.1109/csb.2005.7DOI Listing
May 2007

Robust diagnosis of non-Hodgkin lymphoma phenotypes validated on gene expression data from different laboratories.

Genome Inform 2005 ;16(1):233-44

Center for Systems Biology, Institute for Advanced Study, Princeton, NJ 08540, USA.

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https://www.jsbi.org/pdfs/journal1/IBSB05/IBSB05F001.pdf
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January 2006

A robust meta-classification strategy for cancer detection from MS data.

Proteomics 2006 Jan;6(2):592-604

Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA.

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http://dx.doi.org/10.1002/pmic.200500192DOI Listing
January 2006

Results from modeling of B-Cell receptors binding to antigen.

Authors:
Gyan Bhanot

Prog Biophys Mol Biol 2004 Jun-Jul;85(2-3):343-52

Computational Biology Center, T.J.WatsonResearch Center, IBM Research, Yorktown Height, NY 10598, USA.

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http://dx.doi.org/10.1016/j.pbiomolbio.2004.01.008DOI Listing
July 2004

Dynamical analysis of a degenerate primary and secondary humoral immune response.

Bull Math Biol 2003 May;65(3):535-45

Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA.

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http://dx.doi.org/10.1016/S0092-8240(03)00023-5DOI Listing
May 2003

The importance of thermodynamic equilibrium for high throughput gene expression arrays.

Biophys J 2003 Jan;84(1):124-35

Institute for Advanced Study, Princeton, New Jersey 08540, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1302598PMC
http://dx.doi.org/10.1016/S0006-3495(03)74837-1DOI Listing
January 2003