Fatima Merchant

Faculty

Fatima Merchant, Ph.D.

Research Professor

Phone 713-743-8292

Fax 713-743-0172

Email fmerchant [at] uh.edu

Website Dr. Merchant Research Lab Page

Education

Certificate in Bioinformatics, University of British Columbia, Vancouver, BC, Canada, 2002
Post-doctoral Research Fellow (Advisor: Mehmet Toner), Harvard Medical School/Massachusetts General, Boston, MA, USA, 1997
PhD - Biomedical Engineering (Advisor: Kenneth R. Diller), The University of Texas at Austin, Austin, TX, USA, 1995
MS - Biomedical Engineering (Advisor: Kenneth R. Diller), The University of Texas at Austin, Austin, TX, USA, 1992
BS - Engineering, emphasis on Biomedical Engineering, University of Bombay, Thadomal Shahani Engineering College, Bombay, India, 1989

Other Appointments

Associate Professor, Department of Biomedical Engineering and Department of Electrical & Computer Engineering, Cullen College of Engineering, University of Houston
Associate Professor, Department of Computer Science, College of Natural Sciences and Mathematics, University of Houston
Adjunct Faculty, Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin

Professional Experience

Director, Research Infrastructure Core, NIMHD RCMI HEALTH Center for Addictions Research and Cancer Prevention, 2020-Present
Professor, Department of Engineering Technology, University of Houston, TX, 2020-Present
Associate Professor, Department of Engineering Technology, University of Houston, TX, 2014-2019
Assistant Professor, Department of Engineering Technology, University of Houston, TX, 2008-2013
Adjunct Faculty, Department of Computer Science, University of Houston, TX, 2009-2014
Research Assistant Professor, Department of Chemistry, University of Houston, TX, 2008-2013
Lead Research Engineer, Softimaging LLC, Houston, TX, 2007-2008
Lecturer, Department of Computer Science, University of Houston, Houston, TX, 2001-2006
Lead Research Engineer, IRIS International, subsidiary PSI and ADIR, LLC, Friendswood, TX, 1997-2007
Postdoctoral Research Fellow, Surgery, Harvard Medical School, Boston, MA, 1995-1997
Research/Teaching Assistant, Biomedical Engineering Program, The University of Texas at Austin, Austin, TX, 1990-1995
Assistant Engineer, X-Ray & Electromedicals India Pvt. Ltd., Bombay, India, 1989-1990
Engineering Trainee, Bhabha Atomic Research Center, Govt. of India, Trombay, India, 1988-1989

Professional Service & Affiliations

Session Chair, 10th Intl. Conf. on 3D Body Scanning Technologies, Switzerland, 2019
Associate Editor, Biomedical Engineering Online Journal, USA, 2018-Present
NIH Review Panel for NCI Centers of Cancer Nanotechnology Excellence, 2015
Editorial Board Member, Plastic and Aesthetic Research, China, 2014
Grant Reviewer, Austrian Science Fund (FWF), 2014
Grant Reviewer, Chilean National Science & Technology, FONDECYT 2015 Regular Competition, 2014
Session Chair, 5th International Conference on 3D Body Scanning Technologies, Switzerland, 2014
Affiliate Faculty, Center for Nuclear Receptors and Cellular Signaling, College of Natural Sciences and Mathematics, University of Houston, 2013-Present
MOSS-C NIH Director's New Innovator Award Program Study Section, 2013-Present
Session Chair, 4th International Conference on 3D Body Scanning Technologies, 2013
Chair, Program Committee, IEEE Int. Ph.D. Workshop Multimedia Computing Research, 2013
Editorial Board Member, Computers in Biology & Medicine , USA, 2011-Present
Reviewer, Journal of Computational Surgery, 2011-Present
Co-Chair, Imaging Session, IEEE-EMBS Conference,October 2011, Boston, MA, 2011
Reviewer, Cellular and Molecular Engineering, USA, 2010-Present
Reviewer, Computers in Biology & Medicine, USA, 2010-Present
Reviewer, Journal of Healthcare Engineering, USA, 2009-Present
Reviewer, Optical Society of America, Applied Optics, 2009-Present
Reviewer, Pattern Recognition Letters, 2008-Present
Panelist, Engineering Research Center Proposals, NSF, USA, 2002
Grant Reviewer, National Institute of Health, SBIR, Bethesda, MD, USA, 1999-Present
Grant Reviewer, National Institute of Health, Study Sections, Bethesda, MD, USA, 1999-Present

Institutional Service

Chair, Dean 5th Year Performance Review, Hotel & Restaurant Management, 2020
Chair, Graduate Program Committee, Department of Engineering Technology, 2020
Committee Member, Department of Electrical & Computer Engineering, Research Faculty Search Committee,, 2019
Member, Department of Engineering Technology, Chair Search Committee2019
Member, University of Houston Faculty Senate (CoT Representative), Faculty Governance Committee,, 2019 - Present
Program Coordinator, MS Computational Health Informatics, Department of Engineering Technology, 2018 - Present
Member, University of Houston Faculty Senate (At-large CoT Representative), Faculty Affairs Committee, 2018 - Present
Member, Promotion & Tenure Committee, Department of Engineering Technology, 2017 - Present
Member, University of Houston Title IX Grievance Committee, 2017- Present
Member, University of Houston Student Financial Support Committee, 2016- Present
Member, Professional Engagement, Development & Advancement Initiative, Center for ADVANCING UH Faculty Success, 2015-2020
Member, College of Technology Academic Honesty Committee, 2013-Present
Chair, College of Technology Scholarship Committee, 2013-Present
Member, Biotechnology Program Course Curriculum (PCC) Committee, 2013-Present
Member, Oversight Committee on Renovation of Restroom Facilities in Technology Annex, 2013
Member, Supply Chain and Logistics Tenure-Track Faculty Search Committee, 2013
Member, Biotechnology Instructional Faculty Search Committee, 2012
Volunteer, Cougar Movers, UH Student Housing and Residential Life, 2012-2013
Member, UH PAL (Personal Access Liaison), Cougar Success Initiative, 2011-Present
Member, UH Imaging Core Committee, 2011-2012
Member, Preparation of the UH grant application to the NSF ADVANCE Grant for Advancement of Women in STEM Fields program, 2011
Member, MS Imaging Option Committee, ECE/CS/Math/ET, 2011
Proctor, Programming Competition at USAA Association of Information Technology Professionals (AITP) Region 3 Student Conference, Hosted by ILT COT, 2010
Member, College of Technology Scholarship Committee, 2010-2012
Member, Biotechnology Tenure-Track Faculty Search Committee, 2009
Coordinator, Bioinformatics Track in the Biotechnology Program, Department of Engineering Technology, College of Technology, 2008-Present

Classes

BTEC 3301 - Genomics/Proteomics & Bioinformatics
BTEC 4300 - Principles of Bioinformatics
BTEC 6304 - Computational Methods in Biotechnology
ELET 2300 - Introduction to C++ Programming
ELET 4350/6350 - Intro. to Computational Health Informatics
ELET 4354/6354 - Biomedical Image Analysis
ELET 4356/6356 - Health Analytics & Visualization

Research Interests

Computational Cytogenetics
Angiogenesis and Revascularization
Multi-dimensional Image Cytometry
Cancer Diagnostics

Grants

Name	Duration	Amount	Maker
3D Image Analysis Software for Breast Reconstruction Surgical Planning, Outcome Assessment & Clinical Consultation	(4/1/2022 - 03/31/2023)	$399,000	NIH NCI R41 CA272122
HEALTH Center for Addictions Research and Cancer Prevention	(9/11/2020 - 08/31/2025)	$11,800,000	NIH NIMHD U54 MD015946-01 (Total funded $11,800,000)
Impact of cell microenvironment on differentiation and physiology of induced pluripotent stem cells (iPSCs) into pancreatic islet cells	(05/01/2020 - 05/30/2021)	$30,000	UH-Baylor College Medicine Collaborative (UH-BCM)
Investigating efficacy of epigenetic therapy in ovarian cancer	(05/01/2020 - 05/30/2021)	$30,000	UH Health Research Institute (HRI) Pilot Award
Novel Substrates for in-vitro mechanotransduction and cellular patterning	(05/01/19- 09/31/21)	$62,000	UH High Priority Area Research Seed Grant
RNA-sequencing of stem cells differentiated into insulin producing cells	(03/01/19- 02/28/20)	$10,000	UH CoT Internal Seed Research Grant
BioMEMS for studying Ovarian Cancer Metastasis	(03/01/18- 02/28/19)	$10,000	UH CoT Internal Seed Research Grant
3D Modeling Based Decision Support for Optimizing Quality of Life following Breast Reconstruction	(03/01/16 - 02/28/22)	$447,850	NIH R01CA203984 (Total funded $3,400,000)
Micropatterned Substrates for Generation of Insulin Producing Cells from Adult Human Bone Marrow Mesenchymal Stem Cells	(09/01/15 - 08/31/16)	$3,000	UH Small Grants Award
Quality Enhancement Plan (QEP) Award (Integrating Information-Driven Research Into An Undergraduate Bioinformatics Course)	8/2013-12/2013	$4,425	UH Office of Undergraduate Research
Lab Grant Award (for purchase of disposables)	7/2012	$1,000	Grenier Bio-One North America, Inc.
3D Computer Modeling for Optimizing Body Image following Breast Reconstruction (UH Subcontract)	2010-2015	$341,958	National Institutes of Health (Grant R01CA143190)
New Faculty Award (Improving Prenatal Genetic Diagnosis for Invitro Fertilization)	1/2009-12/2009	$6,000	UH Office of the Provost
Small Grants Award (BioMEMS for pancreatic islet revascularization)	2009-2010	$3,000	UH Division of Research
Higher Education Assistance Fund (HEAF)	2008-2010	$150,000	UH Office of the Provost
Start-up Fund	2008-2012	$75,000	UH College of Technology
Graduate Student Support	2008-2010	$75,000	UH College of Natural Science and Mathematics
Equipment Award, Optical Imaging Equipment	9/2008	~$75,000	Iris International, Inc.
A Virtual Reality Environment for Genomic Data Visualization	2007-2008	$125,000	National Institutes of Health (Grant 1R43GM075849)
3D Breast Anatomy Analysis in Cancer Treatment Planning	2007-2008	$125,000	National Institutes of Health (Grant 1R43CA121646-01)
Improved Automated Urinalysis	2007-2008	$100,000	National Institutes of Health (Grant 1R43DK078365)
Low Cost Urinalysis Using Spectral Data	2005-2006	$100,000	National Institutes of Health (Grant 1R43DK067750)
Automated Detection of Gene Duplications or Deletions	204-2007	$750,000	National Institutes of Health (Grant 2R44GM060894)
Semi-Automated Prenatal Screening Using Maternal Blood	2003-2004	$650,000	National Institutes of Health (Grant 2R44HD037308)
Improved Imaging for Precise Cryptic Anomaly Detection	2002-2004	$745,258	National Institutes of Health (Grant 2R44HD038150)
Automated Detection of Gene Duplications or Deletions	2000-2001	$97,470	National Institutes of Health (Grant 1R43GM060894)
Automated Detection of Cryptic Rearrangements	3/2000-12/2000	$98,001	National Institutes of Health (Grant 1R43HD038150)
Semi-Automated Prenatal Screening Using Maternal Blood	1999-2000	$99,918	National Institutes of Health (Grant 1R43HD037308)
Automated Prenatal Screening Using Maternal Blood	1999-2001	$742,927	National Institutes of Health (Grant 2R44HD034719)

Awards & Honors

UH 50-in-5 Scholar Honoree, 2021
UH 50-in-5 Scholar Honoree, 2020
Service Excellence Award, College of Technology, University of Houston, 2020
Provosts' Global Faculty Development Award, University of Houston, 2017
Teaching Excellence Award, College of Technology, University of Houston, 2017
Research Excellence Award, College of Technology, University of Houston, 2016
Provost's Faculty Travel Award, University of Houston, 2014
Provost's Faculty Travel Award, University of Houston, 2011
Travel Award, Association of Biomolecular Resource Facilities, USA, 2007
Senior Member, IEEE, USA, 2007
European Molecular Biology Organization Fellowship, Heidelberg, Germany, 1999
Tayside Travel Grant, Society of Low Temperature Biology, Scotland, 1996
Travel Grant, European Society of Microcirculation, Germany, 1996
Yasuda Award, Society for Physical Regulation in Biology & Medicine, USA, 1996
Travel Award, 32 nd Annual Meeting, Society for Cryobiology, USA, 1995
J. N. Tata Scholarship, Bombay, India, 1990
Wadia Trust Award, Bombay, India, 1990
Lotus Trust Award, Bombay, India, 1990
First Rank in Biomedical Engineering (Sophomore, Junior and Senior years), India, 1987-1989

Theses and Dissertation

Estimation of the heamatocrit percentage in blood non-invasively. B.E. Thesis, Major: Biomedical Engineering, Thadomal Shahani Engineering College, University of Bombay, 1989.
Assaying viability of cryopreserved pancreatic islets and determining the 3-D distribution of damaged cells using laser scanning confocal microscopy. M.S. Thesis, Major: Biomedical Engineering, The University of Texas at Austin, 1992.
In vivo analysis of angiogenesis and revascularization of transplanted pancreatic islets using confocal microscope images. Ph.D. Dissertation, Major: Biomedical Engineering, The University of Texas at Austin, 1995. Nominated for the Best Dissertation of the year award.

Books

Microscope Image Processing, Editors: Qiang Wu, Fatima Merchant, Kenneth Castleman, Publisher: Academic Press; 1st edition, 2008

Articles in Peer-Reviewed Journals

Oujja A, Abid MR, Boumhidi J, Bourhnane S, Mourhir A, Merchant FA, Benhaddou D, "High-performance computing for SARS-CoV-2 RNAs clustering: a data science-based genomics approach." Genomics & Informatics, 19(4), 2021.
Nicklaus KM, Bui T, Bordes MC, Liu J, Chopra D, Hoffman AS, Reece GP, Hanson SE, Merchant FA, Markey MK, "Goldilocks principle: preference for change in breast size in breast cancer reconstruction patients." Frontiers in Psychology, Volume 12, September 2021.
Nicklaus KM, Wang H, Bordes MC, Zaharan A, Sampathkumar U, Cheong AL, Reece GP, Hanson SE, Merchant FA, Markey MK, "Potential of intra-operative 3D photography and 3D visualization in breast reconstruction." PRS-GO, Oct 7;9(10):e3845, 2021.
Sampathkumar U, Nowroozilarki Z, Bordes MC, Reece GP, Hanson SE, Markey MK, Merchant FA. Review of Quantitative Imaging for Objective Assessment of Fat Grafting Outcomes in Breast Surgery. Aesthetic Surgery Journal. 41(Suppl 1):S39-S49, 2021.
Friguglietti, J, Das S, Le P, Fraga D, Quintela M, Gazze SA, McPhail D, Gu J, Sabek O, Gaber AO, Francis LW, Zagozdzon-Wosik W, Merchant FA. Novel silicon Titanium Diboride Micropatterned Substrates for Cellular Patterning. Biomaterials, 244:119927, 2020.
Jung, S., Cui, Y., Barnes, M., Satam, C., Zhang, S., Chowdhury, R.A., Adumbumkulath, A., Sahin, O., Miller, C., Sajadi, S.M., Sassi, L., Bennett, M., Yu, M., Friguglietti, J., Merchant, FA, Verduzco, R., Roy, S., Vajtai, R., Meredith, J., Youngblood, J., Koratkar, N., Rahman, M., and Ajayan, P. Multifunctional Bio-Nanocomposite Coatings for Perishable Fruits. Advanced Materials, 2020: p. 1908291, 2020.
Chapman BV, Lei X, Patil P, Tripathi S, Nicklaus KM, Grossberg AJ, Shaitelman SF, Thompson AM, Hunt KK, Buchholz TA, Merchant FA, Markey MK, Smith BD, Reddy JP. Quantitative 3-Dimensional Photographic Assessment of Breast Cosmesis After Whole Breast Irradiation for Early Stage Breast Cancer: A Secondary Analysis of a Randomized Clinical Trial. Adv Radiat Oncol. Sep-Oct; 5(5): 824-833, 2020.
Cheong AL, Liu J, Reece GP, Nicklaus KM, Bordes MC, Hanson SE, Markey MK, and Merchant FA. Natural Breast Symmetry in Pre-Operative Breast Cancer Patients. Plastic and Reconstructive Surgery Global Open, 7(7):e2297, 2019.
Teo I, Reece GP, Huang SC, Mahajan K, Andon J, Khanal P, Sun C, Nicklaus K, Merchant FA, Markey MK, Fingeret MC. Body image dissatisfaction in patients undergoing breast reconstruction: Examining the roles of breast symmetry and appearance investment. Psychooncology, 27(3):857-863, 2018. PMID: 29152816, PMCID: PMC5839959
Reddy JP, Lei X, Huang SC, Nicklaus KM†, Fingeret MC, Shaitelman SF, Kelly KK, Thomas A. Buchholz TA, Merchant FA, Markey MK, and Smith BD. Quantitative assessment of breast cosmetic outcome following whole breast irradiation. International Journal of Radiation Oncology, Biology, Physics, 97(5):894-902, 2017.
Blessing AM†, Rajapakshe K, Bollu LR, Shi Y, White MA, Pham AH, Lin C, Jonsson P, Cortes CJ, Cheung E, La Spada AR, Bast RC, Merchant FA, Coarfa C, and Frigo DE. Transcriptional regulation of core autophagy and lysosomal genes by the androgen receptor promotes prostate cancer progression, Autophagy, 13(3):506-521, 2017.
McCollum CW, Vancells JC, Hans C†, Vazquez-Chantada M, Kleinstreuer N, Tal T, Knudsen T, Shah SS, Merchant FA, Finnell RH, Gustafsson JA, Cabrera R, Bondesson M. Identification of vascular disruptor compounds by analysis in zebrafish embryos and mouse embryonic endothelial cells. Reprod Toxicol., 70:60-69, 2017.
Li D, Cheong A, Reece GP, Crosby MA, Fingeret MC, Merchant FA. Computation of breast ptosis from 3D surface scans of the female torso. Comput Biol Med., 78:18-28, 2016.
Zhao L, Cheong A, Reece GP, Fingeret MC, Shah S, Merchant FA. Inferior Breast-Chest Contour Detection in 3D Images of the Female Torso. IEEE Journal of Translational Engineering in Health and Medicine. vol. 4, pp. 1-10, 2016.
Recce GP, Merchant FA, Andon J, Khatam H, Ravi-Chandar K, Weston J, Fingeret M, Lane C, Duncan K, Markey M. 3D surface imaging of the human female torso in upright to supine positions, Medical Engineering & Physics, 37:375-383, 2015.
Tal T, McCollum CW, Harris PS, Olin J, Kleinstreuer N, Wood CE, Hans C, Shah S, Merchant FA, Bondesson M, Knudsen TB, Padilla S, Hemmer MJ. Immediate and long-term consequences of vascular toxicity during zebrafish development. Reproductive Toxicology, 48:51-61, 2014.
Tsouko E, Khan AS, White MA, Han JJ, Shi Y, Merchant FA, Sharpe MA, Xin L, Frigo DE. Regulation of the pentose phosphate pathway by an androgen receptor-mTOR-mediated mechanism and its role in prostate cancer cell growth. Oncogenesis, e103:1-10, 2014.
McCollum CW, Hans C, Shah S, Merchant FA, Gustafsson JA, Bondesson M. Embryonic exposure to sodium arsenite perturbs vascular development in zebrafish. Aquat Toxicol., 152C:152-163, 2014.
Mukherjee M, Byrd T, Brawley VS, Bielamowicz K, Li XN, Merchant FA, Maitra S, Sumazin P, Fuller G, Kew Y, Sun D, Powell SZ, Ahmed NM, Zhang N, Pati D. Overexpression and Constitutive Nuclear Localization of Cohesin Protease Separase Protein Correlates with High Incidence of Relapse and Reduced Overall Survival in Glioblastoma Multiforme. J Neurooncol., 119(1):27-35, 2014.
Shete A, Rao P, Pati D, Merchant FA. Spatial quantitation of FISH signals in diploid versus aneuploid nuclei. Cytometry A, 85(4):339-52, 2014.
Sun, CS, Markey MK, Merchant F, Krishnaswamy RC, Fingeret MC, Reece GP. 3D computer technology addresses body-image issues of breast reconstruction. In SPIE Newsroom: Biomedical Optics & Medical Imaging, 1-4, 2013.
Hegde M, Corder A, Chow KK, Mukherjee M, Ashoori A, Kew Y, Zhang YJ, Baskin DS, Merchant FA, Brawley VS, Byrd TT, Krebs S, Wu MF, Liu H, Heslop HE, Gottschalk S, Yvon E, Ahmed N.. Combinational targeting offsets antigen escape and enhances effector functions of adoptively transferred T cells in Glioblastoma. Mol. Cancer Ther., 21(11):2087-101, 2013.
Kawale M, Reece GP, Crosby MA, Beahm EK, Fingeret MC, Markey MK, and Merchant FA. Automated identification of fiducial points on 3D Torso Images. Biomedical Engineering and Computational Biology, 5:57-68, 2013.
Shi Y, Han JJ, Tennakoon JB, Mehta FF, Merchant FA, Burns AR, Howe MK, McDonnell DP, and Frigo DE. Androgens Promote Prostate Cancer Cell Growth through Induction of Autophagy. Mol Endocrinol., 27(2):280-295, 2013.
Lee J, Kawale M, Merchant FA, Weston J, Fingeret MC, Ladewig D, Reece GP, Crosby MA, Beahm EK, and Markey MK. Validation of stereophotogrammetry of the human torso. Breast Cancer: Basic and Clinical Research, 5:15-25, 2011.
Kawale M, Lee J, Leung SY, Fingeret MC, Reece GP, Crosby MA, Beahm EK, Markey MK, and Merchant FA. 3D symmetry measure invariant to subject pose during image acquisition. Breast Cancer: Basic and Clinical Research, 5:131-142, 2011.
Dabeer M, Kim E, Reece G, Merchant FA, Crosby M, Beahm E, and Markey M. Automatic calculation of symmetry measure on clinical photographs. Journal of Evaluation in Clinical Practice. 17(6):1129-1136, 2011.
Gurkan D and Merchant FA. Interoperable Medical Instrument Networking and Access System with Security Considerations for Critical Care. Journal of Healthcare Engineering, 1(4):637-654, 2010.
Thigpen J, Merchant FA, and Shah S. Photometric calibration for quantitative spectral microscopy under transmitted illumination. Journal of Microscopy, 239(3):200-214, 2010.
Meyer R, Fofanov V, Panigrahi A, Merchant FA, Zhang N, and Pati D. Overexpression and Mislocalization of the Chromosomal Segregation Protein Separase in Multiple Human Cancers. Clinical Cancer Research, 15(8):2703-2710, 2009.
Thigpen J, Shah S, and Merchant FA. Cell Differentiation in Multispectral Image Cytology. Journal of Algorithms and Computational Technology, 2(4):469-499, 2008.
Dabeer M, Merchant FA, Reece GP, Beahm EK, and Markey MK. A research agenda for appearance changes due to breast cancer treatment. Breast Cancer: Basic and Clinical Research, 2:1-3, 2008.
Merchant FA and Castleman KR. Strategies for automated fetal cell screening. Human Reproduction Update, 8(6):509-521, 2002.
Merchant FA, Holmes WH, Capelli-Schellpfeffer, M, Lee RC, and Toner M. P-188 enhances functional recovery of heat shocked fibroblasts. J. Surg. Res., 74:131-140, 1998.
de Freitas RC, Diller KR, Lachenbruch CA and Merchant FA. Network thermodynamic model of coupled transport in a multicellular tissue-The islet of Langerhans. Ann N Y Acad Sci., 858:191-204, 1998.
Merchant FA, Diller KR, Aggarwal SJ, and Bovik AC. Angiogenesis in cultured and cryopreserved pancreatic islet grafts. Transplantation, 63:1652-1660, 1997.
Merchant FA, Diller KR, Aggarwal SJ, and Bovik AC. Viability analysis of cryopreserved rat pancreatic islets using laser scanning confocal microscopy. Cryobiology, 33:236-252, 1996.
Merchant FA, Aggarwal SJ, Diller KR, and Bovik AC. In-vivo analysis of angiogenesis and revascularization of transplanted pancreatic islets using confocal microscopy. Journal of Microscopy, 176: 262-275, 1994.
Merchant FA, Aggarwal SJ, Diller KR, Bartels KA, and Bovik AC. Three-dimensional distribution of damaged cells in cryopreserved pancreatic islets as determined by laser scanning confocal microscopy. Journal of Microscopy, 169: 329-338, 1993.

Articles in Peer-Reviewed Conference Proceedings

Sampathkumar U, Nowroozilarki N, Reece GP, Hanson SE, Merchant FA. Spherical harmonics for modeling shape transformations of breasts following breast surgery. Proc. of SPIE Medical Imaging 2020: Image-Guided Procedures, Robotic Interventions, and Modeling, 11315:113152H, 2020.
Nowroozilarki Z, Bordes MC, Sampathkumar U, Hanson SE, Reece GP, Markey MK, and Merchant FA. Investigation of Smallest Volume Difference Measurable Using 3D Imaging. Proceedings of the 11th International Conference and Exhibition on 3D Body Scanning and Processing Technologies (3DBODY.TECH), Virtual Conference, 2020. https://doi.org/10.15221/20.26
Sampathkumar U, Cheong A, Reece GP, Bordes MC, Hanson SE, Markey MK, Merchant FA. Interactive visualization of breast shape for breast surgery. Proceedings of the 10th International Conference and Exhibition on 3D Body Scanning and Processing Technologies (3DBODY.TECH), Lugano Switzerland, pp 34-42, 2019.
Nicklaus KM, Jewett E, Liu C, Liu J, Reece GP, Hanson SE, Merchant FA, Markey MK. Trends in breast measurements of unilateral breast reconstruction patients to inform bra design. Proceedings of the 10th International Conference and Exhibition on 3D Body Scanning and Processing Technologies (3DBODY.TECH), Lugano Switzerland, 2019.
Cheong AL, Hanson SE, Reece GP, Markey MK, Merchant FA. Potential of 3D surface imaging for quantitative analysis of fat grafting. Proceedings of the 9th International Conference and Exhibition on 3D Body Scanning and Processing Technologies (3DBODY.TECH), Lugano Switzerland, pp 57 - 63, 2018. doi: 10.15221/18.057
Yen F, Pati D, Merchant FA. 3D modeling of chromosomes territories in normal and aneuploid nuclei. Proc. SPIE 10578, Medical Imaging 2018: Biomedical Applications in Molecular, Structural, and Functional Imaging, 105782K, 12 March, pp 105782K-1 - 105782K-9, 2018.
Nicklaus KM, Chu J, Liu C, Reece GP, Merchant FA, Fingeret MC, Markey MK. Correspondence of breast measurements for bra design after reconstruction surgery. Proceedings of the 8th International Conference and Exhibition on 3D Body Scanning and Processing Technologies (3DBODY.TECH), Montreal Canada, pp 106-112, 2017. doi:10.15221/17.106
Cheong AL, Reece GP, Markey MK, Fingeret MC, Merchant FA. Quantitative analysis of localized changes in breast shape. Proceedings of the 8th International Conference and Exhibition on 3D Body Scanning and Processing Technologies (3DBODY.TECH), Montreal Canada, pp 130-138, 2017. doi:10.15221/17.130
Hans C, McCollum C, Bondesson M, Shah S, Merchant FA. Gradient Weighted Co-HOG for Analysis of Caudal Vein Structural Changes in Toxin Exposed Zebrafish Embryo, Proceedings of IEEE International Symposium of Biomedical Imaging, New York, In Press, 2015.
Zhao L, Reece GP, Fingeret MC, and Merchant FA. Multi-View 3D Data Fusion for Visualization of the Inframammary Fold in Women with Ptotic Breasts. Proc. 5th International Conference and Exhibition on 3D Body Scanning Technologies, 5:29-38, Oct. 2014.
Cheong A, Reece GP, Fingeret MC, and Merchant FA. Visualization and Quantification of Female Breast Morphology During Breast Reconstruction. Proc. 5th International Conference and Exhibition on 3D Body Scanning Technologies, 5:21-38, Oct. 2014.
Zhao L, Shah S, and Merchant FA. Longitudinal Characterization of Breast Morphology during Reconstructive Surgery. Multimedia (ISM), IEEE International Symposium, pp. 407-408, 2013.
Hans C, McCollum C, Bondesson M, Gustafsson J-A, Shah S, and Merchant FA. Automated Analysis of Zebrafish Images for Screening Toxicants. Proc IEEE Eng. Med. Biol. Soc., 2013: 3004-3007, 2013.
Li D, Reece G, Crosby M, Fingeret M, and Merchant FA. Computation of Breast Ptosis from 3D Surface Scans of the female torso. Proc. 4th International Conference and Exhibition on 3D Body Scanning Technologies, 4:98-106, November 2013.
Zhao L, Shah S, Reece G, Crosby M, Fingeret M, and Merchant FA. Automated Detection of Breast Contour in 3D Images of the Female Torso. Proc. 4th International Conference and Exhibition on 3D Body Scanning Technologies, 4:273-278, November 2013.
Zhao L, Shah S, Reece GP, Crosby MA, Beahm EK, Fingeret MC, Markey MK and Merchant FA. Semi-Automated Registration of 3D Torso Images from Breast Reconstruction Surgery. Proc. 3D Body Scanning Technologies, 3:179-188, 2012.
Bose A, Shah S, Reece GP, Crosby MA, Beahm EK, Fingeret MC, Markey MK, and Merchant FA. Automated Spatial Alignment of 3D Torso Images. Proc. IEEE Eng. Med. Biol. Soc., 2011:8455-8458, 2011.
Hans C, Shete A, Shah S, McCollum C, Bondesson M, and Merchant FA. 3D Imaging for Quantitative assessment of Toxicity on Vascular Development in Zebrafish. Proc. IEEE Eng. Med. Biol. Soc., 2011:5969-5972, 2011.
Hans C, Merchant FA, and Shah S. Decision Fusion for Urine Particle Classification in Multispectral Images. Proc. of 7th Indian conference on Computer Vision, Graphics, and Image Processing, 1:419-426, 2010.
Mujumdar S, McKneely PK, Thongpithoonrat P, Gurkan D, Chapman F and Merchant FA, Performance Analysis of a Proposed Tightly-Coupled Medical Instrument Network Based on CAN Protocol. Proc. IEEE Eng. Med. Biol. Soc., 2010: 360-364, 2010.
Shah S and Merchant FA. I-FISH: Increasing Detection Efficiency for Fluorescent Dot Counting in Cell Nuclei. 6th International Conference on Advances in Pattern Recognition, 1:220-225, 2007.
Thigpen J, Shah S, Merchant FA, and Castleman KR. Calibrating Multispectral Imaging System for Biological Particle Analysis under Transmitted Illumination. Proceedings of Microscopy and Microanalysis, 12(2):1678-1679, 2006.
Shah S and Merchant FA. Fluorescence Dot Counting Efficiency in Radiance Mapped Images. Proceedings of Microscopy and Microanalysis, 12(2):1676-1677, 2006.
Shah S, Thigpen J, Merchant FA, and Castleman KR. Photometric Calibration for Automated Multispectral Imaging of Biological Samples. Proc. 1st workshop on microscopic image analysis with applications in biology (in conjunction with MICCAI (Medical Image Computing and Computer Assisted Intervention), Copenhagen), 1:27-33, 2006.
Merchant FA, Good KN, Choi H, and Castleman KR. Automated detection of chromosomal rearrangements in multi-color fluorescence in-situ hybridization images. Proc. IEEE Eng. Med. Biol. Soc., 2002: 1074-1075, 2002.
Bischoff FZ, Marquez-Do D, Simpson JL, Elias S, Castleman KR, and Merchant FA. Semi-automated screening of nucleated red blood cells for prenatal diagnosis using fetal cells in maternal blood. J Soc. Gyn. Invest., 7:1, 2000.
Merchant FA, and Toner M. Spatial and dynamic characterization of the interaction of Staphylococcal Aureus a-toxin with cell membranes. Advances in Heat and Mass Transfer in Biotechnology, HTV 355 / BED, 37: 3-8, 1997.
Merchant FA, Holmes W, Yarmush M, and Toner, M. Poloxamer 188 enhances functional recovery of lethally heat shocked fibroblasts. Advances in Heat and Mass Transfer in Biotechnology, HTV 355 / BED, 37: 161-166, 1997.
Merchant FA, Holmes WH, and Toner M. Analysis of functional recovery in cells treated with co-block polymers after thermal injury. Proc. IEEE Eng. Med. Biol. Soc., 5: 2182-2183, 1996.
Merchant FA, Aggarwal SJ, Diller KR, and Bovik AC. Semi-automatic morphological measurements of 2-D and 3-D microvascular images. Proc. IEEE International Conference on Image Processing, 1:416-420, 1994.
Merchant FA, Aggarwal SJ, Diller KR, and Bovik, AC. Analysis of 3-D microscope images of cryopreserved rat pancreatic islets for determination of viability. Proc. 3rd International Conference on Advances in Pattern Recognition and Digital Techniques, 1: 500-506, 1993.
Merchant FA, Aggarwal SJ, Diller KR, Bartels KA, and Bovik AC. Analysis of volumetric changes in rat pancreatic islets under osmotic stress using laser scanning confocal microscopy. Biomedical Sciences Instrumentation, 29:111-119, 1993.
Merchant FA, Aggarwal SJ, Diller KR, Bartels KA, and Bovik AC. Confocal microscopy and 3-D visualization of cryopreserved pancreatic islets. Biomedical Image Processing and Three-Dimensional Microscopy: SPIE, 1660:774-783, 1992.

Book Chapters

Wu X, Shah S, and Merchant FA. Automated Prototype Generation for Multi-Color Karyotyping. Lecture Notes in Computational Vision and Biomechanics, 6:145-163, 2013.
Merchant FA and Castleman KR. Computer-Assisted Microscopy. The Essential Guide to Image Processing, (ed. A.C. Bovik), Academic Press, pp. 777-828, 2009.
Merchant FA, Shah SK, and Castleman KR. Object Measurements. Microscope Image Processing, (eds. Q.J. Wu, F.A. Merchant, & K.R. Castleman), 1st Edition, Elsiever, pp. 195-214, 2008.
Merchant FA and Periasamy A. Fluorescence Microscopy. Microscope Image Processing, (eds. Q.J. Wu, F.A. Merchant, & K.R. Castleman), 1st Edition, Elsiever, pp. 247-290, 2008.
Merchant FA. Three-dimensional Imaging. Microscope Image Processing, (eds. Q.J. Wu, F.A. Merchant, & K.R. Castleman), 1st Edition, Elsiever, pp. 329-289, 2008.
Merchant FA, and Castleman KR. Computer Assisted Microscopy. Handbook of Image and Video Processing, (ed. A.C. Bovik), 2nd Edition, Academic Press, pp. 1311-1340, 2005.
Bovik AC, Aggarwal SJ, Merchant FA, Kim NH, and Diller KR. Automatic area and volume measurement from digital biomedical images. Image Analysis: Methods and Applications, (ed. D.P. Häder), 2nd Edition, CRC Press, pp. 23-64, 2001.
Merchant FA, Bartels KA, Bovik AC, and Diller KR. Confocal Microscopy. Handbook of Image and Video Processing, (ed. A.C. Bovik), Academic Press, pp. 853-868, 2000.
Diller KR, and Merchant FA. Network thermodynamic modeling of coupled osmotic and viscoelastic behavior of a tissue during cryopreservation. Macroscopic and Microscopic Heat Transfer in Biomedical Engineering, (eds. K.R. Diller & A. Shitzer), Elsevier Press, pp. 327-342, 1992.

Meeting Abstracts

(excluding conference articles)

Bui T, Sampathkumar U, Nowroozilarki Z, Liu J , Bordes MC , Hanson SE, Reece GP, Markey MK, Merchant FA. Symmetry of breasts following reconstructive surgery," San Antonio Breast Cancer Symposium 2020. In Press.
Chapman BV, Lei X, Patil P, Tripathi S, Nicklaus KM, Fingeret MC, Shaitelman SF, Hunt K, Buchholz T, Merchant FA, Markey MK, Smith B, Reddy JP. Quantitative 3D Assessment of Breast Cosmesis After Conventional (CF-WBI) versus Hypofractionated Whole Breast Radiation (HF-WBI): Results of a Randomized Clinical Trial. International Journal of Radiation Oncology, Biology, Physics, Volume 103, Issue 5, pp. E19, 2019.
Nicklaus KM, Ali K, Merchant FA, Hanson SE, Reece GP, Markey MK, "Development of an expert surgeon validation tool for breast reconstruction decision-making", Biomedical Engineering Society Annual Meeting, 2018.
Zaharan A, Nicklaus KM, Bordes MC, Reece GP, Hanson SE, Merchant FA, Markey MK, "Developing a Microsoft HoloLens application for mastectomy specimen visualizations," Biomedical Engineering Society (BMES) Annual Meeting, 2018.
Nicklaus KM, Cheong AL, Liu J, Reece GP, Bordes MC, Hanson SE, Markey MK, and Merchant FA, "3D Symmetry of Pre-operative Breasts in Cancer Patients," San Antonio Breast Cancer Symposium 2018.
Nicklaus KM, Teo I, Reece GP, Huang SC, Mahajan K, Andon J, Khanal P, Sun C, Merchant FA, Markey MK, Fingeret MC, "Relationships among breast symmetry, appearance investment, and body image dissatisfaction in breast cancer patients undergoing reconstruction," San Antonio Breast Cancer Symposium, 2017.
Fingeret MC, Weston J, Bordes MC, Huang SC, Reece GP, Merchant FA, Cantor SB, Markey MK, "Understanding the unmet needs of women with breast cancer undergoing reconstructive surgery," Appearance Matters 7 Conference, 2016.
Weston J, Bordes MC, Huang SC, Reece GP, Merchant FA, Cantor SB, Markey MK, Fingeret MC, "Patient preferences for visualizing possible outcomes of breast reconstruction," American Medical Informatics Association Annual Symposium, 2016.
Reddy J, Lei X, Huang H, Nicklaus KM, Fingeret MC, Shaitelman SF, Hunt KK, Buchholz TA, Merchant FA, Markey MK, and Smith BD, "Using quantitative metrics of breast cosmesis to compare fractionation regimens for whole-breast irradiation," ASTRO, 2016.
Loera E, Nicklaus KM, Bordes MC, Lee J, Cheong AL, Fingeret MC, Merchant FA, Reece GP, Markey MK, "Design of stereoscopic visualization of mastectomy specimens for augmented reality glasses," Biomedical Engineering Society (BMES) Annual Meeting, 2016.
Blessing AM†, Shi Y, Bollu LR, Drake JM, Faltermeier CM, Jonsson P, Sung YY, Han JJ, Merchant FA, Cheung E, Pienta KJ, Witte ON, and Frigo DE. Dissecting the Role and Regulation of Autophagy in Prostate Cancer. Autophagy Keystone Symposia, Breckenridge, Colorado, 2015.
Blessing AM†, Shi Y, Bollu LR, Drake JM, Faltermeier CM, Jonsson P, Sung YY, Han JJ, Merchant FA, Cheung E, Pienta KJ, Witte ON, and Frigo DE. The Role and Regulation of Autophagy in Prostate Cancer. National Graduate Student Symposium St. Jude Children's Research Hospital. Memphis, Tennessee, 2015.
Fingeret M, Reece G, Merchant FA, Ravi-Chandra K, Cantor S, and Markey, M. 3D Computer-Based Decision Support for Optimizing Body Image Following Breast Reconstruction. World Congress of Psycho-Oncology, Washington DC, USA, 2015.
Reece G, Merchant FA, Khatam H, Ravi-Chandra K., Weston J., Fingeret M., Lane C., Duncan K, and Markey, M. 3D Surface Imaging of the Human Female Torso in Upright to Supine Positions. Biomedical Engineering Society 2014 Annual Meeting, San Antonio, TX, 2014.
Wosik W., Das S., Zuo Z., and Merchant FA. The role of substrate materials in controlled culture of endothelial cells. Biomedical Engineering Society 2014 Annual Meeting, San Antonio, TX, 2014.
Hans C, McCollum C, Bondesson M., Gustafsson J., Shah S, Merchant FA. Automated Quantification of Caudal Vein Plexus in Zebrafish to Study Vascular Disruptors. Biomedical Engineering Society 2014 Annual Meeting, San Antonio, TX, 2014.
McCollum, C.W., Hans, C., Shah, S. Merchant, FA., Bondesson, M. and Gustafsson, J-A. Arsenic disrupts vascular development in zebrafish. A Collaborative Workshop on Aquatic Models and 21st Century Toxicology, Raleigh, NC, 2014.
McCollum CW, Hans C, Shah S, Merchant FA, Bondesson M, and Gustafsson JA. Identifying vascular disrupting chemicals using zebrafish. Society of Toxicology Annual Meeting: SOT 2013, San Antonio, TX, 2013.
Yan S, Tennakoon J, Han J, Merchant FA, Howe M, Ilkayeva O, Newgard C, McDonnell D, and Frigo D. Autophagy Is Required for Androgen Receptor-Mediated Prostate Cell Growth and Survival. Endocr. Rev., 33 (03_MeetingAbstracts): SUN-535, 2012.
Das S, Zagozdzon-Wosik W, and Merchant FA. BioMEMS Substrates for Endothelial Cells Network Formation, Biomedical Engineering Society 2012 Annual Meeting, Atlanta, Georgia, October 2012.
Shah T, Wu X, Chen J, Kakadiaris I, Shah S, and Merchant FA. Semi-Automated segmentation of branching patterns from optical projection tomography images of the bronchial tree. Biomedical Engineering Society 2012 Annual Meeting, Georgia, October 2012.
Das S, Merchant FA, and Zagozdzon-Wosik W. BioMEMS for Growth of Endothelial Cells. Mater. Res. Soc. Symposium, Boston, MA, November, 2011.
Kawale M, Reece G, Beahm E, Crosby M, Markey M, and Merchant FA. Automated Identification of Fiducial Points in 3D Torso Images. 3rd Annual International Conference in Computational Surgery, Houston, Texas, January, 2011.
Kawale M, Reece G, Crosby M, Beahm E, Markey M, and Merchant FA. Automated Localization of Fiducial Points in Three-Dimensional Torso Images. Biomedical Engineering Society Conference 2010, Austin, TX, October 2010.
Hogins J, Lee J, Szeto C, Reece G, Markey M, and Merchant FA. Effect of Patient Posture on Linear Assessment of Breast Appearance. Biomedical Engineering Society Conference 2009, Pittsburgh, PA, October 2009.
Farooqui H, Gurkan D, and Merchant FA. Tools for Optimizing HIPAA Compliance and Penetration Testing for EHR. Biomedical Engineering Society Conference 2009, Pittsburgh, PA, October 2009.
Valenzuela N, Rao P, Shah S, and Merchant FA. Automated Prototype Generation for Multi-Color Karyotyping, Biomedical Engineering Society Conference 2009, Pittsburgh, PA, October 2009.
Kawale M, Reece G, Crosby M, Beahm E, Markey M, and Merchant FA. Automated Nipple Identification in Three-Dimensional Surface Scans of Torso. Biomedical Engineering Society Conference 2009, Pittsburgh, PA, October 2009.
Merchant FA, Castleman K, Gibas Y, and Jackson L. Automated Prenatal Screening using Maternal Blood. Biomedical Imaging: Beyond Diagnostics, Workshop Abstracts, University of Michigan, pp. 22-23, September 1999.
Merchant FA, Holmes, WH, and Toner M. Role of co-block polymers in cell recovery after thermal injury. 16th Annual Meeting of the Society for Physical Regulation in Biology and Medicine, Chicago, Illinois, 1996.
Merchant FA, Diller KR, and Bovik AC. Quantitative analysis of confocal micrographs to measure the 3-D neovasculature in transplanted pancreas islets. Annals of Biomedical Engineering, 1996 Annual Fall Meeting, S-27, 1996.
Merchant FA, Diller KR, Aggarwal SJ, and Bovik AC. Evaluation of the angiogenesis process in cryopreserved islet grafts using laser scanning confocal microscopy. 32nd Annual Meeting of the Society for Cryobiology, Cryobiology 32: 539, Madison, Wisconsin, 1995.
Merchant FA, Diller KR, Aggarwal SJ, and Bovik AC. Analysis of the 3-D distribution of injury to pancreas islets during cryopreservation: Computer evaluation of laser scanning confocal micrographs. Proc. of the 31st Annual Technical Meeting of the Society of Engineering Science, College Station, Texas, 1994.
Merchant FA, Diller KR, Aggarwal SJ, and Bovik AC. Digital analysis of confocal micrographs for estimation of damage to cryopreserved islets and evaluation of the angiogenesis process in cryopreserved islets transplanted at renal subcapsular site in rats. 31st Annual Meeting of the Society for Cryobiology, Cryobiology 31: 590, Kyoto, Japan, 1994.
Diller KR, Merchant FA, Aggarwal SJ, Bartels KA, and Bovik AC. Measurement of the osmotic properties of multicellular tissues for understanding and predicting behavior during cryopreservation. 30th Annual Meeting of the Society for Cryobiology, Cryobiology 30: 618, Atlanta, Georgia, 1993.
Merchant FA, Aggarwal SJ, Diller KR, and Bovik AC. Assaying viability of cryopreserved pancreatic islets using laser scanning confocal microscopy. 29th Annual Meeting of the Society for Cryobiology, Cryobiology 29: 715, Ithaca, New York, 1992.

Invited Presentations

Merchant FA. 3D image based computational modeling to facilitate shared decision making in breast reconstruction surgery. UT School of Biomedical Informatics, Houston, Texas, November 13, 2019.
Merchant FA. 3D Modeling of Chromosomes Territories in Normal and Aneuploid Nuclei. Imaging-based Single Cell Analytics: Applications for Cancer Cell Biology and Therapeutics, BioScience Research Collaborative, Houston, Texas, February 25-27, 2019.
Merchant FA. Quantitative Imaging in Biology and Medicine. Department of Computer Science, University of Houston, Oct. 29, 2014.
Merchant FA. Research Topics in Bioengineering. Biomedical Engineering Society, University of Houston, April 5, 2012.
Merchant FA. 3D Modeling of the Spatial Nuclear Localization of Diploid and Aneuploid Chromosomes in Human Embryonic Stem Cells. Center of Nuclear Receptors and Cell Signaling, University of Houston, October 14, 2011.
Merchant FA. Optical Imaging in Medicine and Biology, Department of Electrical and Computer Engineering, University of Houston, April 1, 2011.
Merchant FA. and Farooqui H. Technology in Telemedicine. The University of Texas Health Science Center at Houston, School of Health Information Sciences, October 2009.
Merchant FA. Imaging Techniques for Molecular Cytogenetics, The Association of Biomolecular Resource Facilities, Creating the Biological Roadmap, March 31 - April 3, 2007, Tampa Florida.
Merchant FA. Automated Detection of Fetal Cells in Maternal Blood. National Institute of Child Health and Development, Sharpening the tools: Workshop on new technologies for detection of fetal cells in maternal blood for early prenatal diagnosis, Bethesda, 2003.
Merchant FA, Diller KR, Aggarwal SJ, and Bovik AC. Analysis of angiogenesis in pancreatic islet grafts using laser scanning confocal microscopy. 6th World Congress for Microcirculation, Munich, Germany, 1996.
Merchant FA, Diller KR, Aggarwal SJ, and Bovik AC. Confocal Microscopy of rat pancreatic islets: Cultured, cryopreserved and transplanted. 7th Annual Meeting of the Society of Low Temperature Biology, Dundee, Scotland, 1996.