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Soumyaroop Bhattacharya, M.S., Ed.D.

Soumyaroop Bhattacharya, M.S., Ed.D.

About Me

Faculty Appointments

Research Assistant Professor - Department of Pediatrics, Neonatology (SMD)

Credentials

Education

Ed.D. | University of Rochester. Education. 2023

MEd | Fitchburg State University. Science Education. 2006

MS | University of Pittsburgh. Biomedical Informatics. 2004

MS | U of Massachusetts-Lowell. Biological Science. 2002

BS | India-Banaras Hindu U, Varanasi. Agriculture. 2000

Diploma in Software Engineering | APTECH Computer Education. 1999

Awards

Doctoral Student Dissertation Funding. 2023

PAS Trainee Registration Grant. 2021

Abstract Scholarship Award. 2019 - 2019

Abstract Scholarship Award. 2019

Best Poster (Faculty). 2019

American Thoracic Society Abstract Scholarship Award. 2015

Associate Chair. 2015 - 2015

Travel Fellowship. 2005

Best E-Poster. 2003

Graduate Research Grant Award. 2001 - 2002

National Talent Search Scholarship. 1993

Research

Soumyaroop Bhattacharya is an Assistant in Neonatology Division of Pediatrics Department. His research interests include gene expression analysis of lung development and diseases, involving biomarker discovery and algorithm development for data analysis, and he is currently leading multiple project...
Soumyaroop Bhattacharya is an Assistant in Neonatology Division of Pediatrics Department. His research interests include gene expression analysis of lung development and diseases, involving biomarker discovery and algorithm development for data analysis, and he is currently leading multiple projects on Genome-wide expression profiling studies on lung diseases and development. He is also collaborating with investigators in numerous other bioinformatics studies.
Dr. Bhattacharya has over two decades of experience in applying state-of-the-art analytical approaches on high-throughput functional genomics data generated from multiple species using multiple omics platforms. He has demonstrated expertise in developing algorithms for high-throughput genomic data analysis, their application in studying gene expression changes during human lung development, and its aberrations, as well as in adult lung diseases.

Research Lab

Soumyaroop Bhattacharya's research interests include gene expression analysis of lung development and diseases, involving biomarker discovery and algorithm development for data analysis.

Visit Research Lab Website

Publications

Journal Articles

Bulk RNA Sequencing of Human Pediatric Lung Cell Populations Reveals Unique Transcriptomic Signature Associated with Post-natal Pulmonary Development.

Bandyopadhyay G, Jehrio MG, Baker C, Bhattacharya S, Misra RS, Huyck HL, Chu CY, Myers JR, Ashton J, Polter S, Cochran M, Bushnell T, Dutra J, Katzman PJ, Deutsch GH, Mariani TJ, Pryhuber GS

American journal of physiology. Lung cellular and molecular physiology.. 2024 March 5 Epub 03/05/2024.

Single-Cell Transcriptomic Profiling Identifies Molecular Phenotypes of Newborn Human Lung Cells.

Bhattacharya S, Myers JA, Baker C, Guo M, Danopoulos S, Myers JR, Bandyopadhyay G, Romas ST, Huyck HL, Misra RS, Dutra J, Holden-Wiltse J, McDavid AN, Ashton JM, Al Alam D, Potter SS, Whitsett JA, Xu Y, Pryhuber GS, Mariani TJ

Genes.. 2024 February 2615 (3)Epub 02/26/2024.

A Trisomy 21 Lung Cell Atlas.

Bhattacharya S, Cherry C, Deutsch G, , Glass IA, Mariani TJ, Alam DA, Danopoulos S

bioRxiv : the preprint server for biology.. 2023 April 3 Epub 04/03/2023.

Multiple Genes of Candida albicans Influencing Echinocandin Susceptibility in Caspofungin-Adapted Mutants.

Sah SK, Bhattacharya S, Yadav A, Husain F, Ndiaye ABKT, Kruppa MD, Hayes JJ, Rustchenko E

Antimicrobial agents and chemotherapy.. 2022 November 10 :e0097722. Epub 11/10/2022.

Use of Host Response to Refine the Diagnosis of Group A Streptococcal Pharyngitis.

Yu J, Tycksen E, Yang W, Mariani TJ, Bhattacharya S, Falsey AR, Topham DJ, Storch GA

Journal of the Pediatric Infectious Diseases Society.. 2022 September 25 Epub 09/25/2022.

Dysregulation of bile acids, lipids, and nucleotides in psoriatic arthritis revealed by unbiased profiling of serum metabolites.

Paine A, Brookes PS, Bhattacharya S, Li D, Garcia-Hernandez ML, Tausk F, Ritchlin C

Arthritis & rheumatology.. 2022 July 11 Epub 07/11/2022.

Transcriptional Characterization Suggests Accelerated Epithelial Differentiation in Trisomy 21 Lungs.

Danopoulos S, Bhattacharya S, Cherry C, Deutsch G, Mariani T, Al Alam D

FASEB journal : official publication of the Federation of American Societies for Experimental Biology.. 2022 May 36 Suppl 1 Epub 1900 01 01.

Gene Expression Risk Scores for COVID-19 Illness Severity.

Peterson DR, Baran AM, Bhattacharya S, Branche AR, Croft DP, Corbett AM, Walsh EE, Falsey AR, Mariani TJ

The Journal of infectious diseases.. 2021 November 30 Epub 11/30/2021.

Proteomic Analysis of Human Lung Development.

Clair G, Bramer LM, Misra R, McGraw MD, Bhattacharya S, Kitzmiller JA, Feng S, Danna VG, Bandyopadhyay G, Bhotika H, Huyck HL, Deutsch GH, Mariani TJ, Carson J, Whitsett JA, Pryhuber GS, Adkins JN, Ansong C

American journal of respiratory and critical care medicine.. 2021 November 9 Epub 11/09/2021.

The effect of air pollution on the transcriptomics of the immune response to respiratory infection.

Croft DP, Burton DS, Nagel DJ, Bhattacharya S, Falsey AR, Georas SN, Hopke PK, Johnston CJ, Kottmann RM, Litonjua AA, Mariani TJ, Rich DQ, Thevenet-Morrison K, Thurston SW, Utell MJ, McCall MN

Scientific reports.. 2021 September 3011 (1):19436. Epub 09/30/2021.

Gene Expression Risk Scores for COVID-19 Illness Severity.

Peterson DR, Baran AM, Bhattacharya S, Branche AR, Croft DP, Corbett AM, Walsh EE, Falsey AR, Mariani TJ

bioRxiv : the preprint server for biology.. 2021 August 24 Epub 08/24/2021.

Prenatal histological, cellular, and molecular anomalies in Trisomy 21 lung.

Danopoulos S, Bhattacharya S, Deutsch G, Nih LR, Slaunwhite C, Mariani TJ, Al Alam D

The Journal of pathology.. 2021 May 29 Epub 05/29/2021.

A novel in vitro model of primary human pediatric lung epithelial cells.

Wang Q, Bhattacharya S, Mereness JA, Anderson C, Lillis JA, Misra RS, Romas S, Huyck H, Howell A, Bandyopadhyay G, Donlon K, Myers JR, Ashton J, Pryhuber GS, Mariani TJ

Pediatric research.. 2020 February 87 (3):511-517. Epub 02/18/2019.

Lymphocyte-Specific Biomarkers Associated With Preterm Birth and Bronchopulmonary Dysplasia.

Bhattacharya S, Mereness JA, Baran AM, Misra RS, Peterson DR, Ryan RM, Reynolds AM, Pryhuber GS, Mariani TJ

Frontiers in immunology.. 2020 11 :563473. Epub 01/21/2021.

Collagen VI Deficiency Results in Structural Abnormalities in the Mouse Lung.

Mereness JA, Bhattacharya S, Ren Y, Wang Q, Anderson CS, Donlon K, Dylag AM, Haak J, Angelin A, Bonaldo P, Mariani TJ

The American journal of pathology.. 2019 December 13 Epub 12/13/2019.

CX3CR1 as a respiratory syncytial virus receptor in pediatric human lung.

Anderson CS, Chu CY, Wang Q, Mereness JA, Ren Y, Donlon K, Bhattacharya S, Misra RS, Walsh EE, Pryhuber GS, Mariani TJ

Pediatric research.. 2019 November 14 Epub 11/14/2019.

Disruption of normal patterns of FOXF1 expression in a lethal disorder of lung development.

Steiner LA, Getman M, Schiralli Lester GM, Iqbal MA, Katzman P, Szafranski P, Stankiewicz P, Bhattacharya S, Mariani T, Pryhuber G, Lin X, Young JL, Dean DA, Scheible K

Journal of medical genetics.. 2019 October 29 Epub 10/29/2019.

Transcriptional Characterisation of Human Lung Cells Identifies Novel Mesenchymal Lineage Markers.

Danopoulos S, Bhattacharya S, Mariani TJ, Al Alam D

The European respiratory journal.. 2019 October 16 Epub 10/16/2019.

Author Correction: Transcriptional Regulation on Aneuploid Chromosomes in Diverse Candida albicans Mutants.

Tucker C, Bhattacharya S, Wakabayashi H, Bellaousov S, Kravets A, Welle SL, Myers J, Hayes JJ, Bulger M, Rustchenko E

Scientific reports.. 2019 July 59 (1):10019. Epub 07/05/2019.

Integration of transcriptomic and proteomic data identifies biological functions in cell populations from human infant lung.

Du Y, Clair GC, Al Alam, Danopoulos S, Schnell D, Kitzmiller JA, Misra RS, Bhattacharya S, Warburton D, Mariani TJ, Pryhuber GS, Whitsett JA, Ansong C, Xu Y

American journal of physiology. Lung cellular and molecular physiology.. 2019 July 3 Epub 07/03/2019.

Host Gene Expression in Nose and Blood for the Diagnosis of Viral Respiratory Infection.

Yu J, Peterson DR, Baran AM, Bhattacharya S, Wylie TN, Falsey AR, Mariani TJ, Storch GA

The Journal of infectious diseases.. 2019 April 1219 (7):1151-1161. Epub 1900 01 01.

Exome sequencing identifies gene variants and networks associated with extreme respiratory outcomes following preterm birth.

Hamvas A, Feng R, Bi Y, Wang F, Bhattacharya S, Mereness J, Kaushal M, Cotten CM, Ballard PL, Mariani TJ,

BMC genetics.. 2018 October 2019 (1):94. Epub 10/20/2018.

Dissociation, cellular isolation, and initial molecular characterization of neonatal and pediatric human lung tissues.

Bandyopadhyay G, Huyck HL, Misra RS, Bhattacharya S, Wang Q, Mereness J, Lillis JA, Myers JR, Ashton J, Bushnell T, Cochran M, Holden-Wiltse J, Katzman P, Deutsch GH, Whitsett JA, Xu Y, Mariani TJ, Pryhuber GS

American journal of physiology. Lung cellular and molecular physiology.. 2018 October 1315 (4):L576-L583. Epub 07/05/2018.

Transcriptional Regulation on Aneuploid Chromosomes in Divers Candida albicans Mutants.

Tucker C, Bhattacharya S, Wakabayashi H, Bellaousov S, Kravets A, Welle SL, Myers J, Hayes JJ, Bulger M, Rustchenko E

Scientific reports.. 2018 January 268 (1):1630. Epub 01/26/2018.

Type VI collagen promotes lung epithelial cell spreading and wound-closure.

Mereness JA, Bhattacharya S, Wang Q, Ren Y, Pryhuber GS, Mariani TJ

PloS one.. 2018 13 (12):e0209095. Epub 12/14/2018.

Transcriptomic Biomarkers to Discriminate Bacterial from Nonbacterial Infection in Adults Hospitalized with Respiratory Illness.

Bhattacharya S, Rosenberg AF, Peterson DR, Grzesik K, Baran AM, Ashton JM, Gill SR, Corbett AM, Holden-Wiltse J, Topham DJ, Walsh EE, Mariani TJ, Falsey AR

Scientific reports.. 2017 July 267 (1):6548. Epub 07/26/2017.

Lung Gene Expression Analysis (LGEA): an integrative web portal for comprehensive gene expression data analysis in lung development.

Du Y, Kitzmiller JA, Sridharan A, Perl AK, Bridges JP, Misra RS, Pryhuber GS, Mariani TJ, Bhattacharya S, Guo M, Potter SS, Dexheimer P, Aronow B, Jobe AH, Whitsett JA, Xu Y

Thorax.. 2017 May 72 (5):481-484. Epub 01/09/2017.

MicroRNA expression profiling defines the impact of electronic cigarettes on human airway epithelial cells.

Solleti SK, Bhattacharya S, Ahmad A, Wang Q, Mereness J, Rangasamy T, Mariani TJ

Scientific reports.. 2017 April 247 (1):1081. Epub 04/24/2017.

Flow-based sorting of neonatal lymphocyte populations for transcriptomics analysis.

Misra RS, Bhattacharya S, Huyck HL, Wang JE, Slaunwhite CG, Slaunwhite SL, Wightman TR, Secor-Socha S, Misra SK, Bushnell TP, Reynolds AM, Ryan RM, Quataert SA, Pryhuber GS, Mariani TJ

Journal of immunological methods.. 2016 October 437 :13-20. Epub 07/18/2016.

The Healthy Infant Nasal Transcriptome: A Benchmark Study.

Chu CY, Qiu X, Wang L, Bhattacharya S, Lofthus G, Corbett A, Holden-Wiltse J, Grier A, Tesini B, Gill SR, Falsey AR, Caserta MT, Walsh EE, Mariani TJ

Scientific reports.. 2016 September 236 :33994. Epub 09/23/2016.

Serpine2 deficiency results in lung lymphocyte accumulation and bronchus-associated lymphoid tissue formation.

Solleti SK, Srisuma S, Bhattacharya S, Rangel-Moreno J, Bijli KM, Randall TD, Rahman A, Mariani TJ

FASEB journal : official publication of the Federation of American Societies for Experimental Biology.. 2016 July 30 (7):2615-26. Epub 04/08/2016.

Recurrent copy number variants associated with bronchopulmonary dysplasia.

Ahmad A, Bhattacharya S, Sridhar A, Iqbal AM, Mariani TJ

Pediatric research.. 2016 June 79 (6):940-5. Epub 03/14/2016.

Airway epithelial cell PPAR? modulates cigarette smoke-induced chemokine expression and emphysema susceptibility in mice.

Solleti SK, Simon DM, Srisuma S, Arikan MC, Bhattacharya S, Rangasamy T, Bijli KM, Rahman A, Crossno JT, Shapiro SD, Mariani TJ

American journal of physiology. Lung cellular and molecular physiology.. 2015 August 1309 (3):L293-304. Epub 05/29/2015.

Alterations in gene expression and DNA methylation during murine and human lung alveolar septation.

Cuna A, Halloran B, Faye-Petersen O, Kelly D, Crossman DK, Cui X, Pandit K, Kaminski N, Bhattacharya S, Ahmad A, Mariani TJ, Ambalavanan N

American journal of respiratory cell and molecular biology.. 2015 July 53 (1):60-73. Epub 1900 01 01.

Integrated genomic analyses in bronchopulmonary dysplasia.

Ambalavanan N, Cotten CM, Page GP, Carlo WA, Murray JC, Bhattacharya S, Mariani TJ, Cuna AC, Faye-Petersen OM, Kelly D, Higgins RD,

The Journal of pediatrics.. 2015 March 166 (3):531-7.e13. Epub 11/06/2014.

The genome-wide transcriptional response to neonatal hyperoxia identifies Ahr as a key regulator.

Bhattacharya S, Zhou Z, Yee M, Chu CY, Lopez AM, Lunger VA, Solleti SK, Resseguie E, Buczynski BW, Mariani TJ, O'Reilly MA

American journal of physiology. Lung cellular and molecular physiology.. 2014 October 1307 (7):L516-23. Epub 08/22/2014.

Systems biology approaches to identify developmental bases for lung diseases.

Bhattacharya S, Mariani TJ

Pediatric research.. 2013 April 73 (4 Pt 2):514-22. Epub 01/11/2013.

Genome-wide transcriptional profiling reveals connective tissue mast cell accumulation in bronchopulmonary dysplasia.

Bhattacharya S, Go D, Krenitsky DL, Huyck HL, Solleti SK, Lunger VA, Metlay L, Srisuma S, Wert SE, Mariani TJ, Pryhuber GS

American journal of respiratory and critical care medicine.. 2012 August 15186 (4):349-58. Epub 06/21/2012.

Identification of FGF7 as a novel susceptibility locus for chronic obstructive pulmonary disease.

Brehm JM, Hagiwara K, Tesfaigzi Y, Bruse S, Mariani TJ, Bhattacharya S, Boutaoui N, Ziniti JP, Soto-Quiros ME, Avila L, Cho MH, Himes B, Litonjua AA, Jacobson F, Bakke P, Gulsvik A, Anderson WH, Lomas DA, Forno E, Datta S, Silverman EK, Celedón JC

Thorax.. 2011 December 66 (12):1085-90. Epub 09/15/2011.

SOX5 is a candidate gene for chronic obstructive pulmonary disease susceptibility and is necessary for lung development.

Hersh CP, Silverman EK, Gascon J, Bhattacharya S, Klanderman BJ, Litonjua AA, Lefebvre V, Sparrow D, Reilly JJ, Anderson WH, Lomas DA, Mariani TJ,

American journal of respiratory and critical care medicine.. 2011 June 1183 (11):1482-9. Epub 02/17/2011.

Peripheral blood gene expression profiles in COPD subjects.

Bhattacharya S, Tyagi S, Srisuma S, Demeo DL, Shapiro SD, Bueno R, Silverman EK, Reilly JJ, Mariani TJ

Journal of clinical bioinformatics. 2011 April 241 (1):12. Epub 04/24/2011.

Fibroblast growth factor receptors control epithelial-mesenchymal interactions necessary for alveolar elastogenesis.

Srisuma S, Bhattacharya S, Simon DM, Solleti SK, Tyagi S, Starcher B, Mariani TJ

American journal of respiratory and critical care medicine.. 2010 April 15181 (8):838-50. Epub 01/21/2010.

Transcriptomic analysis of human lung development.

Kho AT, Bhattacharya S, Tantisira KG, Carey VJ, Gaedigk R, Leeder JS, Kohane IS, Weiss ST, Mariani TJ

American journal of respiratory and critical care medicine.. 2010 January 1181 (1):54-63. Epub 10/08/2009.

Integration of genomic and genetic approaches implicates IREB2 as a COPD susceptibility gene.

DeMeo DL, Mariani T, Bhattacharya S, Srisuma S, Lange C, Litonjua A, Bueno R, Pillai SG, Lomas DA, Sparrow D, Shapiro SD, Criner GJ, Kim HP, Chen Z, Choi AM, Reilly J, Silverman EK

American journal of human genetics.. 2009 October 85 (4):493-502. Epub 1900 01 01.

Array of hope: expression profiling identifies disease biomarkers and mechanism.

Bhattacharya S, Mariani TJ

Biochemical Society transactions.. 2009 August 37 (Pt 4):855-62. Epub 1900 01 01.

Platform dependence of inference on gene-wise and gene-set involvement in human lung development.

Du R, Tantisira K, Carey V, Bhattacharya S, Metje S, Kho AT, Klanderman BJ, Gaedigk R, Lazarus R, Mariani TJ, Leeder JS, Weiss ST

BMC bioinformatics.. 2009 June 1910 :189. Epub 06/19/2009.

Molecular biomarkers for quantitative and discrete COPD phenotypes.

Bhattacharya S, Srisuma S, Demeo DL, Shapiro SD, Bueno R, Silverman EK, Reilly JJ, Mariani TJ

American journal of respiratory cell and molecular biology.. 2009 March 40 (3):359-67. Epub 10/10/2008.

Expression profiles of the mouse lung identify a molecular signature of time-to-birth.

Kho AT, Bhattacharya S, Mecham BH, Hong J, Kohane IS, Mariani TJ

American journal of respiratory cell and molecular biology.. 2009 January 40 (1):47-57. Epub 07/29/2008.

Gene expression profiling of Epstein-Barr virus-positive and -negative monomorphic B-cell posttransplant lymphoproliferative disorders.

Craig FE, Johnson LR, Harvey SA, Nalesnik MA, Luo JH, Bhattacharya SD, Swerdlow SH

Diagnostic molecular pathology : the American journal of surgical pathology, part B.. 2007 September 16 (3):158-68. Epub 1900 01 01.

Progression-associated genes in astrocytoma identified by novel microarray gene expression data reanalysis.

MacDonald TJ, Pollack IF, Okada H, Bhattacharya S, Lyons-Weiler J

Methods in molecular biology.. 2007 377 :203-22. Epub 1900 01 01.

Microarray data-based prioritization of chronic obstructive pulmonary disease susceptibility genes.

Bhattacharya S, Srisuma S, Demeo DL, Reilly JJ, Bueno R, Silverman EK, Mariani TJ

Proceedings of the American Thoracic Society.. 2006 August 3 (6):472. Epub 1900 01 01.

Epithelial cell PPARgamma is an endogenous regulator of normal lung maturation and maintenance.

Simon DM, Arikan MC, Srisuma S, Bhattacharya S, Andalcio T, Shapiro SD, Mariani TJ

Proceedings of the American Thoracic Society.. 2006 August 3 (6):510-1. Epub 1900 01 01.

Epithelial cell PPAR[gamma] contributes to normal lung maturation.

Simon DM, Arikan MC, Srisuma S, Bhattacharya S, Tsai LW, Ingenito EP, Gonzalez F, Shapiro SD, Mariani TJ

FASEB journal : official publication of the Federation of American Societies for Experimental Biology.. 2006 July 20 (9):1507-9. Epub 05/23/2006.

Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling.

Bhattacharya S, Mariani TJ

Nucleic acids research.. 2005 October 1333 (18):e157. Epub 10/13/2005.

A classification-based machine learning approach for the analysis of genome-wide expression data.

Lyons-Weiler J, Patel S, Bhattacharya S

Genome research.. 2003 March 13 (3):503-12. Epub 1900 01 01.

Overcoming confounded controls in the analysis of gene expression data from microarray experiments.

Bhattacharya S, Long D, Lyons-Weiler J

Applied bioinformatics. 2003 2 (4):197-208. Epub 1900 01 01.

Books

2013 Systems Biology Approaches to Identify Developmental Bases for Lung Diseases (2013)

Chapter: Systems biology approaches to identify developmental bases for lung diseases

Authors: Bhattacharya S and Mariani TJ,.

Publisher: Pediatric Res 2013

Array of hope: Expression profiling identifies disease biomarkers and mechanism (2009)

Authors: Bhattacharya S and Mariani, TJ,

Publisher: Biochem Soc Trans. 2009

Methods in Molecular Biology (2007)

Chapter: Progression-associated genes in astrocytoma identified by microarray gene expression data re-analysis: Microarray Data Analysis: Methods and Applications

Authors: MacDonald TJ, Pollack IF, Okada H, Bhattacharya S, Lyons-Weiler J.

Publisher: Humana Press Inc. 2007