Vijaya Kolachalama | Profiles RNS

Vijaya B. Kolachalama, PhD, FAHA

Assistant Professor

Boston University School of Medicine

Dept of Medicine

Computational Biomedicine

BS, Indian Institute of Technology, Kharagpur, India
PhD, University of Southampton, UK

Websites

	Kolachalama Laboratory
	BU Computer Science
	Faculty of Computing & Data Sciences
	Google Scholar
	GitHub

ORCID : 0000-0002-5312-8644

The Kolachalama laboratory is broadly focused on developing advanced machine learning algorithms to tackle complex biomedical datasets, with particular emphasis on medical imaging.

Phenotyping neurodegeneration using machine learning: We build machine learning frameworks to process multimodal data and identify specific signatures of neurodegeneration. We have experience in dealing with large data cohorts such as the Framingham Heart Study and established several computational pipelines to efficiently process volumetric images of the brain, neuropathology and other modes of data and use them for further analysis.

Digital pathology: We develop computational frameworks based on deep learning to assist the pathologist. Our current application areas include kidney disease, lung cancer and colorectal cancer.

Machine learning for musculoskeletal diseases: We develop machine learning frameworks to bring efficiency to the analysis of large-scale studies such as Osteoarthritis Initiative (OAI) and Multicenter osteoarthritis (MOST) study. We are particularly interested to quantify structures that are responsible for pain and factors that contribute to the progression of knee osteoarthritis.

Member
Boston University
Whitaker Cardiovascular Institute

Member
Boston University
Evans Center for Interdisciplinary Biomedical Research

Founding Assistant Professor
Boston University School of Medicine, Graduate Medical Sciences
Computing & Data Sciences Administration

2020 Faculty of Computing & Data Sciences, Boston University: Founding Member

2019 Institute for Health System Innovation & Policy, Boston University: Institute Fellow

2019 American Heart Association: Fellow

2018 Hariri Institute for Computing and Computational Science & Engineering, Boston University: Junior Faculty Fellow

2008 United States Food and Drug Administration: ORISE Fellowship

2005 Massachusetts Institute of Technology: Young Researcher Fellowship

BU Research

Integrated Digital Technology Platform for Optimization of Precision Brain Health
07/01/2020 - 06/30/2024 (Co-PI)
PI: Rhoda Au, PhD
American Heart Association

PRISTINE: Pre-cancer histology identification of Endobronchial biopsies using deep learning
09/01/2020 - 08/31/2022 (Co-PI)
PI: Jennifer E. Beane-Ebel, PhD
NIH/National Cancer Institute
1R21CA253498-01

Mechanisms of drug-coated balloon therapy
07/01/2017 - 06/30/2021 (PI)
American Heart Association

Biomarkers of lung squamous premalignant progression using deep learning on pathology imagesBiomarkers of lung squamous premalignant progression using deep learning on pathology images
06/01/2020 - 05/31/2021 (Co-PI)
PI: Jennifer E. Beane-Ebel, PhD
Johnson & Johnson Enterprise Innovation, Inc.

Novel antibody design using deep learning
01/01/2018 - 12/31/2019 (PI)
Visterra, Inc.

Title

Yr	Title	Project-Sub Proj	Pubs

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Chang GH, Felson DT, Qiu S, Guermazi A, Capellini TD, Kolachalama VB. Correction to: Assessment of knee pain from MR imaging using a convolutional Siamese network. Eur Radiol. 2020 Dec; 30(12):6968.View Related Profiles.

Guermazi, Ali
Felson, David
Kolachalama, Vijaya

PMID: 32700018

Xu D, Zhou F, Sun W, Chen L, Lan L, Li H, Xiao F, Li Y, Kolachalama VB, Li Y, Wang X, Xu H. Relationship Between serum SARS-CoV-2 nucleic acid(RNAemia) and Organ Damage in COVID-19 Patients: A Cohort Study. Clin Infect Dis. 2020 Jul 28. PMID: 32720678

Qiu S, Joshi PS, Miller MI, Xue C, Zhou X, Karjadi C, Chang GH, Joshi AS, Dwyer B, Zhu S, Kaku M, Zhou Y, Alderazi YJ, Swaminathan A, Kedar S, Saint-Hilaire MH, Auerbach SH, Yuan J, Sartor EA, Au R, Kolachalama VB. Development and validation of an interpretable deep learning framework for Alzheimer's disease classification. Brain. 2020 06 01; 143(6):1920-1933.View Related Profiles.

Dwyer, Brigid
Sartor, Emmett
Kaku, Michelle
Au, Rhoda
Auerbach, Sanford
Zhu, Shuhan
Kolachalama, Vijaya

PMID: 32357201

Azar D, Lott JT, Jabbarzadeh E, Shazly T, Kolachalama VB. Surface Modification Using Ultraviolet-Ozone Treatment Enhances Acute Drug Transfer in Drug-Coated Balloon Therapy. Langmuir. 2020 05 05; 36(17):4645-4653. PMID: 32271583

Richard D, Liu Z, Cao J, Kiapour AM, Willen J, Yarlagadda S, Jagoda E, Kolachalama VB, Sieker JT, Chang GH, Muthuirulan P, Young M, Masson A, Konrad J, Hosseinzadeh S, Maridas DE, Rosen V, Krawetz R, Roach N, Capellini TD. Evolutionary Selection and Constraint on Human Knee Chondrocyte Regulation Impacts Osteoarthritis Risk. Cell. 2020 04 16; 181(2):362-381.e28. PMID: 32220312

Chang GH, Felson DT, Qiu S, Guermazi A, Capellini TD, Kolachalama VB. Assessment of knee pain from MR imaging using a convolutional Siamese network. Eur Radiol. 2020 Jun; 30(6):3538-3548.View Related Profiles.

Guermazi, Ali
Felson, David
Kolachalama, Vijaya

PMID: 32055951

Wollacott AM, Xue C, Qin Q, Hua J, Bohnuud T, Viswanathan K, Kolachalama VB. Quantifying the nativeness of antibody sequences using long short-term memory networks. Protein Eng Des Sel. 2019 12 31; 32(7):347-354. PMID: 31504835

Joshi PS, Heydari M, Kannan S, Alvin Ang TF, Qin Q, Liu X, Mez J, Devine S, Au R, Kolachalama VB. Temporal association of neuropsychological test performance using unsupervised learning reveals a distinct signature of Alzheimer's disease status. Alzheimers Dement (N Y). 2019; 5:964-973.View Related Profiles.

Mez, Jesse
Au, Rhoda
Devine, Sherral
Kolachalama, Vijaya

PMID: 31921970

Walker JA, Richards S, Belghasem ME, Arinze N, Yoo SB, Tashjian JY, Whelan SA, Lee N, Kolachalama VB, Francis J, Ravid K, Sherr D, Chitalia VC. Temporal and tissue-specific activation of aryl hydrocarbon receptor in discrete mouse models of kidney disease. Kidney Int. 2020 03; 97(3):538-550.View Related Profiles.

Sherr, David
Francis, Jean
Walker, Joshua
Ravid, Katya
Belghasem, Mostafa
Kolachalama, Vijaya
Chitalia, Vipul

PMID: 31932072

Azar D, Torres WM, Davis LA, Shaw T, Eberth JF, Kolachalama VB, Lessner SM, Shazly T. Geometric determinants of local hemodynamics in severe carotid artery stenosis. Comput Biol Med. 2019 11; 114:103436. PMID: 31521900

Showing 10 of 45 results. Show More

Zhu H, Tao Q, Ang TFA, Massaro J, Gan Q, Salim S, Zhu RY, Kolachalama VB, Zhang X, Devine S, Auerbach SH, DeCarli C, Au R, Qiu WQ. Association of Plasma Amylin Concentration With Alzheimer Disease and Brain Structure in Older Adults. JAMA Netw Open. 2019 08 02; 2(8):e199826.View Related Profiles.

Zhu, Haihao
Massaro, Joseph
Au, Rhoda
Auerbach, Sanford
Ang, Ting Fang Alvin
Kolachalama, Vijaya

PMID: 31433485

Chang GH, Azar DA, Lyle C, Chitalia VC, Shazly T, Kolachalama VB. Intrinsic coating morphology modulates acute drug transfer in drug-coated balloon therapy. Sci Rep. 2019 05 02; 9(1):6839.View Related Profiles.

Kolachalama, Vijaya
Chitalia, Vipul

PMID: 31048704

Lee Y, Kim MT, Rhodes G, Sack K, Son SJ, Rich CB, Kolachalama VB, Gabel CV, Trinkaus-Randall V. Sustained Ca2+ mobilizations: A quantitative approach to predict their importance in cell-cell communication and wound healing. PLoS One. 2019; 14(4):e0213422.View Related Profiles.

Gabel, Christopher
Trinkaus-Randall, Vickery
Kolachalama, Vijaya

PMID: 31017899

Kannan S, Morgan LA, Liang B, Cheung MG, Lin CQ, Mun D, Nader RG, Belghasem ME, Henderson JM, Francis JM, Chitalia VC, Kolachalama VB. Segmentation of Glomeruli Within Trichrome Images Using Deep Learning. Kidney Int Rep. 2019 Jul; 4(7):955-962.View Related Profiles.

Francis, Jean
Henderson, Joel
Belghasem, Mostafa
Kolachalama, Vijaya
Chitalia, Vipul

PMID: 31317118

Gopal DM, Ayalon N, Wang YC, Siwik D, Sverdlov A, Donohue C, Perez A, Downing J, Apovian C, Silva V, Panagia M, Kolachalama V, Ho JE, Liang CS, Gokce N, Colucci WS. Galectin-3 Is Associated With Stage B Metabolic Heart Disease and Pulmonary Hypertension in Young Obese Patients. J Am Heart Assoc. 2019 04 02; 8(7):e011100.View Related Profiles.

Sverdlov, Aaron
Apovian, Caroline
Siwik, Deborah
Gopal, Deepa
Panagia, Marcello
Ayalon, Nir
Gokce, Noyan
Kolachalama, Vijaya
Colucci, Wilson

PMID: 30929550

Xue C, Lott JT, Kolachalama VB. Estimation of Size and Contact Angle of Evaporating Sessile Liquid Drops Using Texture Analysis. Langmuir. 2019 Mar 12; 35(10):3672-3679. PMID: 30707587

Qiu S, Chang GH, Panagia M, Gopal DM, Au R, Kolachalama VB. Fusion of deep learning models of MRI scans, Mini-Mental State Examination, and logical memory test enhances diagnosis of mild cognitive impairment. Alzheimers Dement (Amst). 2018; 10:737-749.View Related Profiles.

Gopal, Deepa
Panagia, Marcello
Au, Rhoda
Kolachalama, Vijaya

PMID: 30480079

Kolachalama VB, Garg PS. Machine learning and medical education. NPJ Digit Med. 2018; 1:54.View Related Profiles.

Garg, Priya
Kolachalama, Vijaya

PMID: 31304333

Kumaradevan S, Lee SY, Richards S, Lyle C, Zhao Q, Tapan U, Jiangliu Y, Ghumman S, Walker J, Belghasem M, Arinze N, Kuhnen A, Weinberg J, Francis J, Hartshorn K, Kolachalama VB, Cifuentes D, Rahimi N, Chitalia VC. c-Cbl Expression Correlates with Human Colorectal Cancer Survival and Its Wnt/ß-Catenin Suppressor Function Is Regulated by Tyr371 Phosphorylation. Am J Pathol. 2018 08; 188(8):1921-1933.View Related Profiles.

Kuhnen, Angela
Cifuentes, Daniel
Weinberg, Janice
Francis, Jean
Walker, Joshua
Hartshorn, Kevan
Belghasem, Mostafa
Rahimi, Nader
Zhao, Qing
Tapan, Umit
Kolachalama, Vijaya
Chitalia, Vipul

PMID: 30029779; DOI: 10.1016/j.ajpath.2018.05.007;

Kolachalama VB, Shashar M, Alousi F, Shivanna S, Rijal K, Belghasem ME, Walker J, Matsuura S, Chang GH, Gibson CM, Dember LM, Francis JM, Ravid K, Chitalia VC. Uremic Solute-Aryl Hydrocarbon Receptor-Tissue Factor Axis Associates with Thrombosis after Vascular Injury in Humans. J Am Soc Nephrol. 2018 03; 29(3):1063-1072.View Related Profiles.

Francis, Jean
Ravid, Katya
Belghasem, Mostafa
Matsuura, Shinobu
Kolachalama, Vijaya
Chitalia, Vipul

PMID: 29343519; DOI: 10.1681/ASN.2017080929;

Kolachalama VB, Singh P, Lin CQ, Mun D, Belghasem ME, Henderson JM, Francis JM, Salant DJ, Chitalia VC. Association of Pathological Fibrosis With Renal Survival Using Deep Neural Networks. Kidney Int Rep. 2018 Mar; 3(2):464-475.View Related Profiles.

Salant, David
Francis, Jean
Henderson, Joel
Belghasem, Mostafa
Kolachalama, Vijaya
Chitalia, Vipul

PMID: 29725651

Li J, Ogrodnik M, Kolachalama VB, Lin H, Au R. Assessment of the Mid-Life Demographic and Lifestyle Risk Factors of Dementia Using Data from the Framingham Heart Study Offspring Cohort. J Alzheimers Dis. 2018; 63(3):1119-1127.View Related Profiles.

Lin, Honghuang
Au, Rhoda
Kolachalama, Vijaya

PMID: 29710704

Shashar M, Belghasem ME, Matsuura S, Walker J, Richards S, Alousi F, Rijal K, Kolachalama VB, Balcells M, Odagi M, Nagasawa K, Henderson JM, Gautam A, Rushmore R, Francis J, Kirchhofer D, Kolandaivelu K, Sherr DH, Edelman ER, Ravid K, Chitalia VC. Targeting STUB1-tissue factor axis normalizes hyperthrombotic uremic phenotype without increasing bleeding risk. Sci Transl Med. 2017 Nov 22; 9(417).View Related Profiles.

Gautam, Amitabh
Sherr, David
Francis, Jean
Henderson, Joel
Walker, Joshua
Ravid, Katya
Belghasem, Mostafa
Rushmore, Richard
Matsuura, Shinobu
Kolachalama, Vijaya
Chitalia, Vipul

PMID: 29167396; DOI: 10.1126/scitranslmed.aam8475;

Tapan U, Lee SY, Weinberg J, Kolachalama VB, Francis J, Charlot M, Hartshorn K, Chitalia V. Racial differences in colorectal cancer survival at a safety net hospital. Cancer Epidemiol. 2017 08; 49:30-37.View Related Profiles.

Weinberg, Janice
Francis, Jean
Hartshorn, Kevan
Charlot, Marjory
Tapan, Umit
Kolachalama, Vijaya
Chitalia, Vipul

PMID: 28538169

Shashar M, Siwak J, Tapan U, Lee SY, Meyer RD, Parrack P, Tan J, Khatami F, Francis J, Zhao Q, Hartshorn K, Kolachalama VB, Rahimi N, Chitalia V. c-Cbl mediates the degradation of tumorigenic nuclear ß-catenin contributing to the heterogeneity in Wnt activity in colorectal tumors. Oncotarget. 2016 11 01; 7(44):71136-71150.View Related Profiles.

Francis, Jean
Tan, Josenia
Hartshorn, Kevan
Rahimi, Nader
Zhao, Qing
Tapan, Umit
Kolachalama, Vijaya
Chitalia, Vipul

PMID: 27661103; DOI: 10.18632/oncotarget.12107;

Mandal PK, Sarifuddin, Kolachalama VB. Computational Model of Drug-Coated Balloon Delivery in a Patient-Specific Arterial Vessel with Heterogeneous Tissue Composition. Cardiovasc Eng Technol. 2016 Dec; 7(4):406-419. PMID: 27443840

O'Brien CC, Kolandaivelu K, Brown J, Lopes AC, Kunio M, Kolachalama VB, Edelman ER. Constraining OCT with Knowledge of Device Design Enables High Accuracy Hemodynamic Assessment of Endovascular Implants. PLoS One. 2016; 11(2):e0149178. PMID: 26906566; PMCID: PMC4764338; DOI: 10.1371/journal.pone.0149178;

O'Brien CC, Lopes AC, Kolandaivelu K, Kunio M, Brown J, Kolachalama VB, Conway C, Bailey L, Markham P, Costa M, Ware J, Edelman ER. Vascular Response to Experimental Stent Malapposition and Under-Expansion. Ann Biomed Eng. 2016 Jul; 44(7):2251-60. PMID: 26732391; PMCID: PMC4893976; DOI: 10.1007/s10439-015-1518-x;

Ferdous J, Kolachalama VB, Kolandaivelu K, Shazly T. Degree of bioresorbable vascular scaffold expansion modulates loss of essential function. Acta Biomater. 2015 Oct; 26:195-204. PMID: 26277377; PMCID: PMC4584207; DOI: 10.1016/j.actbio.2015.08.009;

Kolandaivelu K, O'Brien CC, Shazly T, Edelman ER, Kolachalama VB. Enhancing physiologic simulations using supervised learning on coarse mesh solutions. J R Soc Interface. 2015 Mar 6; 12(104):20141073. PMID: 25652458; PMCID: PMC4345474; DOI: 10.1098/rsif.2014.1073;

Alshareef M, Krishna V, Ferdous J, Alshareef A, Kindy M, Kolachalama VB, Shazly T. Effect of spinal cord compression on local vascular blood flow and perfusion capacity. PLoS One. 2014; 9(9):e108820. PMID: 25268384; PMCID: PMC4182502; DOI: 10.1371/journal.pone.0108820;

Martorell J, Santomá P, Kolandaivelu K, Kolachalama VB, Melgar-Lesmes P, Molins JJ, Garcia L, Edelman ER, Balcells M. Extent of flow recirculation governs expression of atherosclerotic and thrombotic biomarkers in arterial bifurcations. Cardiovasc Res. 2014 Jul 1; 103(1):37-46. PMID: 24841070; PMCID: PMC4670884; DOI: 10.1093/cvr/cvu124;

Kolachalama VB, Pacetti SD, Franses JW, Stankus JJ, Zhao HQ, Shazly T, Nikanorov A, Schwartz LB, Tzafriri AR, Edelman ER. Mechanisms of tissue uptake and retention in zotarolimus-coated balloon therapy. Circulation. 2013 May 21; 127(20):2047-55. PMID: 23584359; PMCID: PMC3748613; DOI: 10.1161/CIRCULATIONAHA.113.002051;

O'Brien CC, Kolachalama VB, Barber TJ, Simmons A, Edelman ER. Impact of flow pulsatility on arterial drug distribution in stent-based therapy. J Control Release. 2013 Jun 10; 168(2):115-24. PMID: 23541929; PMCID: PMC3697861; DOI: 10.1016/j.jconrel.2013.03.014;

Ferdous J, Kolachalama VB, Shazly T. Impact of polymer structure and composition on fully resorbable endovascular scaffold performance. Acta Biomater. 2013 Apr; 9(4):6052-61. PMID: 23261926; PMCID: PMC4104616; DOI: 10.1016/j.actbio.2012.12.011;

Baker AB, Gibson WJ, Kolachalama VB, Golomb M, Indolfi L, Spruell C, Zcharia E, Vlodavsky I, Edelman ER. Heparanase regulates thrombosis in vascular injury and stent-induced flow disturbance. J Am Coll Cardiol. 2012 Apr 24; 59(17):1551-60. PMID: 22516446; PMCID: PMC4191917; DOI: 10.1016/j.jacc.2011.11.057;

Kniazeva T, Epshteyn AA, Hsiao JC, Kim ES, Kolachalama VB, Charest JL, Borenstein JT. Performance and scaling effects in a multilayer microfluidic extracorporeal lung oxygenation device. Lab Chip. 2012 May 7; 12(9):1686-95. PMID: 22418858; PMCID: PMC3320667; DOI: 10.1039/c2lc21156d;

Shazly T, Kolachalama VB, Ferdous J, Oberhauser JP, Hossainy S, Edelman ER. Assessment of material by-product fate from bioresorbable vascular scaffolds. Ann Biomed Eng. 2012 Apr; 40(4):955-65. PMID: 22042625; PMCID: PMC4616251; DOI: 10.1007/s10439-011-0445-8;

Kolandaivelu K, Swaminathan R, Gibson WJ, Kolachalama VB, Nguyen-Ehrenreich KL, Giddings VL, Coleman L, Wong GK, Edelman ER. Stent thrombogenicity early in high-risk interventional settings is driven by stent design and deployment and protected by polymer-drug coatings. Circulation. 2011 Apr 5; 123(13):1400-9. PMID: 21422389; PMCID: PMC3131199; DOI: 10.1161/CIRCULATIONAHA.110.003210;

Kolachalama VB, Levine EG, Edelman ER. Luminal flow amplifies stent-based drug deposition in arterial bifurcations. PLoS One. 2009; 4(12):e8105. PMID: 19956555; PMCID: PMC2781163; DOI: 10.1371/journal.pone.0008105;

Tzafriri AR, Vukmirovic N, Kolachalama VB, Astafieva I, Edelman ER. Lesion complexity determines arterial drug distribution after local drug delivery. J Control Release. 2010 Mar 19; 142(3):332-8. PMID: 19925836; PMCID: PMC2994187; DOI: 10.1016/j.jconrel.2009.11.007;

Kolachalama VB, Tzafriri AR, Arifin DY, Edelman ER. Luminal flow patterns dictate arterial drug deposition in stent-based delivery. J Control Release. 2009 Jan 5; 133(1):24-30. PMID: 18926864; PMCID: PMC2836846; DOI: 10.1016/j.jconrel.2008.09.075;

Kolachalama VB, Bressloff NW, Nair PB, Shearman CP. Predictive haemodynamics in a one-dimensional human carotid artery bifurcation. Part II: Application to graft design. IEEE Trans Biomed Eng. 2008 Mar; 55(3):1176-84. PMID: 18334411; DOI: 10.1109/TBME.2007.912398;

Kolachalama VB, Bressloff NW, Nair PB. Mining data from hemodynamic simulations via Bayesian emulation. Biomed Eng Online. 2007; 6:47. PMID: 18078522; PMCID: PMC2231366; DOI: 10.1186/1475-925X-6-47;

Kolachalama VB, Bressloff NW, Nair PB, Shearman CP. Predictive haemodynamics in a one-dimensional human carotid artery bifurcation. Part I: Application to stent design. IEEE Trans Biomed Eng. 2007 May; 54(5):802-12. PMID: 17518276; DOI: 10.1109/TBME.2006.889188;

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 45 publications over 13 distinct years, with a maximum of 10 publications in 2019

Bar chart showing 45 publications over 13 distinct years, with a maximum of 10 publications in 2019

Year	Publications
2007	2
2008	2
2009	2
2011	2
2012	3
2013	2
2014	2
2015	2
2016	4
2017	2
2018	6
2019	10
2020	6

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In addition to these self-described keywords below, a list of MeSH based concepts is available here.

Machine learning
Artificial intelligence
Deep learning
Computer vision
Digital pathology
Computational pathology
Deep neural networks
Adversarial learning
Alzheimer's disease
Osteoarthritis
Chronic kidney disease
Vascular drug delivery
Drug coated balloons
Drug eluting stents

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