Papers


  • Some papers can be downloaded directly from the links below.
  • To get a copy of other papers, please email vkola(AT)bu.edu.

  1. 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 Jun 1;143(6):1920-1933. 
  2. 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 May 5;36(17):4645-4653.
  3. 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 Apr 16;181(2):362-381.e28.
  4. Chang GH, Felson DT, Qiu S, Guermazi A, Capellini TD, Kolachalama VBAssessment of knee pain from MR imaging using a convolutional Siamese network. Eur Radiol. 2020 Jun;30(6):3538-3548.
  5. 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 Mar;97(3):538-550.
  6. Joshi PS, Heydari M, Kannan S, Ang TFA, 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 Dec 28;5:964-973.
  7. 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 Nov;114:103436.
  8. 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 Dec 31;32(7):347-354.
  9. 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 Aug 2;2(8):e199826.
  10. Kannan S, Morgan LA, Cheung M, Liang B, Lin CQ, Mun D, Francis JM, Chitalia VC, Henderson JMKolachalama VB. Segmentation of glomeruli within trichrome images using deep learning. Kidney Int Rep. 2019 Apr 15;4(7):955-962.
  11. Chang GH, Azar DA, Lyle C, Chitalia VC, Shazly T, Kolachalama VBIntrinsic coating morphology modulates acute drug transfer in drug-coated balloon therapySci Rep. 2019 May 2;9(1):6839.
  12. 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 healingPLoS One. 2019 Apr 24;14(4):e0213422.
  13. Gopal DM, Ayalon N, Wang YC, Siwik D, Sverdlov A, Donohue C, Perez A, Downing J, Apovian C, Silva V, Panagia M, Kolachalama VB, Ho JE, Liang CS, Gokce N, Colucci WS. Galectin-3 Is Associated With Stage B Metabolic Heart Disease and Pulmonary Hypertension in Young Obese PatientsJ Am Heart Assoc. 2019 Apr 2;8(7):e011100.

  14. Xue C, Lott JT, Kolachalama VB. Estimation of size and contact angle of evaporating sessile liquid drops using texture analysis. Langmuir, 2019, 35 (10), pp 3672–3679.

  15. 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 Sep 28;10:737-749.
  16. Kolachalama VB, Garg PS. Machine learning and medical education. NPJ Digit Med. 2018 Sep 27;1:54.
  17. 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/β-Catenin Suppressor Function Is Regulated by Tyr371 Phosphorylation. Am J Pathol. 2018 Aug;188(8):1921-1933.
  18. 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 NetworksKidney Int Rep (2018) 3, 464–475.PowerPoint Presentation
  19. 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.jad2018
  20. 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 Mar;29(3):1063-1072.Screen Shot 2018-01-23 at 10.44.04 PM
  21. 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).F3.large
  22. 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 May 21;49:30-37.Screen Shot 2017-05-26 at 12.22.43 PM
  23. Shashar M, Siwak J, Tapan U, Lee SY, Meyer R, 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 β-catenin contributing to the heterogeneity in Wnt activity in colorectal tumorsOncotarget. 2016 Nov 1;7(44):71136-71150.12107-182224-1-pb
  24. Mandal PK, Sarifuddin, Kolachalama VBComputational model of drug-coated balloon delivery in a patient-specific arterial vessel with heterogeneous tissue compositionCardiovasc Eng Technol. 2016 Dec;7(4):406-419.screen-shot-2017-01-04-at-1-35-37-pm
  25. 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):2251-60.10439_2015_1518_fig1_html
  26. 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 Feb 23;11(2):e0149178.journal-pone-0149178-g003
  27. Ferdous J, Kolachalama VB, Kolandaivelu K, Shazly T. Degree of bioresorbable vascular scaffold expansion modulates loss of essential functionActa Biomater. 2015 Oct;26:195-204.nihms717531f1
  28. Kolandaivelu K, O’Brien CC, Shazly T, Edelman ER, Kolachalama VBEnhancing physiologic simulations using supervised learning on coarse mesh solutions. J R Soc Interface. 2015 Mar 6;12(104).f5-medium
  29. 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 Sep 30;9(9):e108820.pone-0108820-g003
  30. 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 bifurcationsCardiovasc Res. 2014 Jul 1;103(1):37-46.f3-large
  31. 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.nihms479003f1
  32. O’Brien CC, Kolachalama VB, Barber TJ, Simmons A, Edelman ER. Impact of flow pulsatility on arterial drug distribution in stent-based therapyJ Control Release. 2013 Jun 10;168(2):115-24.NIHMS468946.html
  33. Ferdous J, Kolachalama VB, Shazly T. Impact of polymer structure and composition on fully resorbable endovascular scaffold performanceActa Biomater. 2013 Apr;9(4):6052-61.nihms603713f4
  34. 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.nihms729800f2
  35. 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.nihms366332f1
  36. 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 disturbanceJ Am Coll Cardiol. 2012 Apr 24;59(17):1551-60.1-s2-0-s0735109712005013-gr5
  37. 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.nihms280987f6
  38. 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.NIHMS159865.html
  39. Kolachalama VB, Levine EG, Edelman ER. Luminal flow amplifies stent-based drug deposition in arterial bifurcationsPLoS One. 2009 Dec 2;4(12):e8105.journal-pone-0008105-g001
  40. Kolachalama VB, Tzafriri AR, Arifin DY, Edelman ER. Luminal flow patterns dictate arterial drug deposition in stent-based delivery. J Control Release. 2009 Jan 133(1): 24-30.NIHMS86794.html
  41. 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. 4384221-fig-4-large
  42. Kolachalama VB, Bressloff NW, Nair PB. Mining data from hemodynamic simulations via Bayesian emulation. Biomed Eng Online. 2007 Dec 13;6:47.1475-925x-6-47-2
  43. 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):802-12.4155000-fig-6-large