Research Overview

In his research, Alvin Kho builds mathematical models of developing biological systems to identify developmental programs that underwrite pathobiology in these systems with the aim of translating this knowledge into clinically-relevant endpoints. He has investigated transcriptomes of the developing central nervous system (PMID:15075291), skeletal muscle (PMID:21337346) and lung (PMID:16800721, 19815808, 18664640) and identified molecular correlates associated with (normal) organ-specific function and disease traits in these systems. Recently, he has focused on the role of in utero exposures (e.g., vitamin D, corticosteroids) in the pathobiology of chronic disease that occur later in life such as asthma and COPD (PMID:22983352, 24188128, 24668408).

Researcher Services

Researcher Areas

  • Bioinformatics
  • Multi scale Mathematical Models of Developing and Pathogenic Systems
  • Fetal Programming
  • Systems Analysis

Research Departments

Researcher Programs

PUBLICATIONS

Publications powered by Harvard Catalyst Profiles

  1. Qiao D, Ameli A, Prokopenko D, Chen H, Kho AT, Parker MM, Morrow J, Hobbs BD, Liu Y, Beaty TH, Crapo JD, Barnes KC, Nickerson DA, Bamshad M, Hersh CP, Lomas DA, Agusti A, Make BJ, Calverley PMA, Donner CF, Wouters EF, Vestbo J, Paré PD, Levy RD, Rennard SI, Tal-Singer R, Spitz MR, Sharma A, Ruczinski I, Lange C, Silverman EK, Cho MH. Whole exome sequencing analysis in severe chronic obstructive pulmonary disease. Hum Mol Genet. 2018 Nov 01; 27(21):3801-3812. View abstract
  2. Kho AT, McGeachie MJ, Moore KG, Sylvia JM, Weiss ST, Tantisira KG. Circulating microRNAs and prediction of asthma exacerbation in childhood asthma. Respir Res. 2018 06 26; 19(1):128. View abstract
  3. Davis JS, Sun M, Kho AT, Moore KG, Sylvia JM, Weiss ST, Lu Q, Tantisira KG. Circulating microRNAs and association with methacholine PC20 in the Childhood Asthma Management Program (CAMP) cohort. PLoS One. 2017; 12(7):e0180329. View abstract
  4. Boudreault F, Pinilla-Vera M, Englert JA, Kho AT, Isabelle C, Arciniegas AJ, Barragan-Bradford D, Quintana C, Amador-Munoz D, Guan J, Choi KM, Sholl L, Hurwitz S, Tschumperlin DJ, Baron RM. Zinc deficiency primes the lung for ventilator-induced injury. JCI Insight. 2017 Jun 02; 2(11). View abstract
  5. McGeachie MJ, Davis JS, Kho AT, Dahlin A, Sordillo JE, Sun M, Lu Q, Weiss ST, Tantisira KG. Asthma remission: Predicting future airways responsiveness using an miRNA network. J Allergy Clin Immunol. 2017 Aug; 140(2):598-600.e8. View abstract
  6. McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Strunk RC, Weiss ST. Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma. Am J Respir Crit Care Med. 2016 12 15; 194(12):1465-1474. View abstract
  7. Zhang H, Kho AT, Wu Q, Halayko AJ, Limbert Rempel K, Chase RP, Sweezey NB, Weiss ST, Kaplan F. CRISPLD2 (LGL1) inhibits proinflammatory mediators in human fetal, adult, and COPD lung fibroblasts and epithelial cells. Physiol Rep. 2016 09; 4(17). View abstract
  8. Beauchemin KJ, Wells JM, Kho AT, Philip VM, Kamir D, Kohane IS, Graber JH, Bult CJ. Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development. PeerJ. 2016; 4:e2318. View abstract
  9. Kho AT, Sharma S, Davis JS, Spina J, Howard D, McEnroy K, Moore K, Sylvia J, Qiu W, Weiss ST, Tantisira KG. Circulating MicroRNAs: Association with Lung Function in Asthma. PLoS One. 2016; 11(6):e0157998. View abstract
  10. Kho AT, Chhabra D, Sharma S, Qiu W, Carey VJ, Gaedigk R, Vyhlidal CA, Leeder JS, Tantisira KG, Weiss ST. Age, Sexual Dimorphism, and Disease Associations in the Developing Human Fetal Lung Transcriptome. Am J Respir Cell Mol Biol. 2016 06; 54(6):814-21. View abstract
  11. McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Weiss ST, Strunk RC. Patterns of Growth and Decline in Lung Function in Persistent Childhood Asthma. N Engl J Med. 2016 May 12; 374(19):1842-1852. View abstract
  12. Oh DY, Dowling DJ, Ahmed S, Choi H, Brightman S, Bergelson I, Berger ST, Sauld JF, Pettengill M, Kho AT, Pollack HJ, Steen H, Levy O. Adjuvant-induced Human Monocyte Secretome Profiles Reveal Adjuvant- and Age-specific Protein Signatures. Mol Cell Proteomics. 2016 06; 15(6):1877-94. View abstract
  13. Prilutsky D, Kho AT, Palmer NP, Bhakar AL, Smedemark-Margulies N, Kong SW, Margulies DM, Bear MF, Kohane IS. Gene expression analysis in Fmr1KO mice identifies an immunological signature in brain tissue and mGluR5-related signaling in primary neuronal cultures. Mol Autism. 2015; 6:66. View abstract
  14. Haas DM, Lai D, Sharma S, Then J, Kho A, Flockhart DA, Tantisira K, Foroud T. Steroid Pathway Genes and Neonatal Respiratory Distress After Betamethasone Use in Anticipated Preterm Birth. Reprod Sci. 2016 May; 23(5):680-6. View abstract
  15. Park JA, Kim JH, Bi D, Mitchel JA, Qazvini NT, Tantisira K, Park CY, McGill M, Kim SH, Gweon B, Notbohm J, Steward R, Burger S, Randell SH, Kho AT, Tambe DT, Hardin C, Shore SA, Israel E, Weitz DA, Tschumperlin DJ, Henske EP, Weiss ST, Manning ML, Butler JP, Drazen JM, Fredberg JJ. Unjamming and cell shape in the asthmatic airway epithelium. Nat Mater. 2015 Oct; 14(10):1040-8. View abstract
  16. Sharma S, Kho AT, Chhabra D, Qiu W, Gaedigk R, Vyhlidal CA, Leeder JS, Barraza-Villarreal A, London SJ, Gilliland F, Raby BA, Weiss ST, Tantisira KG. Glucocorticoid genes and the developmental origins of asthma susceptibility and treatment response. Am J Respir Cell Mol Biol. 2015 May; 52(5):543-53. View abstract
  17. Chhabra D, Sharma S, Kho AT, Gaedigk R, Vyhlidal CA, Leeder JS, Morrow J, Carey VJ, Weiss ST, Tantisira KG, DeMeo DL. Fetal lung and placental methylation is associated with in utero nicotine exposure. Epigenetics. 2014 Nov; 9(11):1473-84. View abstract
  18. Crosslin DR, Carrell DS, Burt A, Kim DS, Underwood JG, Hanna DS, Comstock BA, Baldwin E, de Andrade M, Kullo IJ, Tromp G, Kuivaniemi H, Borthwick KM, McCarty CA, Peissig PL, Doheny KF, Pugh E, Kho A, Pacheco J, Hayes MG, Ritchie MD, Verma SS, Armstrong G, Stallings S, Denny JC, Carroll RJ, Crawford DC, Crane PK, Mukherjee S, Bottinger E, Li R, Keating B, Mirel DB, Carlson CS, Harley JB, Larson EB, Jarvik GP. Genetic variation in the HLA region is associated with susceptibility to herpes zoster. Genes Immun. 2015 Jan-Feb; 16(1):1-7. View abstract
  19. Sharma S, Chhabra D, Kho AT, Hayden LP, Tantisira KG, Weiss ST. The genomic origins of asthma. Thorax. 2014 May; 69(5):481-7. View abstract
  20. Kho AT, Sharma S, Qiu W, Gaedigk R, Klanderman B, Niu S, Anderson C, Leeder JS, Weiss ST, Tantisira KG. Vitamin D related genes in lung development and asthma pathogenesis. BMC Med Genomics. 2013 Nov 05; 6:47. View abstract
  21. Kho AT, Liu K, Visner G, Martin T, Boudreault F. Identification of dedifferentiation and redevelopment phases during postpneumonectomy lung growth. Am J Physiol Lung Cell Mol Physiol. 2013 Oct 15; 305(8):L542-54. View abstract
  22. Alexander MS, Kawahara G, Motohashi N, Casar JC, Eisenberg I, Myers JA, Gasperini MJ, Estrella EA, Kho AT, Mitsuhashi S, Shapiro F, Kang PB, Kunkel LM. MicroRNA-199a is induced in dystrophic muscle and affects WNT signaling, cell proliferation, and myogenic differentiation. Cell Death Differ. 2013 Sep; 20(9):1194-208. View abstract
  23. Patel NR, Bole M, Chen C, Hardin CC, Kho AT, Mih J, Deng L, Butler J, Tschumperlin D, Fredberg JJ, Krishnan R, Koziel H. Cell elasticity determines macrophage function. PLoS One. 2012; 7(9):e41024. View abstract
  24. Carpe N, Mandeville I, Kho AT, Qiu W, Martin JG, Tantisira KG, Raby BA, Weiss ST, Kaplan F. Maternal allergen exposure reprograms the developmental lung transcriptome in atopic and normoresponsive rat pups. Am J Physiol Lung Cell Mol Physiol. 2012 Nov 15; 303(10):L899-911. View abstract
  25. Melén E, Kho AT, Sharma S, Gaedigk R, Leeder JS, Mariani TJ, Carey VJ, Weiss ST, Tantisira KG. Expression analysis of asthma candidate genes during human and murine lung development. Respir Res. 2011 Jun 23; 12:86. View abstract
  26. Alexander MS, Kawahara G, Kho AT, Howell MH, Pusack TJ, Myers JA, Montanaro F, Zon LI, Guyon JR, Kunkel LM. Isolation and transcriptome analysis of adult zebrafish cells enriched for skeletal muscle progenitors. Muscle Nerve. 2011 May; 43(5):741-50. View abstract
  27. Ning M, Sarracino DA, Kho AT, Guo S, Lee SR, Krastins B, Buonanno FS, Vizcaíno JA, Orchard S, McMullin D, Wang X, Lo EH. Proteomic temporal profile of human brain endothelium after oxidative stress. Stroke. 2011 Jan; 42(1):37-43. View abstract
  28. Liu F, Mih JD, Shea BS, Kho AT, Sharif AS, Tager AM, Tschumperlin DJ. Feedback amplification of fibrosis through matrix stiffening and COX-2 suppression. J Cell Biol. 2010 Aug 23; 190(4):693-706. View abstract
  29. Carpe N, Mandeville I, Ribeiro L, Ponton A, Martin JG, Kho AT, Chu JH, Tantisira K, Weiss ST, Raby BA, Kaplan F. Genetic influences on asthma susceptibility in the developing lung. Am J Respir Cell Mol Biol. 2010 Dec; 43(6):720-30. View abstract
  30. Kojic N, Chung E, Kho AT, Park JA, Huang A, So PT, Tschumperlin DJ. An EGFR autocrine loop encodes a slow-reacting but dominant mode of mechanotransduction in a polarized epithelium. FASEB J. 2010 May; 24(5):1604-15. View abstract
  31. Kho AT, Bhattacharya S, Tantisira KG, Carey VJ, Gaedigk R, Leeder JS, Kohane IS, Weiss ST, Mariani TJ. Transcriptomic analysis of human lung development. Am J Respir Crit Care Med. 2010 Jan 01; 181(1):54-63. View abstract
  32. Du R, Tantisira K, Carey V, Bhattacharya S, Metje S, Kho AT, Klanderman BJ, Gaedigk R, Lazarus R, Mariani TJ, Leeder JS, Weiss ST. Platform dependence of inference on gene-wise and gene-set involvement in human lung development. BMC Bioinformatics. 2009 Jun 19; 10:189. View abstract
  33. Arashiro P, Eisenberg I, Kho AT, Cerqueira AM, Canovas M, Silva HC, Pavanello RC, Verjovski-Almeida S, Kunkel LM, Zatz M. Transcriptional regulation differs in affected facioscapulohumeral muscular dystrophy patients compared to asymptomatic related carriers. Proc Natl Acad Sci U S A. 2009 Apr 14; 106(15):6220-5. View abstract
  34. Schüller U, Heine VM, Mao J, Kho AT, Dillon AK, Han YG, Huillard E, Sun T, Ligon AH, Qian Y, Ma Q, Alvarez-Buylla A, McMahon AP, Rowitch DH, Ligon KL. Acquisition of granule neuron precursor identity is a critical determinant of progenitor cell competence to form Shh-induced medulloblastoma. Cancer Cell. 2008 Aug 12; 14(2):123-34. View abstract
  35. Kho AT, Bhattacharya S, Mecham BH, Hong J, Kohane IS, Mariani TJ. Expression profiles of the mouse lung identify a molecular signature of time-to-birth. Am J Respir Cell Mol Biol. 2009 Jan; 40(1):47-57. View abstract
  36. Gobezie R, Kho A, Krastins B, Sarracino DA, Thornhill TS, Chase M, Millett PJ, Lee DM. High abundance synovial fluid proteome: distinct profiles in health and osteoarthritis. Arthritis Res Ther. 2007; 9(2):R36. View abstract
  37. Frank NY, Kho AT, Schatton T, Murphy GF, Molloy MJ, Zhan Q, Ramoni MF, Frank MH, Kohane IS, Gussoni E. Regulation of myogenic progenitor proliferation in human fetal skeletal muscle by BMP4 and its antagonist Gremlin. J Cell Biol. 2006 Oct 09; 175(1):99-110. View abstract
  38. Schüller U, Kho AT, Zhao Q, Ma Q, Rowitch DH. Cerebellar 'transcriptome' reveals cell-type and stage-specific expression during postnatal development and tumorigenesis. Mol Cell Neurosci. 2006 Nov; 33(3):247-59. View abstract
  39. Hung KE, Kho AT, Sarracino D, Richard LG, Krastins B, Forrester S, Haab BB, Kohane IS, Kucherlapati R. Mass spectrometry-based study of the plasma proteome in a mouse intestinal tumor model. J Proteome Res. 2006 Aug; 5(8):1866-78. View abstract
  40. Cerletti M, Molloy MJ, Tomczak KK, Yoon S, Ramoni MF, Kho AT, Beggs AH, Gussoni E. Melanoma cell adhesion molecule is a novel marker for human fetal myogenic cells and affects myoblast fusion. J Cell Sci. 2006 Aug 01; 119(Pt 15):3117-27. View abstract
  41. Liu H, Kho AT, Kohane IS, Sun Y. Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development. PLoS Med. 2006 Jul; 3(7):e232. View abstract
  42. Gazda HT, Kho AT, Sanoudou D, Zaucha JM, Kohane IS, Sieff CA, Beggs AH. Defective ribosomal protein gene expression alters transcription, translation, apoptosis, and oncogenic pathways in Diamond-Blackfan anemia. Stem Cells. 2006 Sep; 24(9):2034-44. View abstract
  43. Kho AT, Kang PB, Kohane IS, Kunkel LM. Transcriptome-scale similarities between mouse and human skeletal muscles with normal and myopathic phenotypes. BMC Musculoskelet Disord. 2006 Mar 07; 7:23. View abstract
  44. Cerletti M, Molloy MJ, Tomczak KK, Yoon S, Ramoni MF, Kho AT, Beggs AH and Gussoni E. Melanoma Cell Adhesion Molecule is a novel marker for human fetal myogenic cells and affects myoblast fusion. J Cell Sci. 119, 3117-27, 2006. 2006; 119(Pt 15):3117-27. View abstract
  45. Gazda HT, Kho AT, Sanoudou D, JM, Kohane IS, Sieff CA, Beggs AH. Alteration of ribosomal protein gene expression, transcription, apoptosis and cancer pathways in Diamond-Blackfan anemia. Stem Cells. 2006; 24(9):2033-44. View abstract
  46. Haslett JN, Kang PB, Han M, Kho AT, Sanoudou D, Volinski JM, Beggs AH, Kohane IS, Kunkel LM. The influence of muscle type and dystrophin deficiency on murine expression profiles. Mamm Genome. 2005 Oct; 16(10):739-48. View abstract
  47. Kang PB, Kho AT, Sanoudou D, Haslett JN, Dow CP, Han M, Blasko JM, Lidov HG, Beggs AH, Kunkel LM. Variations in gene expression among different types of human skeletal muscle. Muscle Nerve. 2005 Oct; 32(4):483-91. View abstract
  48. Liadaki K, Kho AT, Sanoudou D, Schienda J, Flint A, Beggs AH, Kohane IS, Kunkel LM. Side population cells isolated from different tissues share transcriptome signatures and express tissue-specific markers. Exp Cell Res. 2005 Feb 15; 303(2):360-74. View abstract
  49. Ligon KL, Alberta JA, Kho AT, Weiss J, Kwaan MR, Nutt CL, Louis DN, Stiles CD, Rowitch DH. The oligodendroglial lineage marker OLIG2 is universally expressed in diffuse gliomas. J Neuropathol Exp Neurol. 2004 May; 63(5):499-509. View abstract
  50. Sanoudou D, Frieden LA, Haslett JN, Kho AT, Greenberg SA, Kohane IS, Kunkel LM, Beggs AH. Molecular classification of nemaline myopathies: "nontyping" specimens exhibit unique patterns of gene expression. Neurobiol Dis. 2004 Apr; 15(3):590-600. View abstract
  51. Kho AT, Zhao Q, Cai Z, Butte AJ, Kim JY, Pomeroy SL, Rowitch DH, Kohane IS. Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers. Genes Dev. 2004 Mar 15; 18(6):629-40. View abstract
  52. Lennon NJ, Kho A, Bacskai BJ, Perlmutter SL, Hyman BT, Brown RH. Dysferlin interacts with annexins A1 and A2 and mediates sarcolemmal wound-healing. J Biol Chem. 2003 Dec 12; 278(50):50466-73. View abstract
  53. Haslett JN, Sanoudou D, Kho AT, Han M, Bennett RR, Kohane IS, Beggs AH, Kunkel LM. Gene expression profiling of Duchenne muscular dystrophy skeletal muscle. Neurogenetics. 2003 Aug; 4(4):163-71. View abstract
  54. Sanoudou D, Haslett JN, Kho AT, Guo S, Gazda HT, Greenberg SA, Lidov HG, Kohane IS, Kunkel LM, Beggs AH. Expression profiling reveals altered satellite cell numbers and glycolytic enzyme transcription in nemaline myopathy muscle. Proc Natl Acad Sci U S A. 2003 Apr 15; 100(8):4666-71. View abstract
  55. Haslett JN, Sanoudou D, Kho AT, Bennett RR, Greenberg SA, Kohane IS, Beggs AH, Kunkel LM. Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscle. Proc Natl Acad Sci U S A. 2002 Nov 12; 99(23):15000-5. View abstract
  56. Isaac S. Kohane, Alvin T. Kho, Atul J. Butte . Microarrays for an Integrative Genomics Microarrays for an Integrative Genomics. 2002; 326. View abstract
  57. Zhao Q, Kho A, Kenney AM, Yuk Di DI, Kohane I, Rowitch DH. Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach. Proc Natl Acad Sci U S A. 2002 Apr 16; 99(8):5704-9. View abstract
  58. Tsien CL, Libermann TA, Gu X, Kho A, Kohane IS. CHIP TUNER: a web tool for evidence-based noise reduction in gene discovery. Proc AMIA Symp. 2002; 810-4. View abstract
  59. Katsoulakis MA, Kho AT (3) 265-290, 2001. Stochastic mean curvature flows: Asymptotic derivation, level set formulation and numerics. Interfaces and Free Boundaries. 2001; 3:265-90. View abstract
  60. Alvin Thong-Juak Kho. Multi-scale analysis for microscropic models in materials science and cell biology. 2000. View abstract