Isaac Kohane

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance
    Peter J Park
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology, Center of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 25:3121-7. 2009
  2. pmc Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cells
    Erxi Wu
    Informatics Program, Children s Hospital Boston, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 3:e3794. 2008
  3. pmc Does collocation inform the impact of collaboration?
    Kyungjoon Lee
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 5:e14279. 2010
  4. ncbi request reprint Can we measure autism?
    Isaac S Kohane
    Isaac S Kohane is Co Director of the Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, and the Lawrence J Henderson Professor of Pediatrics, Children s Hospital, Boston, MA 02115, USA
    Sci Transl Med 5:209ed18. 2013
  5. pmc The co-morbidity burden of children and young adults with autism spectrum disorders
    Isaac S Kohane
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 7:e33224. 2012
  6. pmc Taxonomizing, sizing, and overcoming the incidentalome
    Isaac S Kohane
    Children s Hospital Informatics Program, Children s Hospital, Boston, Massachusetts, USA
    Genet Med 14:399-404. 2012
  7. doi request reprint (Mis)treating the pharmacogenetic incidentalome
    Isaac S Kohane
    Harvard Medical School Center for Biomedical Informatics, 10 Shattuck Street, Boston, Massachusetts 02115, USA
    Nat Rev Drug Discov 11:89-90. 2012
  8. pmc An unsupervised classification method for inferring original case locations from low-resolution disease maps
    John S Brownstein
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology, 1 Autumn St, Boston, MA, USA
    Int J Health Geogr 5:56. 2006
  9. pmc The twin questions of personalized medicine: who are you and whom do you most resemble?
    Isaac S Kohane
    Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
    Genome Med 1:4. 2009
  10. pmc Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia
    Jennifer Cohen
    Children s Hospital, Boston, Division of Newborn Medicine, Boston, Longwood Avenue, Boston, MA 02115, USA
    Genome Biol 8:R210. 2007

Research Grants

  1. Training Grant in Bioinformatics and Functional Genomics
    Isaac Kohane; Fiscal Year: 2005
  2. Index and Retrieval of Pathology Specimens
    Isaac Kohane; Fiscal Year: 2005
  3. GPing: Informatics for Personal Control of Genomic Data
    Isaac Kohane; Fiscal Year: 2007
  4. GPing: Informatics for Personal Control of Genomic Data
    Isaac Kohane; Fiscal Year: 2009
  5. Preventing the Incidentalome
    Isaac Kohane; Fiscal Year: 2009
  6. Preventing the Incidentalome
    Isaac S Kohane; Fiscal Year: 2010
  7. GPing: Informatics for Personal Control of Genomic Data
    Isaac S Kohane; Fiscal Year: 2010

Detail Information

Publications114 found, 100 shown here

  1. pmc Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance
    Peter J Park
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology, Center of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 25:3121-7. 2009
    ..We asked whether these heterogeneous models can be integrated to provide consistent and robust biological insights into the biology of insulin resistance...
  2. pmc Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cells
    Erxi Wu
    Informatics Program, Children s Hospital Boston, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 3:e3794. 2008
    ..Furthermore, some signaling is solely modulated through heterodimeric PDGFRalpha/beta...
  3. pmc Does collocation inform the impact of collaboration?
    Kyungjoon Lee
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 5:e14279. 2010
    ..We asked whether the physical proximity of collaborators remained a strong predictor of the scientific impact of their research as measured by citations of the resulting publications...
  4. ncbi request reprint Can we measure autism?
    Isaac S Kohane
    Isaac S Kohane is Co Director of the Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA, and the Lawrence J Henderson Professor of Pediatrics, Children s Hospital, Boston, MA 02115, USA
    Sci Transl Med 5:209ed18. 2013
    ..Newly released definitions of autism spectrum disorder demonstrate the need for precise diagnoses informed by the integration of clinical, molecular, and biochemical characteristics in a patient-information commons. ..
  5. pmc The co-morbidity burden of children and young adults with autism spectrum disorders
    Isaac S Kohane
    Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS ONE 7:e33224. 2012
    ..Use electronic health records Autism Spectrum Disorder (ASD) to assess the comorbidity burden of ASD in children and young adults...
  6. pmc Taxonomizing, sizing, and overcoming the incidentalome
    Isaac S Kohane
    Children s Hospital Informatics Program, Children s Hospital, Boston, Massachusetts, USA
    Genet Med 14:399-404. 2012
    ..The false-positive incidental findings are of particular clinical concern. We provide estimates on the size of these false-positive findings and classify them into four broad categories...
  7. doi request reprint (Mis)treating the pharmacogenetic incidentalome
    Isaac S Kohane
    Harvard Medical School Center for Biomedical Informatics, 10 Shattuck Street, Boston, Massachusetts 02115, USA
    Nat Rev Drug Discov 11:89-90. 2012
    ..However, this goal could be undermined if care is not taken to minimize the impact of pharmacogenomic associations that turn out to have narrower implications than suggested by initial studies...
  8. pmc An unsupervised classification method for inferring original case locations from low-resolution disease maps
    John S Brownstein
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology, 1 Autumn St, Boston, MA, USA
    Int J Health Geogr 5:56. 2006
    ..In this report, a method is presented to evaluate whether patient privacy is being breached in the publication of low-resolution disease maps...
  9. pmc The twin questions of personalized medicine: who are you and whom do you most resemble?
    Isaac S Kohane
    Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA
    Genome Med 1:4. 2009
    ..These characterizations are readily represented probabilistically and can be used to drive decision-making in a rational manner that maximizes the positive outcomes for the patient...
  10. pmc Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia
    Jennifer Cohen
    Children s Hospital, Boston, Division of Newborn Medicine, Boston, Longwood Avenue, Boston, MA 02115, USA
    Genome Biol 8:R210. 2007
    ..Sections of umbilical cord were obtained at birth from 20 infants who later developed BPD and from 34 of their peers who did not develop BPD...
  11. pmc Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers
    Kamila Naxerova
    Children s Hospital Informatics Program, Harvard MIT Division of Health Sciences and Technology, Longwood Avenue, Boston, MA 02115, USA
    Genome Biol 9:R108. 2008
    ....
  12. pmc Transcriptome-scale similarities between mouse and human skeletal muscles with normal and myopathic phenotypes
    Alvin T Kho
    Children s Hospital Informatics Program, Harvard MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, USA
    BMC Musculoskelet Disord 7:23. 2006
    ..Mouse and human skeletal muscle transcriptome profiles vary by muscle type, raising the question of which mouse muscle groups have the greatest molecular similarities to human skeletal muscle...
  13. pmc Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms
    Dominic J Allocco
    Children s Hospital Informatics Program at Harvard MIT Division of Health Sciences and Technology, Boston, MA, USA
    BMC Genomics 8:68. 2007
    ....
  14. pmc Inter-species differences of co-expression of neighboring genes in eukaryotic genomes
    Yutaka Fukuoka
    Department of Biosystem Modeling, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
    BMC Genomics 5:4. 2004
    ..Also, no cross-species comparison has been made so far. We analyzed the effect of CD as well as normalized distance (ND) using expression data in six eukaryotic species: yeast, fruit fly, worm, rat, mouse and human...
  15. pmc Availability and quality of paraffin blocks identified in pathology archives: a multi-institutional study by the Shared Pathology Informatics Network (SPIN)
    Ashokkumar A Patel
    Department of Pathology, Center for Pathology Informatics, Benedum Oncology Informatics Center, University of Pittsburgh, Pittsburgh, PA, USA
    BMC Cancer 7:37. 2007
    ..This paper examines if tissue blocks, identified by localized computer searches at participating institutions, can be retrieved in adequate quantity and quality to support medical researchers...
  16. pmc Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks
    Cecily J Wolfe
    Children s Hospital Informatics Program and Harvard MIT Division of Health Sciences and Technology, 300 Longwood Avenue, Boston, MA 02115, USA
    BMC Bioinformatics 6:227. 2005
    ..This has informed the guilt-by-association (GBA) heuristic, widely invoked in functional genomics. Yet although the idea of GBA is accepted, the breadth of GBA applicability is uncertain...
  17. pmc Reproducibility of gene expression across generations of Affymetrix microarrays
    Ashish Nimgaonkar
    Informatics Program, Children s Hospital, Harvard Medical School, Boston, MA, USA
    BMC Bioinformatics 4:27. 2003
    ..In this study the reproducibility of gene expression levels across two generations of Affymetrix GeneChips (HuGeneFL and HG-U95A) was measured...
  18. pmc Quantifying the relationship between co-expression, co-regulation and gene function
    Dominic J Allocco
    Informatics Program, Children s Hospital, Boston, MA, USA
    BMC Bioinformatics 5:18. 2004
    ....
  19. pmc A SNP-centric database for the investigation of the human genome
    Alberto Riva
    Children s Hospital Informatics Program, Children s Hospital Boston, 320 Longwood, Avenue, Boston, MA 02115, USA
    BMC Bioinformatics 5:33. 2004
    ..Retrieving and analyzing such data for a large number of SNPs often represents a major bottleneck in the design of large-scale association studies...
  20. pmc Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements
    Scott L Carter
    Children s Hospital Informatics Program, Harvard Medical School, Boston, MA 02115 USA
    BMC Bioinformatics 6:107. 2005
    ..The NCI-60 gene expression profiles produced by Affymetrix HuFL platform were recalculated using these redefined probe sets and compared to previously published cDNA measurements of the same panel of RNA samples...
  21. pmc MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
    Voichita D Marinescu
    Children s Hospital Boston, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
    BMC Bioinformatics 6:79. 2005
    ..The ability to identify them in a genome-wide manner depends on the availability of accurate models and of search methods able to detect putative regulatory elements with enhanced sensitivity and specificity...
  22. doi request reprint Using electronic health records to drive discovery in disease genomics
    Isaac S Kohane
    Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA
    Nat Rev Genet 12:417-28. 2011
    ....
  23. ncbi request reprint Medicine. Reestablishing the researcher-patient compact
    Isaac S Kohane
    Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
    Science 316:836-7. 2007
  24. ncbi request reprint The incidentalome: a threat to genomic medicine
    Isaac S Kohane
    Center of Biomedical Informatics and Division of Health Sciences Technology, Harvard Medical School, Boston, Mass 02115, USA
    JAMA 296:212-5. 2006
  25. pmc Normalization of plasma 25-hydroxy vitamin D is associated with reduced risk of surgery in Crohn's disease
    Ashwin N Ananthakrishnan
    Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
    Inflamm Bowel Dis 19:1921-7. 2013
    ..Vitamin D may have an immunologic role in Crohn's disease (CD) and ulcerative colitis (UC). Retrospective studies suggested a weak association between vitamin D status and disease activity but have significant limitations...
  26. pmc Improving case definition of Crohn's disease and ulcerative colitis in electronic medical records using natural language processing: a novel informatics approach
    Ashwin N Ananthakrishnan
    Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
    Inflamm Bowel Dis 19:1411-20. 2013
    ....
  27. pmc Serum inflammatory markers and risk of colorectal cancer in patients with inflammatory bowel diseases
    Ashwin N Ananthakrishnan
    Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts Harvard Medical School, Boston, Massachusetts Electronic address
    Clin Gastroenterol Hepatol 12:1342-1348.e1. 2014
    ..No prior studies have examined association between C-reactive protein (CRP) or erythrocyte sedimentation rate (ESR) elevation and risk of CRC in an IBD cohort...
  28. pmc Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls
    Katherine P Liao
    Brigham and Women s Hospital, 75 Francis Street, PBB B3, Boston, MA 02115, USA
    Arthritis Rheum 65:571-81. 2013
    ..The aim of this study was to assess associations of autoantibodies with autoimmune risk alleles and with clinical diagnoses from the electronic medical records (EMRs) among RA cases and non-RA controls...
  29. pmc Association between reduced plasma 25-hydroxy vitamin D and increased risk of cancer in patients with inflammatory bowel diseases
    Ashwin N Ananthakrishnan
    Division of Gastroenterology, Massachusetts General Hospital, Boston, Massachusetts Harvard Medical School, Boston, Massachusetts Electronic address
    Clin Gastroenterol Hepatol 12:821-7. 2014
    ..The effects of low plasma 25-hydroxy vitamin D (25[OH]D) on outcomes other than bone health are understudied in patients with IBD. We examined the association between plasma level of 25(OH)D and risk of cancers in patients with IBD...
  30. pmc Apps to display patient data, making SMART available in the i2b2 platform
    Nich Wattanasin
    Partners HealthCare System, Boston, MA, USA
    AMIA Annu Symp Proc 2012:960-9. 2012
    ..In i2b2, viewing the patient in an EMR-like view enables a natural-feeling medical review process for each patient...
  31. pmc Strategies for maintaining patient privacy in i2b2
    Shawn N Murphy
    Laboratory of Computer Science, Massachusetts General Hospital, Boston, Massachusetts, USA
    J Am Med Inform Assoc 18:i103-8. 2011
    ..Some of these challenges arise from a misperception that the problem should be solved technically when actually the problem needs a holistic solution...
  32. pmc Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements
    Brigham H Mecham
    Division of Pulmonary and Critical Care Medicine, Department of Medicine and Pulmonary Bioinformatics, The Lung Biology Center, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 32:e74. 2004
    ..This strategy allowed a more efficient transfer of classification of breast cancer samples between data sets produced by cDNA microarray and Affymetrix gene-chip platforms...
  33. pmc Association between low density lipoprotein and rheumatoid arthritis genetic factors with low density lipoprotein levels in rheumatoid arthritis and non-rheumatoid arthritis controls
    Katherine P Liao
    Division of Rheumatology, Immunology and Allergy, Brigham and Women s Hospital, Boston, Massachusetts, USA
    Ann Rheum Dis 73:1170-5. 2014
    ..Our objective was to determine the association of established LDL and RA genetic alleles with LDL levels in RA cases compared with non-RA controls...
  34. pmc Lipid and lipoprotein levels and trend in rheumatoid arthritis compared to the general population
    Katherine P Liao
    Brigham and Women s Hospital, Boston, Massachusetts
    Arthritis Care Res (Hoboken) 65:2046-50. 2013
    ..Determining these differences is important in understanding the role of lipids in CV risk in RA...
  35. ncbi request reprint Bayesian approach to discovering pathogenic SNPs in conserved protein domains
    Zhaohui Cai
    Children s Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
    Hum Mutat 24:178-84. 2004
    ..As a result, our model predicted pathogenic variants with a 10% false-positive rate. The high specificity of our prediction algorithm should make it valuable in genetic association studies aimed at identifying pathogenic SNPs...
  36. ncbi request reprint PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applications
    Kyungjoon Lee
    Children s Hospital Informatics Program, 300 Longwood Ave, Boston, MA 02115, USA
    Bioinformatics 19:778-9. 2003
    ..The PGAGENE indexing agent periodically maps all publicly available gene-specific PGA data onto LocusLink using dynamically generated cross-referencing tables...
  37. pmc Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes
    SooHyun Lee
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    BMC Genomics 6:168. 2005
    ..We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories...
  38. pmc Electronic medical records for discovery research in rheumatoid arthritis
    Katherine P Liao
    Brigham and Women s Hospital, Boston, Massachusetts, USA
    Arthritis Care Res (Hoboken) 62:1120-7. 2010
    ..We assessed whether a classification algorithm incorporating narrative EMR data (typed physician notes) more accurately classifies subjects with rheumatoid arthritis (RA) compared with an algorithm using codified EMR data alone...
  39. pmc Serving the enterprise and beyond with informatics for integrating biology and the bedside (i2b2)
    Shawn N Murphy
    Laboratory of Computer Science, Massachusetts General Hospital, Boston, Massachusetts 02129, USA
    J Am Med Inform Assoc 17:124-30. 2010
    ..The current version of this software has been released into the public domain and is available at the URL: http://www.i2b2.org/software...
  40. pmc A set of genes previously implicated in the hypoxia response might be an important modulator in the rat ear tissue response to mechanical stretch
    Vishal Saxena
    Surgery, Brigham and Women s Hospital, Boston, MA, USA
    BMC Genomics 8:430. 2007
    ..The absolute enrichment (AE) algorithm that obtains a combined up and down regulated picture of the expression analysis was implemented...
  41. pmc Induction of the plasminogen activator system by mechanical stimulation of human bronchial epithelial cells
    Eric K Chu
    Brigham and Women s Hospital, Department of Pulmonary and Critical Care Medicine, Harvard School of Public Health, Physiology Program and Children s Hospital Informatics Program, Boston, Massachusetts 02115, USA
    Am J Respir Cell Mol Biol 35:628-38. 2006
    ..Together these observations suggest an integrated response of airway epithelial cells to mechanical stimulation, acting through the plasminogen-activating system to modify the airway microenvironment...
  42. pmc A self-scaling, distributed information architecture for public health, research, and clinical care
    Andrew J McMurry
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology, 300 Longwood Ave, Enders Room 150, Boston, MA 02115, USA
    J Am Med Inform Assoc 14:527-33. 2007
    ..This study sought to define a scalable architecture to support the National Health Information Network (NHIN). This architecture must concurrently support a wide range of public health, research, and clinical care activities...
  43. pmc The MAPPER database: a multi-genome catalog of putative transcription factor binding sites
    Voichita D Marinescu
    Children s Hospital Informatics Program, Children s Hospital Boston, Harvard Medical School, Enders Research Building EN 150 9, 300 Longwood Avenue, Boston, MA 02115, USA
    Nucleic Acids Res 33:D91-7. 2005
    ..Alternatively, the interface allows the user to retrieve binding sites for a single transcription factor of interest in a single gene or in all genes of the human, mouse or fruit fly genomes...
  44. pmc Cluster analysis of gene expression dynamics
    Marco F Ramoni
    Children s Hospital Informatics Program, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 99:9121-6. 2002
    ..A set of gene-expression time series, collected to study the response of human fibroblasts to serum, is used to identify the properties of the method...
  45. pmc Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancers
    Alvin T Kho
    Children s Hospital Informatics Program, Children s Hospital Boston, MA 02115, USA
    Genes Dev 18:629-40. 2004
    ....
  46. ncbi request reprint Analysis of matched mRNA measurements from two different microarray technologies
    Winston Patrick Kuo
    Children s Hospital Informatics Program and Division of Endocrinology, Department of Medicine, Children s Hospital, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Bioinformatics 18:405-12. 2002
    ..Cross-platform utilization of data from different technologies has the potential to reduce the need to duplicate experiments but requires corresponding measurements to be comparable...
  47. ncbi request reprint START: an automated tool for serial analysis of chromatin occupancy data
    Voichita D Marinescu
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
    Bioinformatics 22:999-1001. 2006
    ....
  48. ncbi request reprint Increased measurement accuracy for sequence-verified microarray probes
    Brigham H Mecham
    Division of Pulmonary and Critical Care Medicine, Department of Medicine and Pulmonary Bioinformatics, The Lung Biology Center, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Physiol Genomics 18:308-15. 2004
    ..Our data reveal that the identification and removal of inaccurate probes can significantly improve this technology...
  49. ncbi request reprint Gene regulation and DNA damage in the ageing human brain
    Tao Lu
    Department of Neurology and Division of Neuroscience, The Children s Hospital and Harvard Medical School, Enders 260, 300 Longwood Avenue, Boston, Massachusetts 02115, USA
    Nature 429:883-91. 2004
    ..Thus, DNA damage may reduce the expression of selectively vulnerable genes involved in learning, memory and neuronal survival, initiating a programme of brain ageing that starts early in adult life...
  50. ncbi request reprint Differences in gene expression profiles of diabetic and nondiabetic patients undergoing cardiopulmonary bypass and cardioplegic arrest
    Pierre Voisine
    Division of Cardiothoracic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Mass 02215, USA
    Circulation 110:II280-6. 2004
    ..We sought to compare the cardiac gene expression responses to cardiopulmonary bypass (CPB) and cardioplegic arrest (C) in patients with and without diabetes...
  51. pmc Instrumenting the health care enterprise for discovery research in the genomic era
    Shawn Murphy
    Informatics, Partners HealthCare Systems, Boston, Massachusetts 02115, USA
    Genome Res 19:1675-81. 2009
    ..Even for rare diseases caused by rare, highly penetrant mutations such as Huntington disease (N = 102) and autism (N = 756), these capabilities are also of interest...
  52. pmc Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records
    Fina Kurreeman
    Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
    Am J Hum Genet 88:57-69. 2011
    ....
  53. pmc Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1
    Mary Elizabeth Patti
    Research Division, Joslin Diabetes Center, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 100:8466-71. 2003
    ..Decreased PGC1 expression may be responsible for decreased expression of NRF-dependent genes, leading to the metabolic disturbances characteristic of insulin resistance and DM...
  54. pmc Calculating the return on investment of mobile healthcare
    Nancy E Oriol
    Department of Anesthesia and Critical Care, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
    BMC Med 7:27. 2009
    ..on investment algorithm has been designed to answer is: can the value of the services provided by mobile health programs be quantified in terms of quality adjusted life years saved and estimated emergency department expenditures avoided?..
  55. pmc The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositories
    Griffin M Weber
    Information Technology, Harvard Medical School, 107 Avenue Louis Pasteur, Boston, MA 02115, USA
    J Am Med Inform Assoc 16:624-30. 2009
    ..This will guide us in creating a future technical architecture that is scalable to a national level, compliant with ethical guidelines, and protective of the interests of the participating hospitals...
  56. pmc Chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats
    Asher D Schachter
    Division of Nephrology, Children s Hospital Boston, MA 02115, USA
    Pediatr Nephrol 20:1717-23. 2005
    ..However, TUNEL stains of renal tissue showed no significant difference in the number of apoptotic nuclei. We conclude that chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in rats...
  57. pmc CrossChip: a system supporting comparative analysis of different generations of Affymetrix arrays
    Sek Won Kong
    Bauer Center for Genomics Research, Harvard University, Cambridge, MA, USA
    Bioinformatics 21:2116-7. 2005
    ..Our website supports a within-species comparison for human and mouse GeneChip arrays...
  58. pmc Prediction of chronic obstructive pulmonary disease (COPD) in asthma patients using electronic medical records
    Blanca E Himes
    Channing Laboratory, 181 Longwood Ave, Boston, MA 02115, USA
    J Am Med Inform Assoc 16:371-9. 2009
    ..Identify clinical factors that modulate the risk of progression to COPD among asthma patients using data extracted from electronic medical records...
  59. pmc Parents as partners in obtaining the medication history
    Stephen C Porter
    Division of Emergency Medicine, MA 001, Children s Hospital Boston, 300 Longwood Avenue, Boston, MA 02115, USA
    J Am Med Inform Assoc 12:299-305. 2005
    ..Our specific aims were (1) to estimate the validity of parents' electronically entered medication history for asthma and (2) to compare the parents' kiosk entries regarding medications to the documentation of ED physicians and nurses...
  60. pmc Tissue and process specific microRNA-mRNA co-expression in mammalian development and malignancy
    Hongye Liu
    Informatics Program, Children s Hospital, Boston, MA, USA
    PLoS ONE 4:e5436. 2009
    ..These findings demonstrate the context-dependence of miRNA-mRNA co-expression...
  61. pmc The PING personally controlled electronic medical record system: technical architecture
    William W Simons
    Children s Hospital Informatics Program, Enders 1, 300 Longwood Avenue, Boston, MA 02115, USA
    J Am Med Inform Assoc 12:47-54. 2005
    ....
  62. ncbi request reprint Mechanical stretch is a highly selective regulator of gene expression in human bladder smooth muscle cells
    Rosalyn M Adam
    Urological Diseases Research Center, Department of Urology, Children s Hospital Boston and Harvard Medical School, Boston, Massachusetts 02115, USA
    Physiol Genomics 20:36-44. 2004
    ..Moreover, they suggest that mechanical and growth factor signals converge on common transcriptional regulators that include members of the AP-1 family...
  63. pmc The asthma kiosk: a patient-centered technology for collaborative decision support in the emergency department
    Stephen C Porter
    Department of Medicine, Children s Hospital Boston, Boston, MA 02115, USA
    J Am Med Inform Assoc 11:458-67. 2004
    ..The asthma kiosk successfully links parents' data to guideline recommendations and identifies data critical to health improvements for asthmatic children that otherwise remains undocumented during ED-based care...
  64. pmc Longitudinal histories as predictors of future diagnoses of domestic abuse: modelling study
    Ben Y Reis
    Children s Hospital Informatics Program at the Harvard MIT, Division of Health Sciences and Technology, Children s Hospital Boston, Boston, MA, USA
    BMJ 339:b3677. 2009
    ..To determine whether longitudinal data in patients' historical records, commonly available in electronic health record systems, can be used to predict a patient's future risk of receiving a diagnosis of domestic abuse...
  65. pmc Rapid identification of myocardial infarction risk associated with diabetes medications using electronic medical records
    John S Brownstein
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology, Boston, Massachusetts, USA
    Diabetes Care 33:526-31. 2010
    ..Our use of usual care electronic data sources from a large hospital network represents an innovative approach to rapid safety signal detection that may enable more effective postmarketing drug surveillance...
  66. pmc The contributions of biomedical informatics to the fight against bioterrorism
    Isaac S Kohane
    Children s Hospital and Harvard Medical School, Boston, Massachusetts, 02115, USA
    J Am Med Inform Assoc 9:116-9. 2002
    ..These unique contributions of the discipline of biomedical informatics are reviewed here...
  67. ncbi request reprint Identification of a transcriptional profile associated with in vitro invasion in non-small cell lung cancer cell lines
    Alan S Lader
    Hematology Division, Brigham and Women s Hospital, Boston, Massachusetts 02115, USA
    Cancer Biol Ther 3:624-31. 2004
    ..These and the other genes identified by both analyses represent targets for further study to assess their importance in non-small cell lung cancer invasion and metastasis...
  68. ncbi request reprint A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers
    Scott L Carter
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 38:1043-8. 2006
    ..These results provide a means to assess the potential role of chromosomal instability in determining malignant potential over a broad range of tumors...
  69. pmc Expression profiling reveals altered satellite cell numbers and glycolytic enzyme transcription in nemaline myopathy muscle
    Despina Sanoudou
    Division of Genetics, Children s Hospital, and Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 100:4666-71. 2003
    ..This comprehensive study of downstream molecular consequences of NM gene mutations provides insights in the cellular events leading to the NM phenotype...
  70. ncbi request reprint The value of parental report for diagnosis and management of dehydration in the emergency department
    Stephen C Porter
    Division of Emergency Medicine, Children s Hospital, Boston, MA 02115, USA
    Ann Emerg Med 41:196-205. 2003
    ..We also sought to compare the reports of physical signs related to dehydration made by parents and nurses...
  71. ncbi request reprint Comparing expression profiles of genes with similar promoter regions
    Peter J Park
    Informatics Program and Division of Endocrinology, Children s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
    Bioinformatics 18:1576-84. 2002
    ..We consider the problem in the opposite direction: we seek to find the genes that have similar promoter regions and determine the extent to which these genes have similar expression profiles...
  72. ncbi request reprint Linking gene expression data with patient survival times using partial least squares
    Peter J Park
    Children s Hospital Informatics Program and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115, USA
    Bioinformatics 18:S120-7. 2002
    ..The algorithm is fast, as it does not involve any matrix decompositions in the iterations. We apply our method to data sets from lung carcinoma and diffuse large B-cell lymphoma studies to verify its effectiveness...
  73. pmc Distinctive patterns of microRNA expression in primary muscular disorders
    Iris Eisenberg
    Howard Hughes Medical Institute, Program in Genomics, Division of Genetics, Children s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 104:17016-21. 2007
    ....
  74. pmc Defective ribosomal protein gene expression alters transcription, translation, apoptosis, and oncogenic pathways in Diamond-Blackfan anemia
    Hanna T Gazda
    Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Stem Cells 24:2034-44. 2006
    ..Downregulation of c-myb expression, which causes complete failure of fetal liver erythropoiesis in knockout mice, suggests a link between RPS19 mutations and reduced erythropoiesis in DBA...
  75. pmc The tell-tale heart: population-based surveillance reveals an association of rofecoxib and celecoxib with myocardial infarction
    John S Brownstein
    Children s Hospital Informatics Program at the Harvard MIT Division of Health Sciences and Technology, Boston, Massachusetts, United States of America
    PLoS ONE 2:e840. 2007
    ..COX-2 selective inhibitors are associated with myocardial infarction (MI). We sought to determine whether population health monitoring would have revealed the effect of COX-2 inhibitors on population-level patterns of MI...
  76. pmc An epidemiological network model for disease outbreak detection
    Ben Y Reis
    Children s Hospital Informatics Program, Harvard MIT Division of Health Sciences and Technology, Children s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Med 4:e210. 2007
    ..As a result, public-health crises and major public events threaten to undermine health-surveillance systems at the very times they are needed most...
  77. pmc Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development
    Hongye Liu
    Children s Hospital Informatics Program, Children s Hospital Boston, Boston, Massachusetts, United States of America
    PLoS Med 3:e232. 2006
    ..The histopathologic heterogeneity of lung cancer remains a significant confounding factor in its diagnosis and prognosis-spurring numerous recent efforts to find a molecular classification of the disease that has clinical relevance...
  78. pmc Comorbidity clusters in autism spectrum disorders: an electronic health record time-series analysis
    Finale Doshi-Velez
    Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck St, Boston, MA 02115
    Pediatrics 133:e54-63. 2014
    ..The objective of this study was to investigate the patterns of co-occurrence of medical comorbidities in ASDs...
  79. pmc Similar risk of depression and anxiety following surgery or hospitalization for Crohn's disease and ulcerative colitis
    Ashwin N Ananthakrishnan
    Crohn s and Colitis Center, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
    Am J Gastroenterol 108:594-601. 2013
    ..The objective of this study is to examine whether there is a difference in the risk of psychiatric comorbidity following surgery in CD and UC...
  80. pmc Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolism
    Jong Min Lee
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
    PLoS Genet 3:e135. 2007
    ..Elucidation of this HD CAG-dependent pathway would spur efforts to achieve energy-based therapeutics in HD...
  81. pmc A novel approach to investigate tissue-specific trinucleotide repeat instability
    Jong Min Lee
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
    BMC Syst Biol 4:29. 2010
    ..However progress in this area has been hampered by the lack of sensitive high-throughput instability quantification methods and global approaches to identify the underlying factors...
  82. pmc Absolute enrichment: gene set enrichment analysis for homeostatic systems
    Vishal Saxena
    Department of Surgery, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
    Nucleic Acids Res 34:e151. 2006
    ..This approach lends insights into the feedback mechanisms that may operate, especially when integrated with protein interaction databases...
  83. ncbi request reprint Health-information altruists--a potentially critical resource
    Isaac S Kohane
    Department of Pediatrics, Children s Hospital and Harvard Medical School, Boston, USA
    N Engl J Med 353:2074-7. 2005
  84. pmc Expression profiles of the mouse lung identify a molecular signature of time-to-birth
    Alvin T Kho
    Childrens Hospital Informatics Program, Children s Hospital Boston, Harvard MIT Division of Health Sciences and Technology, Boston, Massachusetts, USA
    Am J Respir Cell Mol Biol 40:47-57. 2009
    ....
  85. pmc A Bayesian dynamic model for influenza surveillance
    Paola Sebastiani
    Department of Biostatistics, Boston University, Boston, MA, USA
    Stat Med 25:1803-16; discussion 1817-25. 2006
    ..Our findings show the importance of modelling the complex dynamics of data collected for influenza surveillance, and suggest that dynamic Bayesian networks could be suitable modelling tools for developing epidemic surveillance systems...
  86. pmc Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscle
    Judith N Haslett
    Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 99:15000-5. 2002
    ....
  87. ncbi request reprint Gene expression profile after cardiopulmonary bypass and cardioplegic arrest
    Marc Ruel
    Division of Cardiothoracic Surgery, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA 02215, USA
    J Thorac Cardiovasc Surg 126:1521-30. 2003
    ..This study examines the cardiac and peripheral gene expression responses to cardiopulmonary bypass and cardioplegic arrest...
  88. ncbi request reprint The influence of muscle type and dystrophin deficiency on murine expression profiles
    Judith N Haslett
    Division of Genetics and Genomics Program, Children s Hospital Boston and Harvard Medical School, Boston, Massachusetts 02115, USA
    Mamm Genome 16:739-48. 2005
    ..Further exploration of the genes that most distinguish these muscles may help explain the origins of the biomechanical differences and the reasons why some muscles are more resistant than others to dystrophin deficiency...
  89. pmc Transcriptomic analysis of human lung development
    Alvin T Kho
    Children s Hospital Informatics Program, Harvard MIT Division of Health Sciences and Technology, Boston, Massachusetts, USA
    Am J Respir Crit Care Med 181:54-63. 2010
    ..Current understanding of the molecular regulation of lung development is limited and derives mostly from animal studies...
  90. pmc Structural, genetic, and functional signatures of disordered neuro-immunological development in autism spectrum disorder
    Vishal Saxena
    Department of Neurology, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
    PLoS ONE 7:e48835. 2012
    ..The underlying pattern may be identified by an integrative approach, especially since ASD is a complex disorder manifested through many loci...
  91. pmc Wireless technology infrastructures for authentication of patients: PKI that rings
    Ulrich Sax
    Children s Hospital Informatics Program, 1 Autumn Street AU543, Boston, MA 02115, USA
    J Am Med Inform Assoc 12:263-8. 2005
    ..The authors propose harnessing this technology for the strong authentication of individuals by creating a registration authority and an authentication service, and examine the problems and promise of such a system...
  92. pmc High throughput single cell bioinformatics
    Kenneth L Roach
    Center for Engineering in Medicine, BioMEMS Resource Center, Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston, MA, USA
    Biotechnol Prog 25:1772-9. 2009
    ..We believe that our microwell array cytometry platform will have general utility for a wide range of questions related to cell population heterogeneity, biological stochasticity, and cell behavior under stress conditions...
  93. doi request reprint Tectonic shifts in the health information economy
    Kenneth D Mandl
    Children s Hospital Informatics Program at the Harvard Massachusetts Institute of Technology Division of Health Sciences and Technology, Children s Hospital Boston, Boston, USA
    N Engl J Med 358:1732-7. 2008
  94. ncbi request reprint Effect of acute aldosterone administration on gene expression profile in the heart
    Alexander Turchin
    Division of Endocrinology, Brigham and Women s Hospital, 221 Longwood Avenue, Boston, Massachusetts 02115, USA
    Endocrinology 147:3183-9. 2006
    ..These results provide the first description of cardiac genetic response to aldosterone and identify several potential mediators of known biochemical sequelae of aldosterone administration in the heart...
  95. pmc Regulation of myogenic progenitor proliferation in human fetal skeletal muscle by BMP4 and its antagonist Gremlin
    Natasha Y Frank
    Division of Genetics, Children s Hospital Boston, Boston, MA 02115, USA
    J Cell Biol 175:99-110. 2006
    ..Together, these studies propose that BMP4 and Gremlin, which are highly expressed by human fetal skeletal muscle SP and MP cells, respectively, are regulators of myogenic progenitor proliferation...
  96. pmc Minimal haplotype tagging
    Paola Sebastiani
    Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
    Proc Natl Acad Sci U S A 100:9900-5. 2003
    ..This result seems to provide further evidence that a severe bottleneck occurred during the founding of Europe and the conjectured "Out of Africa" event...
  97. ncbi request reprint Expression profiling and identification of novel genes involved in myogenic differentiation
    Kinga K Tomczak
    Genetics Division, Children s Hospital, Boston, Massachusetts 02115, USA
    FASEB J 18:403-5. 2004
    ....
  98. ncbi request reprint A submission model for use in the indexing, searching, and retrieval of distributed pathology case and tissue specimens
    Ahmad H Namini
    Laboratory of Computer Science, Massachusetts General Hospital, Boston, MA, USA
    Stud Health Technol Inform 107:1264-7. 2004
    ..With the architecture currently in use by six member institutions, SPIN appears to be a viable, secure methodology to submit pathology information for query and specimen retrieval by investigators..
  99. pmc Human disease classification in the postgenomic era: a complex systems approach to human pathobiology
    Joseph Loscalzo
    Department of Medicine, Brigham and Women s Hospital, Boston, MA 02115, USA
    Mol Syst Biol 3:124. 2007
    ..The purpose of this perspective is to provide a logical basis for a new approach to classifying human disease that uses conventional reductionism and incorporates the non-reductionist approach of systems biomedicine...
  100. ncbi request reprint A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastoma
    Fenghua Liu
    Department of Neurological Surgery, Brigham and Women s Hospital and Harvard Medical School, Boston, MA, USA
    Cancer Res 66:10815-23. 2006
    ..This novel genome-wide approach greatly expanded the list of target genes in glioblastoma and represents a powerful new strategy to identify the upstream determinants of tumor phenotype in a range of human cancers...
  101. pmc Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approach
    Qing Zhao
    Department of Pediatric Oncology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 99:5704-9. 2002
    ..They further show that genome-wide methods are an effective means to identify stage-specific gene expression in the developing granule cell lineage...

Research Grants9

  1. Training Grant in Bioinformatics and Functional Genomics
    Isaac Kohane; Fiscal Year: 2005
    ..The GTP also includes a smaller post-doctoral training track that shares elements with the doctoral track, notably GTP Coupling seminars and a Faculty Advisor system that draws upon GTP Core Faculty. ..
  2. Index and Retrieval of Pathology Specimens
    Isaac Kohane; Fiscal Year: 2005
    ..abstract_text> ..
  3. GPing: Informatics for Personal Control of Genomic Data
    Isaac Kohane; Fiscal Year: 2007
    ..3: Design and evaluate a user interface to communicate disclosure. In concert with appropriate non-discrimination legislation, G-PING lays the groundwork for large-scale genomic cohort studies. ..
  4. GPing: Informatics for Personal Control of Genomic Data
    Isaac Kohane; Fiscal Year: 2009
    ..3: Design and evaluate a user interface to communicate disclosure. In concert with appropriate non-discrimination legislation, G-PING lays the groundwork for large-scale genomic cohort studies. ..
  5. Preventing the Incidentalome
    Isaac Kohane; Fiscal Year: 2009
    ....
  6. Preventing the Incidentalome
    Isaac S Kohane; Fiscal Year: 2010
    ....
  7. GPing: Informatics for Personal Control of Genomic Data
    Isaac S Kohane; Fiscal Year: 2010
    ..3: Design and evaluate a user interface to communicate disclosure. In concert with appropriate non-discrimination legislation, G-PING lays the groundwork for large-scale genomic cohort studies. ..