Research Topics
| Isaac KohaneSummaryAffiliation: Harvard University Country: USA Publications
Research Grants
| Collaborators
|
Detail Information
Publications
The co-morbidity burden of children and young adults with autism spectrum disordersIsaac 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...
Taxonomizing, sizing, and overcoming the incidentalomeIsaac S Kohane
Children s Hospital Informatics Program, Children s Hospital, Boston, Massachusetts, USA
Genet Med 14:399-404. 2012..A new generation of population studies and retooling of the clinical decision-support approach will be required to overcome this threat...- (Mis)treating the pharmacogenetic incidentalomeIsaac 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... - An unsupervised classification method for inferring original case locations from low-resolution disease mapsJohn 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... - 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... - Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasiaJennifer 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... - Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancersKamila 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.... - Transcriptome-scale similarities between mouse and human skeletal muscles with normal and myopathic phenotypesAlvin 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... - Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphismsDominic J Allocco
Children s Hospital Informatics Program at Harvard MIT Division of Health Sciences and Technology, Boston, MA, USA
BMC Genomics 8:68. 2007.... - Inter-species differences of co-expression of neighboring genes in eukaryotic genomesYutaka 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... - 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... - Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networksCecily 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... - Reproducibility of gene expression across generations of Affymetrix microarraysAshish 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... - Quantifying the relationship between co-expression, co-regulation and gene functionDominic J Allocco
Informatics Program, Children s Hospital, Boston, MA, USA
BMC Bioinformatics 5:18. 2004.... - A SNP-centric database for the investigation of the human genomeAlberto 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... - Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurementsScott 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... - MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomesVoichita 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... 
Medicine. Reestablishing the researcher-patient compactIsaac S Kohane
Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
Science 316:836-7. 2007- Using electronic health records to drive discovery in disease genomicsIsaac S Kohane
Harvard Medical School, 10 Shattuck Street, Boston, Massachusetts 02115, USA
Nat Rev Genet 12:417-28. 2011.... - The incidentalome: a threat to genomic medicineIsaac S Kohane
Center of Biomedical Informatics and Division of Health Sciences Technology, Harvard Medical School, Boston, Mass 02115, USA
JAMA 296:212-5. 2006 - Strategies for maintaining patient privacy in i2b2Shawn 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... - Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurementsBrigham 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... - PGAGENE: integrating quantitative gene-specific results from the NHLBI programs for genomic applicationsKyungjoon 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... - Bayesian approach to discovering pathogenic SNPs in conserved protein domainsZhaohui 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... - Electronic medical records for discovery research in rheumatoid arthritisKatherine 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... - Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controlsKatherine P Liao
Brigham and Women s Hospital, Boston, Massachusetts
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... - 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... - A set of genes previously implicated in the hypoxia response might be an important modulator in the rat ear tissue response to mechanical stretchVishal 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... - Analysis of matched mRNA measurements from two different microarray technologiesWinston 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... - Induction of the plasminogen activator system by mechanical stimulation of human bronchial epithelial cellsEric 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... - START: an automated tool for serial analysis of chromatin occupancy dataVoichita 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..Availability: The program is available at http://bio.chip.org/start/. Supplementary information: Supplementary information is available at http://bio.chip.org/doc/start/START-supplementary.pdf.. - Cluster analysis of gene expression dynamicsMarco 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... - The MAPPER database: a multi-genome catalog of putative transcription factor binding sitesVoichita 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... - A self-scaling, distributed information architecture for public health, research, and clinical careAndrew 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... - Conserved mechanisms across development and tumorigenesis revealed by a mouse development perspective of human cancersAlvin T Kho
Children's Hospital Informatics Program, Children's Hospital Boston, MA 02115, USA
Genes Dev 18:629-40. 2004.... - Instrumenting the health care enterprise for discovery research in the genomic eraShawn 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... - Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health recordsFina 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.... - Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomesSooHyun 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... - Coordinated reduction of genes of oxidative metabolism in humans with insulin resistance and diabetes: Potential role of PGC1 and NRF1Mary 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... - Calculating the return on investment of mobile healthcareNancy 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?.. - Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of developmentHongye 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... - Longitudinal histories as predictors of future diagnoses of domestic abuse: modelling studyBen 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... - Rapid identification of myocardial infarction risk associated with diabetes medications using electronic medical recordsJohn 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... - Defective ribosomal protein gene expression alters transcription, translation, apoptosis, and oncogenic pathways in Diamond-Blackfan anemiaHanna 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... - The tell-tale heart: population-based surveillance reveals an association of rofecoxib and celecoxib with myocardial infarctionJohn 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... - A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancersScott 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... - The Shared Health Research Information Network (SHRINE): a prototype federated query tool for clinical data repositoriesGriffin 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... - Tissue and process specific microRNA-mRNA co-expression in mammalian development and malignancyHongye 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... - Prediction of chronic obstructive pulmonary disease (COPD) in asthma patients using electronic medical recordsBlanca 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... - Distinctive patterns of microRNA expression in primary muscular disordersIris 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.... - An epidemiological network model for disease outbreak detectionBen 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... - The contributions of biomedical informatics to the fight against bioterrorismIsaac 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... - CrossChip: a system supporting comparative analysis of different generations of Affymetrix arraysSek 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. AVAILABILITY: http://www.crosschip.org.. - Parents as partners in obtaining the medication historyStephen 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... - The PING personally controlled electronic medical record system: technical architectureWilliam 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.... - Mechanical stretch is a highly selective regulator of gene expression in human bladder smooth muscle cellsRosalyn 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... - Chromosomes 18 and X are quantitative trait loci for nephrotic-range proteinuria in ratsAsher 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... - Expression profiling reveals altered satellite cell numbers and glycolytic enzyme transcription in nemaline myopathy muscleDespina 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... - The value of parental report for diagnosis and management of dehydration in the emergency departmentStephen 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... - Linking gene expression data with patient survival times using partial least squaresPeter 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... - The asthma kiosk: a patient-centered technology for collaborative decision support in the emergency departmentStephen 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... - Identification of a transcriptional profile associated with in vitro invasion in non-small cell lung cancer cell linesAlan 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... - Comparing expression profiles of genes with similar promoter regionsPeter J Park
Informatics Program and Division of Endocrinology, Children s Hospital, 300 Longwood Avenue, Boston, MA 02115, USA
Bioinformatics 18:1576-84. 2002..Overall, we find that considering the relationship between the promoter regions and the expression profiles starting with the regulatory elements is a difficult but useful process that can provide valuable insights... - Apps to display patient data, making SMART available in the i2b2 platformNich Wattanasin
Partners HealthCare System, Boston, MA
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... - A novel approach to investigate tissue-specific trinucleotide repeat instabilityJong 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... - Unbiased gene expression analysis implicates the huntingtin polyglutamine tract in extra-mitochondrial energy metabolismJong 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... - Differences in gene expression profiles of diabetic and nondiabetic patients undergoing cardiopulmonary bypass and cardioplegic arrestPierre Voisine
Division of Cardiothoracic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Mass 02215, USA
Circulation 110:II280-6. 2004..These results have important implications for the design of tailored myocardial protection and operative strategies for diabetic patients undergoing CPB/C... - Gene regulation and DNA damage in the ageing human brainTao 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... - Absolute enrichment: gene set enrichment analysis for homeostatic systemsVishal 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... - Expression profiles of the mouse lung identify a molecular signature of time-to-birthAlvin 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.... - Gene expression profile after cardiopulmonary bypass and cardioplegic arrestMarc 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.... - Transcriptomic analysis of human lung developmentAlvin 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... - Comprehensive dissection of PDGF-PDGFR signaling pathways in PDGFR genetically defined cellsErxi 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... - A Bayesian dynamic model for influenza surveillancePaola 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... - Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscleJudith N Haslett
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
Proc Natl Acad Sci U S A 99:15000-5. 2002.... - Health-information altruists--a potentially critical resourceIsaac S Kohane
Department of Pediatrics, Children's Hospital and Harvard Medical School, Boston, USA
N Engl J Med 353:2074-7. 2005 - The influence of muscle type and dystrophin deficiency on murine expression profilesJudith 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... - Wireless technology infrastructures for authentication of patients: PKI that ringsUlrich 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... - Expression profiling and identification of novel genes involved in myogenic differentiationKinga K Tomczak
Genetics Division, Children's Hospital, Boston, Massachusetts 02115, USA
FASEB J 18:403-5. 2004.... - Minimal haplotype taggingPaola 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... - Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistancePeter 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..Top candidates obtained from our analysis have been confirmed in recent laboratory studies... - Regulation of myogenic progenitor proliferation in human fetal skeletal muscle by BMP4 and its antagonist GremlinNatasha 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... - High throughput single cell bioinformaticsKenneth 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... - Effect of acute aldosterone administration on gene expression profile in the heartAlexander 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... - Tectonic shifts in the health information economyKenneth 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 - A submission model for use in the indexing, searching, and retrieval of distributed pathology case and tissue specimensAhmad H Namini
Laboratory of Computer Science, Massachusetts General Hospital, Boston, MA, USA
Medinfo 11:1264-7. 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.. - Structural, genetic, and functional signatures of disordered neuro-immunological development in autism spectrum disorderVishal 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... - A genome-wide screen reveals functional gene clusters in the cancer genome and identifies EphA2 as a mitogen in glioblastomaFenghua 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... - Human disease classification in the postgenomic era: a complex systems approach to human pathobiologyJoseph 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... - Increased measurement accuracy for sequence-verified microarray probesBrigham 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... - Identification of genes expressed with temporal-spatial restriction to developing cerebellar neuron precursors by a functional genomic approachQing 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... - Visualization and evaluation of clusters for exploratory analysis of gene expression dataJu Han Kim
SNUBI Seoul National University Biomedical Informatics, Seoul National University School of Medicine, 28 Yongon dong Chongno gu, Seoul 110 799, Republic of Korea
J Biomed Inform 35:25-36. 2002.... - Molecular classification of nemaline myopathies: "nontyping" specimens exhibit unique patterns of gene expressionDespina Sanoudou
Genomics Program and Divisison of Genetics, Children's Hospital Boston, and Harvard Medical School, MA 20115, USA
Neurobiol Dis 15:590-600. 2004..Determination of the specific molecular differences in NM subgroups may eventually lead to improved prognostic determinations and treatment of these patients... - Creation and implications of a phenome-genome networkAtul J Butte
Stanford Medical Informatics, Department of Medicine, Stanford University School of Medicine, 251 Campus Drive, Room X 215, Stanford, California 94305 5479, USA
Nat Biotechnol 24:55-62. 2006..We identify novel genes related to concepts such as aging. Comprehensively identifying genes related to phenotype and environment is a step toward the Human Phenome Project... - Comprehensive genomic characterization defines human glioblastoma genes and core pathwaysRoger McLendon
Nature 455:1061-8. 2008..Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer... - Discovering statistically significant pathways in expression profiling studiesLu Tian
Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, 680 North Lake Shore Drive, Chicago, IL 60611, USA
Proc Natl Acad Sci U S A 102:13544-9. 2005..These predictions have been subsequently corroborated by immunohistochemistry... - Gene expression profiling of Duchenne muscular dystrophy skeletal muscleJudith N Haslett
Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
Neurogenetics 4:163-71. 2003..It also highlights a large number of unknown genes whose expression is altered and whose identity therefore becomes important in understanding the pathogenesis of muscular dystrophy... - Evidence of spatially bound gene regulation in Mus musculus: decreased gene expression proximal to microRNA genomic locationHidenori Inaoka
School of Biomedical Science and Institute of Biomaterials and Biomedical Engineering, Tokyo Medical and Dental University, Chiyoda ku, Tokyo 101 0062, Japan
Proc Natl Acad Sci U S A 104:5020-5. 2007..This localization broadens with the shift from developing to mature/differentiated tissues and suggests a developmentally controlled and spatially bound regulation... - GenePING: secure, scalable management of personal genomic dataBen Adida
CSAIL, MIT, Cambridge, MA, USA
BMC Genomics 7:93. 2006..The management of such sizeable, yet fine-grained, data in compliance with privacy laws and best practices presents significant security and scalability challenges... - Gene homology resources on the World Wide WebAlexander Turchin
Department of Medicine, New England Medical Center, Boston 02111, USA
Physiol Genomics 11:165-77. 2002..In this paper, we aim to present a systematic review of the inner details of the most commonly used databases as well as to offer guidelines for their use... - Lower expression of genes near microRNA in C. elegans germlineHidenori Inaoka
Department of Biosystem Modeling, School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
BMC Bioinformatics 7:112. 2006..Because there is mounting evidence for the localized component of transcriptional control, we investigated if there is a distance-dependent effect of miRNA...
Research Grants
- Training Grant in Bioinformatics and Functional GenomicsIsaac 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. ..
- Index and Retrieval of Pathology SpecimensIsaac Kohane; Fiscal Year: 2005..abstract_text> ..
- GPing: Informatics for Personal Control of Genomic DataIsaac 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. ..
- GPing: Informatics for Personal Control of Genomic DataIsaac 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. ..
- Preventing the IncidentalomeIsaac S Kohane; Fiscal Year: 2010....
- GPing: Informatics for Personal Control of Genomic DataIsaac 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. ..