Information

Related Research Units

Emergency Medicine Research

Publications

  1. From Text to Translation: Using Language Models to Prioritize Variants for Clinical Review. medRxiv. 2024 Dec 31. View Abstract
  2. FUSE: Improving the estimation and imputation of variant impacts in functional screening. Cell Genom. 2024 Oct 09; 4(10):100667. View Abstract
  3. Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nat Genet. 2024 May; 56(5):925-937. View Abstract
  4. Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. medRxiv. 2023 Sep 10. View Abstract
  5. Estimating clinical risk in gene regions from population sequencing cohort data. Am J Hum Genet. 2023 06 01; 110(6):940-949. View Abstract
  6. Systematic elucidation of genetic mechanisms underlying cholesterol uptake. Cell Genom. 2023 May 10; 3(5):100304. View Abstract
  7. DeMAG predicts the effects of variants in clinically actionable genes by integrating structural and evolutionary epistatic features. Nat Commun. 2023 04 19; 14(1):2230. View Abstract
  8. Systematic elucidation of genetic mechanisms underlying cholesterol uptake. bioRxiv. 2023 Jan 10. View Abstract
  9. Estimating clinical risk in gene regions from population sequencing cohort data. medRxiv. 2023 Jan 09. View Abstract
  10. Joint estimation and imputation of variant functional effects using high throughput assay data. medRxiv. 2023 Jan 07. View Abstract
  11. The missing link between genetic association and regulatory function. Elife. 2022 12 14; 11. View Abstract
  12. Informing variant assessment using structured evidence from prior classifications (PS1, PM5, and PVS1 sequence variant interpretation criteria). Genet Med. 2023 01; 25(1):16-26. View Abstract
  13. Variants in STXBP3 are Associated with Very Early Onset Inflammatory Bowel Disease, Bilateral Sensorineural Hearing Loss and Immune Dysregulation. J Crohns Colitis. 2021 Nov 08; 15(11):1908-1919. View Abstract
  14. Machine learning based CRISPR gRNA design for therapeutic exon skipping. PLoS Comput Biol. 2021 Jan; 17(1):e1008605. View Abstract
  15. Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. Nat Genet. 2020 11; 52(11):1145-1150. View Abstract
  16. Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics. bioRxiv. 2020 Aug 28. View Abstract
  17. Polygenic background modifies penetrance of monogenic variants for tier 1 genomic conditions. Nat Commun. 2020 08 20; 11(1):3635. View Abstract
  18. Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning. Cell. 2020 07 23; 182(2):463-480.e30. View Abstract
  19. Association of Rare Pathogenic DNA Variants for Familial Hypercholesterolemia, Hereditary Breast and Ovarian Cancer Syndrome, and Lynch Syndrome With Disease Risk in Adults According to Family History. JAMA Netw Open. 2020 04 01; 3(4):e203959. View Abstract
  20. Mutations in RABL3 alter KRAS prenylation and are associated with hereditary pancreatic cancer. Nat Genet. 2019 09; 51(9):1308-1314. View Abstract
  21. Applicability of the Mutation-Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans. Mol Biol Evol. 2019 08 01; 36(8):1701-1710. View Abstract
  22. novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data. Bioinformatics. 2019 04 01; 35(7):1174-1180. View Abstract
  23. Author Correction: Predictable and precise template-free CRISPR editing of pathogenic variants. Nature. 2019 03; 567(7746):E1-E2. View Abstract
  24. Reply to 'Selective effects of heterozygous protein-truncating variants'. Nat Genet. 2019 01; 51(1):3-4. View Abstract
  25. Predictable and precise template-free CRISPR editing of pathogenic variants. Nature. 2018 11; 563(7733):646-651. View Abstract
  26. An integrated clinical program and crowdsourcing strategy for genomic sequencing and Mendelian disease gene discovery. NPJ Genom Med. 2018; 3:21. View Abstract
  27. A literature review at genome scale: improving clinical variant assessment. Genet Med. 2018 09; 20(9):936-941. View Abstract
  28. When "N of 2" is not enough: integrating statistical and functional data in gene discovery. Cold Spring Harb Mol Case Stud. 2017 05; 3(3):a001099. View Abstract
  29. Estimating the selective effects of heterozygous protein-truncating variants from human exome data. Nat Genet. 2017 May; 49(5):806-810. View Abstract
  30. Loss of function mutation in LOX causes thoracic aortic aneurysm and dissection in humans. Proc Natl Acad Sci U S A. 2016 08 02; 113(31):8759-64. View Abstract
  31. An argument for early genomic sequencing in atypical cases: a WISP3 variant leads to diagnosis of progressive pseudorheumatoid arthropathy of childhood. Rheumatology (Oxford). 2016 Mar; 55(3):586-9. View Abstract
  32. Mitigating false-positive associations in rare disease gene discovery. Hum Mutat. 2015 Oct; 36(10):998-1003. View Abstract
  33. Dominance of Deleterious Alleles Controls the Response to a Population Bottleneck. PLoS Genet. 2015 Aug; 11(8):e1005436. View Abstract
  34. Identification of cis-suppression of human disease mutations by comparative genomics. Nature. 2015 Aug 13; 524(7564):225-9. View Abstract
  35. Inherited CHST11/MIR3922 deletion is associated with a novel recessive syndrome presenting with skeletal malformation and malignant lymphoproliferative disease. Mol Genet Genomic Med. 2015 Sep; 3(5):413-23. View Abstract
  36. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol. 2014 Mar 25; 15(3):R53. View Abstract
  37. Large numbers of genetic variants considered to be pathogenic are common in asymptomatic individuals. Hum Mutat. 2013 Sep; 34(9):1216-20. View Abstract
  38. Twitter as a sentinel in emergency situations: lessons from the Boston marathon explosions. PLoS Curr. 2013 Jul 02; 5. View Abstract
  39. A novel, privacy-preserving cryptographic approach for sharing sequencing data. J Am Med Inform Assoc. 2013 Jan 01; 20(1):69-76. View Abstract
  40. Disclosing pathogenic genetic variants to research participants: quantifying an emerging ethical responsibility. Genome Res. 2012 Mar; 22(3):421-8. View Abstract
  41. Automated validation of genetic variants from large databases: ensuring that variant references refer to the same genomic locations. Bioinformatics. 2011 Mar 15; 27(6):891-3. View Abstract
  42. Privacy-Aware Knowledge Discovery: Novel Applications and New Techniques, Chapman Hall / CRC Press. A Survey of Challenges and Solutions for Privacy in Clinical Genomics Data Mining. 2010. View Abstract
  43. AMIA Annu Symp Proc. 2009. Risk of Re-Identification: Privacy Implications for Rare Mutation. 2009. View Abstract
  44. Advances in Disease Surveillance. Expert Meeting on Privacy, Confidentiality, and Other Legal and Ethical Issues in Syndromic Surveillance. 2009; 7(2). View Abstract
  45. Revealing the spatial distribution of a disease while preserving privacy. Proc Natl Acad Sci U S A. 2008 Nov 18; 105(46):17608-13. View Abstract
  46. The Massachusetts Health and Homeland Alert Network: a scalable and secure public health knowledge management and notification system. AMIA Annu Symp Proc. 2008 Nov 06; 893. View Abstract
  47. Re-identification of home addresses from spatial locations anonymized by Gaussian skew. Int J Health Geogr. 2008 Aug 12; 7:45. View Abstract
  48. My sister's keeper?: genomic research and the identifiability of siblings. BMC Med Genomics. 2008 Jul 25; 1:32. View Abstract
  49. Privacy and identifiability in clinical research, personalized medicine, and public health surveillance. 2008. View Abstract
  50. Multi-factor authentication using contents from disparate EHRs. AMIA Annu Symp Proc. 2007 Oct 11; 891. View Abstract
  51. An unsupervised classification method for inferring original case locations from low-resolution disease maps. Int J Health Geogr. 2006 Dec 08; 5:56. View Abstract
  52. No place to hide--reverse identification of patients from published maps. N Engl J Med. 2006 Oct 19; 355(16):1741-2. View Abstract
  53. Proc Symp 2006 Syndromic Surveillance Conf, Baltimore, MD. Evaluating the Performance of a Spatial Scan Statistic Using Simulated Outbreak Characteristics. 2006. View Abstract
  54. A context-sensitive approach to anonymizing spatial surveillance data: impact on outbreak detection. J Am Med Inform Assoc. 2006 Mar-Apr; 13(2):160-5. View Abstract
  55. A software tool for creating simulated outbreaks to benchmark surveillance systems. BMC Med Inform Decis Mak. 2005 Jul 14; 5:22. View Abstract
  56. Reverse geocoding: concerns about patient confidentiality in the display of geospatial health data. AMIA Annu Symp Proc. 2005; 905. View Abstract
  57. International Society of Disease Surveillance Annu Symp Proc. Boston, MA. Geographic Coordinate Transformation Methods to Reduce Privacy Risks Associated with Surveillance. 2004. View Abstract
  58. Measuring outbreak-detection performance by using controlled feature set simulations. MMWR Suppl. 2004 Sep 24; 53:130-6. View Abstract
  59. Spatial outbreak detection analysis tool : a system to create sets of semi-synthetic geo-spatial clusters. 2004. View Abstract

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