Johannes Birgmeier

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Karthik A. JagadeeshPostdoctoral Associate, Broad InstituteVerified email at cs.stanford.edu
Harendra GuturuPh.D., Stanford UniversityVerified email at stanford.edu
Dan BonehProfessor of Computer Science, Stanford UniversityVerified email at cs.stanford.edu
David N. CooperProfessor of Human Molecular Genetics, Cardiff University, UKVerified email at cardiff.ac.uk
Maximilian HaeusslerUC Santa Cruz Genomics Institute, UCSC Genome BrowserVerified email at soe.ucsc.edu
Alan H. Beggs, PhDProfessor of Pediatrics, Harvard Medical School, Director The Manton CenterVerified email at enders.tch.harvard.edu
David WuUniversity of Texas at AustinVerified email at cs.utexas.edu
Alex RatnerAssistant Professor, University of WashingtonVerified email at cs.washington.edu
Christopher RéComputer Science, Stanford UniversityVerified email at cs.stanford.edu
Catherine BrownsteinAssistant Professor at Harvard Medical School, Project Manager at Boston Children's HospitalVerified email at childrens.harvard.edu
Julian A Martinez-AgostoAssociate Professor, University of CaliforniaVerified email at mednet.ucla.edu
Aaron BradleyVerified email at cs.stanford.edu
Georg WeissenbacherProfessor of Computer Science, TU WienVerified email at tuwien.ac.at
Matthew T WheelerAssistant Professor, Stanford UniversityVerified email at stanford.edu
James H. NotwellMapLight TherapeuticsVerified email at maplightrx.com
Susan K. McConnellDepartment of Biology, Stanford UniversityVerified email at stanford.edu
Whitney HeavnerNational Institutes of HealthVerified email at nih.gov
Ethan DyerGoogle Research, Blueshift TeamVerified email at google.com
Andrew TiernoStudent, Stanford UniversityVerified email at stanford.edu
Mark DiekhansUniversity of California, Santa Cruz; UC Santa Cruz Genomics InstituteVerified email at soe.ucsc.edu

Johannes Birgmeier

Department of Computer Science, Stanford University

Verified email at cs.stanford.edu - Homepage

machine learning natural language processing computational genomics Mendelian diseases


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Deriving genomic diagnoses without revealing patient genomes KA Jagadeesh, DJ Wu, JA Birgmeier, D Boneh, G Bejerano Science 357 (6352), 692-695, 2017	135	2017
Emergent high fatality lung disease in systemic juvenile arthritis VE Saper, G Chen, GH Deutsch, RP Guillerman, J Birgmeier, ... Annals of the Rheumatic Diseases 78 (12), 1722-1731, 2019	110	2019
Counterexample to induction-guided abstraction-refinement (CTIGAR) J Birgmeier, AR Bradley, G Weissenbacher International Conference on Computer Aided Verification, 831-848, 2014	68	2014
ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis CA Deisseroth, J Birgmeier, EE Bodle, JN Kohler, DR Matalon, ... Genetics in Medicine, 1, 2018	58	2018
AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature J Birgmeier, M Haeussler, CA Deisseroth, EH Steinberg, KA Jagadeesh, ... Science translational medicine 12 (544), eaau9113, 2020	37	2020
Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization KA Jagadeesh, J Birgmeier, H Guturu, CA Deisseroth, AM Wenger, ... Genetics in Medicine 21 (2), 464-470, 2019	35	2019
CRISPR/Cas9 Genome Engineering in Engraftable Human Brain-Derived Neural Stem Cells DP Dever, SG Scharenberg, J Camarena, EJ Kildebeck, JT Clark, ... iScience 15, 524-535, 2019	23	2019
AMELIE accelerates Mendelian patient diagnosis directly from the primary literature J Birgmeier, M Haeussler, CA Deisseroth, KA Jagadeesh, AJ Ratner, ... bioRxiv, 171322, 2017	21	2017
Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes WE Heavner, S Ji, JH Notwell, ES Dyer, AM Tseng, J Birgmeier, B Yoo, ... Proceedings of the National Academy of Sciences 117 (40), 25074-25084, 2020	17	2020
AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature J Birgmeier, CA Deisseroth, LE Hayward, LMT Galhardo, AP Tierno, ... Genetics in Medicine, 1-9, 2019	16	2019
Biallelic loss‐of‐function WNT5A mutations in an infant with severe and atypical manifestations of Robinow syndrome J Birgmeier, ED Esplin, KA Jagadeesh, H Guturu, AM Wenger, H Chaib, ... American Journal of Medical Genetics Part A 176 (4), 1030-1036, 2018	15	2018
Childhood Arthritis and Rheumatology Research Alliance Registry Investigators. Emergent high fatality lung disease in systemic juvenile arthritis VE Saper, G Chen, GH Deutsch, RP Guillerman, J Birgmeier, ... Ann Rheum Dis 78 (12), 1722-1731, 2019	14	2019
An MTF1 binding site disrupted by a homozygous variant in the promoter of ATP7B likely causes Wilson Disease HI Chen, KA Jagadeesh, J Birgmeier, AM Wenger, H Guturu, S Schelley, ... European Journal of Human Genetics, 1, 2018	13	2018
AMELIE 3: Fully Automated Mendelian Patient Reanalysis at Under 1 Alert per Patient per Year J Birgmeier, E Steinberg, EE Bodle, CA Deisseroth, KA Jagadeesh, ... medRxiv, 2020.12. 29.20248974, 2021	3	2021
InpherNet accelerates monogenic disease diagnosis using patients’ candidate genes’ neighbors B Yoo, J Birgmeier, JA Bernstein, G Bejerano Genetics in Medicine 23 (10), 1984-1992, 2021	1	2021
P127 Lung disease in systemic JIA: an emerging problem linked with young age and anti-IL-1/IL-6 G Chen, V Saper, G Deutsch, RP Guillerman, K Jagadeesh, G Schulert, ... Annals of the Rheumatic Diseases 78 (Suppl 1), A57-A57, 2019	1	2019
Keeping patient phenotypes and genotypes private while seeking disease diagnoses KA Jagadeesh, DJ Wu, JA Birgmeier, D Boneh, G Bejerano bioRxiv, 746230, 2019	1	2019
Using Spectral Clustering to Sample Molecular States and Pathways SH Ahn, J Birgmeier	1	2015
Machine Learning-based Acceleration of Monogenic Disease Diagnosis J Birgmeier Stanford University, 2019		2019
Differential chromatin accessibility in developing projection neurons is correlated with transcriptional regulation of cell fate WE Heavner, S Ji, JH Notwell, ES Dyer, AM Tseng, J Birgmeier, B Yoo, ... bioRxiv, 645572, 2019		2019

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