Nadav Brandes, PhD

Title(s)Postdoctoral Scholar, Medicine
SchoolSchool of Medicine
Address513 Parnassus Avenue, HSE, #901B
San Francisco CA 94143
Phone415-476-6933
ORCID ORCID Icon0000-0002-0510-2546 Additional info
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    The Hebrew University, Jerusalem, IsraelPhD2021Computational Biology
    The Hebrew University, Jerusalem, IsraelMSc2016Mathematics and Bioinformatics
    Bar-Ilan University, Ramat Gan, IsraelBSc2014Mathematics

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    I am a postdoctoral scholar at Jimmie Ye’s lab in UCSF. I’m a CRI and EMBO postdoctoral fellow. I did my PhD in computer science and bioinformatics at The Hebrew University of Jerusalem under the supervision of Professors Michal Linial (Life Sciences) and Nathan Linial (Computer Science and Engineering). In the Ye lab I develop deep learning models and single-cell methods to determine the consequences of genetic variants. My PhD research focused on statistical genetics and proteins. Among other works, I developed algorithms for gene-phenotype mapping and discovery of cancer genes in human.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. ADPKD-Causing Missense Variants in Polycystin-1 Disrupt Cell Surface Localization or Polycystin Channel Function. bioRxiv. 2023 Dec 07. Ha K, Loeb GB, Park M, Pinedo A, Park CH, Brandes N, Ritu F, Ye CJ, Reiter JF, Delling M. PMID: 38106161; PMCID: PMC10723288.
      View in: PubMed   Mentions:
    2. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. Cell. 2023 10 12; 186(21):4567-4582.e20. Tsuchida CA, Brandes N, Bueno R, Trinidad M, Mazumder T, Yu B, Hwang B, Chang C, Liu J, Sun Y, Hopkins CR, Parker KR, Qi Y, Hofman L, Satpathy AT, Stadtmauer EA, Cate JHD, Eyquem J, Fraietta JA, June CH, Chang HY, Ye CJ, Doudna JA. PMID: 37794590; PMCID: PMC10664023.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    3. The genetic underpinnings of variable penetrance and expressivity of pathogenic mutations in cardiometabolic traits. medRxiv. 2023 Sep 18. Wei A, Border R, Fu B, Cullina S, Brandes N, Sankararaman S, Kenny EE, Udler MS, Ntranos V, Zaitlen N, Arboleda VA. PMID: 37745486; PMCID: PMC10516069.
      View in: PubMed   Mentions:
    4. Genome-wide prediction of disease variant effects with a deep protein language model. Nat Genet. 2023 09; 55(9):1512-1522. Brandes N, Goldman G, Wang CH, Ye CJ, Ntranos V. PMID: 37563329; PMCID: PMC10484790.
      View in: PubMed   Mentions: 28     Fields:    Translation:Humans
    5. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. bioRxiv. 2023 Mar 22. Tsuchida CA, Brandes N, Bueno R, Trinidad M, Mazumder T, Yu B, Hwang B, Chang C, Liu J, Sun Y, Hopkins CR, Parker KR, Qi Y, Satpathy AT, Stadtmauer EA, Cate JHD, Eyquem J, Fraietta JA, June CH, Chang HY, Ye CJ, Doudna JA. PMID: 36993359; PMCID: PMC10055432.
      View in: PubMed   Mentions:
    6. Open problems in human trait genetics. Genome Biol. 2022 06 20; 23(1):131. Brandes N, Weissbrod O, Linial M. PMID: 35725481; PMCID: PMC9208223.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    7. ProteinBERT: a universal deep-learning model of protein sequence and function. Bioinformatics. 2022 04 12; 38(8):2102-2110. Brandes N, Ofer D, Peleg Y, Rappoport N, Linial M. PMID: 35020807; PMCID: PMC9386727.
      View in: PubMed   Mentions: 79     Fields:    Translation:Cells
    8. Evolutionary and functional lessons from human-specific amino acid substitution matrices. NAR Genom Bioinform. 2021 Sep; 3(3):lqab079. Shauli T, Brandes N, Linial M. PMID: 34541526; PMCID: PMC8445205.
      View in: PubMed   Mentions: 1  
    9. Genetic association studies of alterations in protein function expose recessive effects on cancer predisposition. Sci Rep. 2021 07 21; 11(1):14901. Brandes N, Linial N, Linial M. PMID: 34290314; PMCID: PMC8295298.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    10. Body Mass Index and Birth Weight Improve Polygenic Risk Score for Type 2 Diabetes. J Pers Med. 2021 Jun 21; 11(6). Moldovan A, Waldman YY, Brandes N, Linial M. PMID: 34205563; PMCID: PMC8233887.
      View in: PubMed   Mentions: 7  
    11. The language of proteins: NLP, machine learning & protein sequences. Comput Struct Biotechnol J. 2021; 19:1750-1758. Ofer D, Brandes N, Linial M. PMID: 33897979; PMCID: PMC8050421.
      View in: PubMed   Mentions: 60  
    12. The FABRIC Cancer Portal: A Ranked Catalogue of Gene Selection in Tumors Over the Human Coding Genome. Cancer Res. 2021 02 15; 81(4):1178-1185. Kelman G, Brandes N, Linial M. PMID: 33277365.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    13. PWAS: proteome-wide association study-linking genes and phenotypes by functional variation in proteins. Genome Biol. 2020 07 14; 21(1):173. Brandes N, Linial N, Linial M. PMID: 32665031; PMCID: PMC7386203.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    14. Substantial batch effects in TCGA exome sequences undermine pan-cancer analysis of germline variants. BMC Cancer. 2019 Aug 07; 19(1):783. Rasnic R, Brandes N, Zuk O, Linial M. PMID: 31391007; PMCID: PMC6686424.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    15. Quantifying gene selection in cancer through protein functional alteration bias. Nucleic Acids Res. 2019 07 26; 47(13):6642-6655. Brandes N, Linial N, Linial M. PMID: 31334812; PMCID: PMC6649814.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    16. Giant Viruses-Big Surprises. Viruses. 2019 04 30; 11(5). Brandes N, Linial M. PMID: 31052218; PMCID: PMC6563228.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    17. ASAP: a machine learning framework for local protein properties. Database (Oxford). 2016; 2016. Brandes N, Ofer D, Linial M. PMID: 27694209; PMCID: PMC5045867.
      View in: PubMed   Mentions: 8     Fields:    
    18. Gene overlapping and size constraints in the viral world. Biol Direct. 2016 05 21; 11:26. Brandes N, Linial M. PMID: 27209091; PMCID: PMC4875738.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
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