Nadav Brandes, PhD
Postdoctoral Scholar
Medicine
School of Medicine

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).

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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.

Education & Training

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• PhD Computational Biology The Hebrew University 2021
• MSc Mathematics and Bioinformatics The Hebrew University 2016
• BSc Mathematics Bar-Ilan University 2014

Interests

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• protein function
• statistical genetics
• deep learning
• single-cell genomics

Websites

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• GitHub (github.com)
• LinkedIn (linkedin.com)
• Google Scholar profile (scholar.google.co.il)
• ResearchGate profile (researchgate.net)
• CRI fellowship (cancerresearch.org)
• Personal website at The Hebrew University (cs.huji.ac.il)
• Personal blog (incrementally.net)
• My online course: Quantitative Biological Research with Python (muddle2.cs.huji.ac.il)

Videos

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• PWAS: Proteome-Wide Association Study | RECOMB 2020 (youtube.com)
• Quantifying gene selection in cancer through protein alteration bias | ISMB 2020 (youtube.com)

Publications (18)

Top publication keywords:
Multifactorial InheritanceMolecular Sequence AnnotationGenes, NeoplasmSequence Analysis, ProteinGenes, OverlappingNeoplasm ProteinsComputational BiologyGenome-Wide Association StudyGenome, ViralCapsidProteomeGiant VirusesSoftwareGenome SizeGenes, Recessive

• ADPKD-Causing Missense Variants in Polycystin-1 Disrupt Cell Surface Localization or Polycystin Channel Function.
  bioRxiv : the preprint server for biology 2023 Ha K, Loeb GB, Park M, Pinedo A, Park CH, Brandes N, Ritu F, Ye CJ, Reiter JF, Delling M
• Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells.
  Cell 2023 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 …
• The genetic underpinnings of variable penetrance and expressivity of pathogenic mutations in cardiometabolic traits.
  medRxiv : the preprint server for health sciences 2023 Wei A, Border R, Fu B, Cullina S, Brandes N, Sankararaman S, Kenny EE, Udler MS, Ntranos V, Zaitlen N, Arboleda VA
• Genome-wide prediction of disease variant effects with a deep protein language model.
  Nature genetics 2023 Brandes N, Goldman G, Wang CH, Ye CJ, Ntranos V
• Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells.
  bioRxiv : the preprint server for biology 2023 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 …

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• Open problems in human trait genetics.
  Genome biology 2022 Brandes N, Weissbrod O, Linial M
• ProteinBERT: a universal deep-learning model of protein sequence and function.
  Bioinformatics (Oxford, England) 2022 Brandes N, Ofer D, Peleg Y, Rappoport N, Linial M
• Evolutionary and functional lessons from human-specific amino acid substitution matrices.
  NAR genomics and bioinformatics 2021 Shauli T, Brandes N, Linial M
• Genetic association studies of alterations in protein function expose recessive effects on cancer predisposition.
  Scientific reports 2021 Brandes N, Linial N, Linial M
• Body Mass Index and Birth Weight Improve Polygenic Risk Score for Type 2 Diabetes.
  Journal of personalized medicine 2021 Moldovan A, Waldman YY, Brandes N, Linial M
• The language of proteins: NLP, machine learning & protein sequences.
  Computational and structural biotechnology journal 2021 Ofer D, Brandes N, Linial M
• The FABRIC Cancer Portal: A Ranked Catalogue of Gene Selection in Tumors Over the Human Coding Genome.
  Cancer research 2020 Kelman G, Brandes N, Linial M
• PWAS: proteome-wide association study-linking genes and phenotypes by functional variation in proteins.
  Genome biology 2020 Brandes N, Linial N, Linial M
• Substantial batch effects in TCGA exome sequences undermine pan-cancer analysis of germline variants.
  BMC cancer 2019 Rasnic R, Brandes N, Zuk O, Linial M
• Quantifying gene selection in cancer through protein functional alteration bias.
  Nucleic acids research 2019 Brandes N, Linial N, Linial M
• Giant Viruses-Big Surprises.
  Viruses 2019 Brandes N, Linial M
• ASAP: a machine learning framework for local protein properties.
  Database : the journal of biological databases and curation 2016 Brandes N, Ofer D, Linial M
• Gene overlapping and size constraints in the viral world.
  Biology direct 2016 Brandes N, Linial M