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Resume  (PDF version)

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Experiences

  • Aug 2022 until now: Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland

    • Lecturer​

    • Participating lectures

      • Systems Genomics

      • Single Cell Technologoes

  • Aug 2021 until now: Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland

    • Established researcher

    • Responsibilities

      • Research projects​

      • Teaching and supervisions

      • Management and maintenance of computational infrastructures

    • Group leader: Prof. Dr. Barbara Treutlein

  • Jan 2019 - Jul 2021: Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland

    • Postdoc​

    • Group leader: Prof. Dr. Barbara Treutlein

  • Jan 2018 - Dec 2018: MPI for Evolutionary Anthropology, Leipzig, Germany

    • Postdoc

    • Group leader: Prof. Dr. Barbara Treutlein

  • Aug 2017 - Dec 2017: Skolkovo Institute of Science and Technology, Moscow, Russia

    • Research scientist

    • Group leader: Prof. Dr. Philipp Khaitovich

  • Mar 2015 - Jan 2018: CAS-MPG Partner Institute for Computational Biology, Shanghai, China

    • Postdoc

    • Group leader: Prof. Dr. Philipp Khaitovich

  • Sep 2015 - Dec 2015: MPI for Evolutionary Anthropology, Leipzig, Germany

    • Visiting scientist

    • Group leader: Dr. Janet Kelso

  • Jul 2008 - Aug 2008: CAS-MPG Partner Institute for Computational Biology, Shanghai, China

    • Research intern

    • Group leader: Prof. Dr. Yudong Cai

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Educations

  • Sep 2009 - Jan 2015: CAS-MPG Partner Institute for Computational Biology, Shanghai, China

    • Degree: PhD

    • Major: Computational Biology

    • Thesis title: Spatial and Temporal Transcriptome Architecture of Primate Brains

    • Thesis supervisor: Prof. Dr. Philipp Khaitovich

  • Sep 2005 - Jul 2009: College of Life Sciences, Zhejiang University, Hangzhou, China

    • Degree: BSc

    • Major: Bioinformatics

    • Thesis title: A Novel SVM-based Method for MicroRNA Target Prediction

    • Thesis supervisor: Prof. Dr. Ming Chen

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Publications

  • 2024

  • 2023​

  • 2022

    • Fleck JS*, Jansen SMJ*, et al., He Z#, Camp JG#, Treutlein B#. Inferring and perturbing cell fate regulomes in human brain organoids. Nature. 2022; https://doi.org/10.1038/s41586-022-05279-8.

    • Wollny D, Vernot B, et al. Characterization of RNA content in individual phase-separated coacervate microdroplets. Nature Communications. 2022; 13:2626.

    • Nikolova MT*, He Z*, et al. Fate and state transitions during human blood vessel organoid development. bioRxiv. 2022; https://www.biorxiv.org/content/10.1101/2022.03.23.485329v1.

  • 2021

    • He Z*, Maynard A*, Jain A*, Gerber T*, et al. Lineage recording in human cerebral organoids. Nature Methods. 2021; https://doi.org/10.1038/s41592-021-01344-8.

    • Kyrousi C, O'Neil AC, et al. Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity. Nature Communications. 2021; 12:6298.

    • Lin HC*, He Z*, Ebert S*, et al. NGN2 induces diverse neuron types from human pluripotency. Stem Cell Reports. 2021; https://doi.org/10.1016/j.stemcr.2021.07.006.

    • Yu Q*, Kilik U*, Holloway EM*, et al. Charting human development using a multi-endodermal organ atlas and organoid models. Cell. 2021; Jun 10;184(12):3281-3298.e22.

    • Brazovskaja A*, Gomes T*, et al. Cell atlas of the regenerating human liver after portal vein embolization. bioRxiv, 2021; https://doi.org/10.1101/2021.06.03.444016.

    • ​Fleck JS*, Sanchís-Calleja F*, He Z, et al. Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases. Cell Stem Cell. 2021; S1934-5909(21)00065-5.

  • 2020​​

    • Dannemann M, He Z, et al. Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions. Stem Cell Reports. 2020; 15(1): 214-225.

    • He Z#, Brazovskaja A, et al. ​CSS: Cluster similarity spectrum integration of single-cell genomics data. Genome Biology 2020; 21(1):224.

  • 2019

    • Kanton S*, Boyle MJ*, He Z*#, et al.​ Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature. 2019; 574:418–422.

  • 2018

    • Yu Q*, He Z*, et al. Lipidome alterations in human prefrontal cortex during development, aging, and cognitive disorders. Molecular Psychiatry. 2018; doi:10.1038/s41380-018-0200-8.

    • Liu C, Wang R, et al. Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells. Stem Cell Report. 2018;11(1):43.

    • He Z#, Yu Q. Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation. BMC Genomics. 2018;19:262.

  • 2017​

    • Shi M, Zhang H, et al. ALYREF mainly binds to the 5′ and the 3′ regions of the mRNA in vivo. Nucleic Acids Research. 2017;45(16):9640

    • Fan J, Kuai B, et al. Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export. The EMBO Journal. 2017; doi:10.15252/embj.201696139.

    • DönertaÅŸ H, Ä°zgi H, et al. Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity.  Scientific Reports. 2017;7:5894.

    • Yu Q, He Z#. Comprehensive investigation of temporal and autism-associated cell type composition-dependent and independent gene expression changes in human brains. Scientific Reports. 2017;7:4121.

    • He Z*, Han D*, et al. Comprehensive transcriptome analysis of neocortical layers in humans, chimpanzees and macaques. Nature Neuroscience. 2017; doi:10.1038/nn.4548.

  • 2016​

    • Mora-Bermúdez F, Badsha F, et al. Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development. eLife. 2016;5:e18683.

    • Kao CY*, He Z*, et al. Fluoxetine treatment rescues energy metabolism pathway alterations in a posttraumatic stress disorder mouse model. Mol Neuropsychiatry. 2016;2:46-59.

    • Kao CY*, He Z*, et al. Fluoxetine treatment prevents the inflammatory response in a mouse model of posttraumatic stress disorder. Journal of Psychiatric Research. 2016 76:74-83.

  • Before 2016

    • Hughes DA, Kircher M, He Z, et al. Evaluating intra- and inter-individual variation in the human placental transcriptome. Genome Biology. 2015 16:54.

    • He Z*, Bammann H*, et al. Conserved expression of lincRNA during human and macaque prefrontal cortex development and maturation. RNA. 2014 Jul;20(7):1103-11.

    • He Z, Chen D, et al. miRPreditor: a Novel MiRNA Target Predictor Based on SVM with Feature Analysis.  Electronic Journal of Biology, 2012 8(4): 79-89.

    • He ZS, Shi XH, et al. A novel sequence-based method for phosphorylation site prediction with feature selection and analysis. Protein Peptide Lett. 2011 Nov; 19(1):70-8.

    • Cai Y, He Z, et al. A novel sequence-based method of predicting protein DNA-binding residues, using a machine learning approach. Mol Cells. 2010 Aug;30(2):99-105

    • He Z#, Zhang J, et al. Predicting drug-target interaction networks based on functional groups and biological features. PLoS One. 2010 Mar 11;5(3):e9603.

(* - equally contributed; # - corresponding author)​

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