About

Dirk Hockemeyer is an Assistant Professor of Molecular and Cell Biology at the University of California, Berkeley, affiliated with the Center for Computational Biology. He is part of the DE Faculty and collaborates within the department to advance research in computational biology. His role involves engaging in research that integrates computational methods with molecular and cell biology, contributing to the understanding of biological systems through a computational lens. He is associated with graduate students such as Shayan Hosseinzadeh and Vincent Pham, and maintains contact via email at hockemeyer@berkeley.edu. His work is situated within a broader institutional framework that supports research, education, and professional development in computational biology.

Research topics

• Computational biology
• Anatomy
• Neuroscience
• Medicine
• Geography
• Environmental health
• Cartography
• Biology

Selected publications

• Calcium Shock Enables Efficient and Programmable Particle Delivery for Genome Editing Applications

  Advanced Science · 2026-03-17

  articleOpen access

  Classical intracellular delivery methods such as transfection and transduction are inefficient, particularly with confluent cells and organoids, and lack cell type-specific programmability. We demonstrate that an innovative methodology called calcium shock (CaSh) dramatically improves particle delivery into single cells, colonies, and organoids, and enables programmable delivery (CaSh-Pro) into specific cell types within heterocellular populations. Calcium shock works by increasing endocytotic uptake while simultaneously disarming cell-cell junctions. CaSh-Pro further incorporates specific molecular targeting agents and amphiphilic peptides for preferential editing of different cell types. Calcium shock improves expression of plasmid, ribonucleoprotein, or adeno-associated viral vectors with minimal toxicity in intact organoids representing diverse lineages. CaSh and CaSh-Pro provide simple, versatile protocols for genome editing in complex systems, to enable biological discovery and therapeutic development.

  PublisherDOI

• iSCORE-PD: scRNA-seq of irradiated WIBR3 hESCs

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

  datasetOpen access

  This Zenodo deposit contains a publicly available description of the Dataset: Title: "iSCORE-PD: scRNA-seq of irradiated WIBR3 hESCs". Description: Single-cell RNA sequencing of WIBR3 human embryonic stem cells (hESCs) exposed to ionizing radiation at doses of 0, 0.5, 2, 5, and 10 Gy. Cells were assayed 24h post-irradiation via multiplexed scRNASeq using MULTI-seq reagents. This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual. This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

  PublisherDOI

• iSCORE-PD: NGS genotyping and zygosity testing of isogenic hESC clones

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

  datasetOpen access

  This Zenodo deposit contains a publicly available description of the Dataset: Title: "iSCORE-PD: NGS genotyping and zygosity testing of isogenic hESC clones". Description: Targeted DNA sequencing data for the iSCORE-PD isogenic hESC clone collection, encompassing three complementary analyses: (1) NGS genotyping of 53 mutant clones across 11 PD-linked genes via amplicon sequencing on Illumina iSeq 100 with CRISPResso2 analysis, (2) zygosity testing of a subset of clones in 6 genes via SNP-PCR (NGS or Sanger) to assess zygosity near CRISPR edit sites, and (3) Sanger sequencing of the wild-type allele in 5 DJ1/PARK7 heterozygous clones. This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual. This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

  PublisherDOI

• iSCORE-PD: NGS genotyping and zygosity testing of isogenic hESC clones

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

  datasetOpen access

  This Zenodo deposit contains a publicly available description of the Dataset: Title: "iSCORE-PD: NGS genotyping and zygosity testing of isogenic hESC clones". Description: Targeted DNA sequencing data for the iSCORE-PD isogenic hESC clone collection, encompassing three complementary analyses: (1) NGS genotyping of 53 mutant clones across 11 PD-linked genes via amplicon sequencing on Illumina iSeq 100 with CRISPResso2 analysis, (2) zygosity testing of a subset of clones in 6 genes via SNP-PCR (NGS or Sanger) to assess zygosity near CRISPR edit sites, and (3) Sanger sequencing of the wild-type allele in 5 DJ1/PARK7 heterozygous clones. This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual. This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

  PublisherDOI

• iSCORE-PD: scRNA-seq of irradiated WIBR3 cortical spheroids

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

  datasetOpen access

  This Zenodo deposit contains a publicly available description of the Dataset: Title: "iSCORE-PD: scRNA-seq of irradiated WIBR3 cortical spheroids". Description: Single-cell RNA sequencing of WIBR3-derived Day 25 cortical spheroids exposed to ionizing radiation at doses of 0, 0.5, 2, 5, and 10 Gy. Spheroids were dissociated and assayed 24h post-irradiation via individual 10x Chromium scRNA-seq libraries per condition. This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual. This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

  PublisherDOI

• iSCORE-PD: scRNA-seq of irradiated WIBR3 cortical spheroids

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

  datasetOpen access

  This Zenodo deposit contains a publicly available description of the Dataset: Title: "iSCORE-PD: scRNA-seq of irradiated WIBR3 cortical spheroids". Description: Single-cell RNA sequencing of WIBR3-derived Day 25 cortical spheroids exposed to ionizing radiation at doses of 0, 0.5, 2, 5, and 10 Gy. Spheroids were dissociated and assayed 24h post-irradiation via individual 10x Chromium scRNA-seq libraries per condition. This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual. This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

  PublisherDOI

• Telomere length of both parents contribute to heritable POT1 cancer-predisposition syndrome

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-11

  articleOpen accessSenior authorCorresponding

  Germline mutations in POT1 are linked to familial cancer predisposition, and somatic POT1 mutations occur recurrently in tumors. These mutations promote oncogenesis by enabling aberrant telomere elongation. For inherited POT1 mutations, a critical question is the extent to which elongated telomeres are transmitted to the next generation from the POT1 carrier parent and whether the inherited hyper-elongated telomeres elevate cancer risk. Using a nanopore sequencing approach that provides haplotype-specific telomere length measurements, we examined telomere inheritance in families harboring POT1 mutations. We found that individuals preferentially inherit their longest telomeres from the carrier parent, consistent with extensive telomere elongation in the carrier germline, whereas their comparatively short telomeres originate from the non-carrier parent. Analysis of carrier and non-carrier siblings showed that both sets of parental telomeres are longer in POT1 carriers, yet the shortest non-carrier-derived telomeres undergo disproportionately greater elongation than those inherited from the carrier parent. This identifies a mechanism of genetic anticipation in which the inheritance of long telomeres from one parent drives excessive extension of shorter telomeres. These findings demonstrate that telomere length inherited from both parents jointly defines the telomere-based tumor suppressor mechanism.

  PublisherDOI

• iSCORE-PD: Whole-genome sequencing and variant calling of isogenic hESC clones and controls

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

  datasetOpen access

  This Zenodo deposit contains a publicly available description of the Dataset: Title: "iSCORE-PD: Whole-genome sequencing and variant calling of isogenic hESC clones and controls". Description: Whole-genome sequencing (WGS) data for the iSCORE-PD isogenic hESC clone collection. 150bp paired-end WGS was performed on Illumina NovaSeq X for 49 mutant clones across 11 PD-linked genes, 12 control lines (8 engineered wild-type subclones, 3 WIBR3 subclones, and the WIBR3 parental line), and 5 DJ1/PARK7 heterozygous clones. Variants were called using DeepVariant and jointly genotyped with GLnexus v1.4.1, producing per-chromosome VCF files aligned to GRCh38. This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual. This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

  PublisherDOI

• iSCORE-PD: scRNA-seq of WT WIBR3 hESC-derived dopaminergic neurons

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

  datasetOpen access

  This Zenodo deposit contains a publicly available description of the Dataset: Title: "iSCORE-PD: scRNA-seq of WT WIBR3 hESC-derived dopaminergic neurons". Description: Single-cell RNA sequencing of WIBR3 hESC-derived dopaminergic neurons differentiated for 35-37 days. Three biological replicates were independently differentiated and assayed via CellPlex-multiplexed 10x Chromium v3.1 scRNA-seq libraries. This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual. This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

  PublisherDOI

• iSCORE-PD: Whole-genome sequencing and variant calling of isogenic hESC clones and controls

  Zenodo (CERN European Organization for Nuclear Research) · 2026-04-15

  datasetOpen access

  This Zenodo deposit contains a publicly available description of the Dataset: Title: "iSCORE-PD: Whole-genome sequencing and variant calling of isogenic hESC clones and controls". Description: Whole-genome sequencing (WGS) data for the iSCORE-PD isogenic hESC clone collection. 150bp paired-end WGS was performed on Illumina NovaSeq X for 49 mutant clones across 11 PD-linked genes, 12 control lines (8 engineered wild-type subclones, 3 WIBR3 subclones, and the WIBR3 parental line), and 5 DJ1/PARK7 heterozygous clones. Variants were called using DeepVariant and jointly genotyped with GLnexus v1.4.1, producing per-chromosome VCF files aligned to GRCh38. This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual. This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset

  PublisherDOI

Recent grants

• Telomerase function in human tumor and stem cell biology

  NIH · $1.7M · 2015–2020

Frequent coauthors

• Hanqin Li

  Research Network (United States)

  89 shared

• Helen S. Bateup

  University of California, Berkeley

  83 shared

• Frank Soldner

  Research Network (United States)

  71 shared

• Oriol Busquets

  Albert Einstein College of Medicine

  60 shared

• Daniel S. Rokhsar

  Innovative Genomics Institute

  54 shared

• Yogendra Verma

  University of California, Berkeley

  44 shared

• Donald C. Rio

  Research Network (United States)

  41 shared

• Khaja Syed

  Research Network (United States)

  41 shared

Labs

• Center for Computational BiologyPI

Education

• Postdoctoral fellow

  Whitehead Institute for Biomedical Research

  2012

• Ph.D

  Rockefeller University

  2007

• Diploma, Biochemistry

  Eberhard Karls Universität Tübingen

  2002