Mapping and modeling the proteome architecture of human cells

Our research is focused on spatial proteomics and cell biology. At the interface between bioimaging, proteomics and artificial intelligence are fundamental aspects of human cell biology systematically assessed at subcellular resolution. The aim is to understand how human proteins are distributed in time and space, and how variations in localization modulate dynamic cell functions and how mislocalization give rise to disease.

A goal is to build the first spatiotemporal proteome model of a human cell. Using machine learning we're interpreting the spatial information from our image collections and integrate it with other datatypes to build whole-proteome multi-scale cell models and demonstrate how they can be used to improve drug discovery.

Part of our work is the creation of the Cell Atlas, of the Human Protein Atlas database, where the subcellular localization of all human proteins is being determined.

We are true believers in Open Science and love to engage more people in our work through crowd-sourced challenges.

People

Lab members

Emma Lundberg

Associate Professor

Ana Martinez Casals

Research Scientist

Devyn James

Administrative Associate

Ulrika Axelsson

Researcher

Frederic Ballllosera Navarro

Research Engineer

Frida Björklund

PH.D. Student

Anna Bäckström

Research Engineer

Anthony Cesnik

Postdoctoral Scholar

Rong Chi

Rotation Student

Nicolai Dorka

PH.D. Student

Jenny Fall

Lab Technician

Alice Finkelstein

Summer Intern

Christian Gnann

PH.D. Student

Ankit Gupta

Postdoctoral Scholar

Jan Hansen

Postdoctoral Scholar

Miguel Angel Hurtado

Lab assistant

Alexandra Johannesson

PH.D. Student

Konstantin Kahnert

Postdoctoral Scholar

Trang Le

PH.D. Student

Will Leineweber

Postdoctoral Scholar

Diana Mahdessian

Researcher

Mariya Mardamshina

Postdoctoral Scholar

Maddie Mitchell

Visiting Student

Emmie Pohjanen

PH.D. Student

Ernst Pulido

PH.D. Student

Sanem Sariyar

PH.D. Student

Katrin Schmitt

Research professional

Alina Sigaeva

Postdoctoral Scholar

Paul Sun

Postdoctoral Scholar

Kalliopi Tzavlaki

Research Engineer

Zoe Wefers

PH.D. Student

Xikun Zhang

PH.D. Student

Alumni

Burcu Ayoglu

Researcher

Ishan Gaur

Master Student

Irene Muñoz

Visiting PH.D. Student

Iva Sutevski

PH.D. Student

Sherry Yang

Rotation Student

Resources

Access our work

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Publications

Browse the ever-growing list of the lab publications over the years

biotech

Lab

Get a virtual tour of our lab and explore its multiple instruments

Human Protein Atlas

The open access resource for human proteins, including our specific contribution to the Cell Atlas

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Protocols

Our contribution to the research community with several protocols and techniques

Antibody HUB

Access and collaborate our CODEX/Phenocycler antybody HUB initiative

Open code

We are committed with open science, our code is freely available in GitHub

memento

Access and take a look at our simple image sharing and annotation tool

PIPEX

Try one of our public available image analysis pipelines, PIPEX

HPAseg

Segment and get data from any immunochemistry stained image available in the HPA site (or bring your own!)

HPAscc

Run the lab's latest single cell classification model based in our 2018 public Kaggle competition

Baserow

Lab data management baserow instance (only for lab members)

Google drive

Lab's google drive shared folders (only for lab members)

Quartzy

Lab's quartzy for equipment requests (only for lab members)

Travelling

Lab's travel form for conferences and symposiums (only for lab members)

Jupyter notebook

Personal jupyter notebook space (only for lab members)

News

Follow the lab

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  • Messages
  • Talks
  • Experiments

Maddie at the IRB Cancer Promotion conference

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Emma Lundberg at Nobel Symposia 2024

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Team building fun!

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Sanem Sariyar PhD defense

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Trang Le won first place in the label-free Light My Cell challenge!

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Way to go, Alice!

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Congratulations on your quals, Ernst!

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Congratulations on your quals, Frida!

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Frederic at the CZI SciTech 2024

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Jan at the FASEB SRC on Biology of Cilia and Flagella

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Emmie for the Flourish Stories

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Christian Gnann PhD defense

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Jan Hansen poster presentation at the Bridge2AI April 2024 All Hands Conference

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Jan Hansen talk at the Bridge2AI April 2024 All Hands Conference

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Microglia study

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Spatial proteomics of cell migration III

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Spatial proteomics of cell migration II

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Spatial proteomics of cell migration I

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Cell Biology at Scale 2024

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Cilia basal bodies in tissue

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Afterwork pizza!

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BioE admit day

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Weekly wet-lab meeting

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CZI AI Resident pilot program kickoff

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R&R award by SPORR

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Emma Lundberg speaking at Bits, Photons & Cells: Exploring Novel Technologies to Unravel Cell Dynamics in Zebrafish

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Lundberg lab in Akoya's #TissueTuesday

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Maddie Mitchell awarded by Rob Clarke Presentation

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Closing dinner at PSB 2024

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Workshop at PSB 2024

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Emma Lundberg at PSB 2024

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Trang Le at PSB 2024

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Frederic Ballllosera at PSB 2024

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Ishan Gaur at PSB 2024

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Ernst Pulido at PSB 2024

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Christmas fika with our swedish colleagues!

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Congrats Emmie on your half-time!

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It's alive!

Experiment

The MS has finally arrived!

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A lot of KOLF2.1J cells to freeze today!

Experiment

Stanford's BioE holiday party!

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Thanks for visiting, Anna Mäkiniemi!

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Cancer Grand Challenge - Future Leaders conference

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Proteomics in Cell Biology and Disease Mechanisms” conference

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CCMI meeting in San Diego

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CZ Biohub confab 2023

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KlarText Preis awarded to Jan Hansen!

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Jan Hansen video portrait from Klartext Award

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Stanford Department of Bioengineering’s 20th anniversary

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Welcome Frida!

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Highly multiplexed image of human kidney

Experiment

Welcome Maddie!

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HPAseg in action!

Experiment

Emma Lundberg at the Angelo lab 2023 Spatial Biology Workshop

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Emma Lundberg at the The Scientific Observer

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Welcome Alice!

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5-plex chromogenic staining

Experiment

Organ Mapping Antibody Panels

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Trang Le in Stanford's instagram

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Poster time in Rotterdam!

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Poster time in Rotterdam!

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PhenoCycler Fusion staining

Experiment

Dual time zone

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“Multi Omics in Metabolic Disease” conference

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A new member of the family!

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SCP conference 2023

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EPIC-XS 2023

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New PhenoCycler Fusion

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Xiuqi Masters thesis project

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BioE retreat at Stanford

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memento is Gold!

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Biohub Confab

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2023 BTP Annual Symposium

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2023 BTP Annual Symposium

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Lab secured!

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Lundberg Lab's Symposium 2022

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Lundberg Lab's Symposium 2022

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Lundberg Lab's Symposium 10.30.2022

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Talk at DataViz+Cancer

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Talk at Condensates

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PIPEX segmentation

Experiment

Cell Mapping Symposium 2018

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Dissecting the spatiotemporal subcellular distribution of the human proteome | Welcome Genome Campus

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Single cell proteome and transcriptome map of the human cell cycle | SCP2021

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Perspectives in Proteomics

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How gamers help science | SVT Gather 2018

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Join us!

Welcome to our lab

Do you want to be part of our work and help us advance open science? We are always interested in new people, ideas and skills! At Lundberg's lab you'll find a dynamic, collaborative, interdisciplinary and Scandinavian culture that will nurture your research, creativity and innovation skills.

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Location:

443 Via Ortega, Stanford, CA 94305

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