scverse Conference 2024

Co-founder & CEO of Lamin

Alex works on an open-source data platform for biology at Lamin. Previously, he created Scanpy and led the build-up of Cellarity’s compute platform.

Angela is the head of computational biology at insitro, working at the forefront of building datasets and ML models to improve understanding of disease mechanisms with the goal to transform drug discovery and development. She is passionate about extracting meaningful information from biomedical datasets and using it to improve disease understanding and drug development. Angela holds a BSc and MSc in Biomedical Engineering and a PhD in Systems Biology. Before moving to insitro, she led the Data Science platform at CZ Biohub. There she made significant contributions for the whole organism cell atlas projects including the first whole mouse cell atlas (Tabula Muris), the first aging cell atlas (Tabula Maris Senis), and Tabula Sapiens, one of the first Human Cell Atlas drafts. She is also a founder and core member of Open Problems in Single Cell, a community effort to improve multimodal data analysis by both generating gold standard datasets and benchmarking metrics and infrastructure.

Behnam Yousefi earned his PhD in Computational Biomedicine from Sorbonne University, Paris, and Pasteur Institute, Paris. He is currently a Postdoctoral Researcher at UKE, Hamburg, and his research focuses on network-based data analysis and deep learning, particularly in personalized medicine, spatial omics, and drug design.

Computer science engineer with a passion for interactive analysis of multidimensional bioimaging and hackathons.

Senior Manager, Informatics
Cho Lab
Pathology, Molecular and Cell Based Medicine
Icahn School of Medicine at Mount Sinai

Christina Leslie is a Member of the Computational and Systems Biology Program at MSKCC in New York and a Professor of Physiology, Biophysics, and Systems Biology in the Tri-I Computational Biology and Medicine Program through Weill Cornell Graduate School. Her group develops statistical and machine learning methods for single-cell and regulatory genomics, with applications to basic and cancer immunology, cancer epigenetics, and stem cell biology and development.

I’m a bioinformatics scientist exploring the intersection of spatial genomics, ML/AI, and cell biology. I am currently a Postdoctoral Researcher in the Yeo Lab at UC San Diego, recently graduated from the UC San Diego Bioinformatics & Systems Biology PhD Program, co-advised by Dr. Gene Yeo and Dr. Hannah Carter. During my PhD, I created bento-tools, an open-source Python toolkit that unifies novel machine learning algorithms and statistics for studying RNA and cell biology. Outside of the lab, I enjoy spending time with my dog in sunny San Diego, CA at my favorite coffee shops and breweries.

Elyas Heidari is a PhD student specialising in AI in Oncology at the German Cancer Research Center (DKFZ) in Heidelberg. He completed his Bachelor's in Computer Science and Mathematics at Sharif University of Technology in Iran and holds a Master’s degree from ETH Zurich, department of Biological Science and Systems Engineering. During his internship at EMBL-EBI, he focused on spatial omics and computational genomics. Elyas has developed packages such as MUVIS (R) and SageNet (python) for biomedical data science and machine learning and is currently interested in developing computational methods for the analysis and integration of spatial omics data at scale.

Director of Helmholtz Munich Computational Health Center and Scientific Director of the Helmholtz Artificial Intelligence Cooperation Unit (Helmholtz AI)

Fabian Theis is a Full Professor at the Technical University of Munich, Associate Faculty at the Wellcome Trust Sanger Institute and member and/or coordinator of various initiatives. He uses artificial intelligence to unlock the secrets of human cells.

Felix Petschko is currently a Master's student in Computer Science at the University of Innsbruck. He is conducting his Master's thesis research within the Computational Biomedicine Group at the Institute of Molecular Biology and the Digital Science Center (DiSC) at the University of Innsbruck, Austria.

Idris graduated from the University of Science and Technology Houari Boumediene in Algiers with a master degree in theoretical physics, then obtained a diploma in quantitative life sciences from the Abdus Salam International Centre for Theoretical Physics (ICTP).

He is currently working on using neural ordinary differential equations for systems biology with Guido Sanguinetti and Andrea Sottoriva.

Bachelor and Master studies in Chemical Biology at University Konstanz. PhD at Helmholtz Center Munich on the development of a novel spatial transcriptomics technology. Now postdoctoral researcher at the Institute of Pathology of the Technical University Munich combining in situ sequencing, pathology and computational analysis to dissect the intra-tumoral heterogeneity of different cancer entities.

John Hawkins is an AI Health Innovation Cluster Postdoctoral Fellow at the European Molecular Biology Laboratory (EMBL) working in the labs of Lars Steinmetz and Oliver Stegle. He earned his Ph.D. in Computational Science, Engineering, and Mathematics at The University of Texas at Austin in the labs of Ilya Finkelstein and Bill Press. His interests are in developing high accuracy DNA barcodes and decoding software, and applying this technology for the creation of higher throughput and more informative CRISPR perturbation screens.

Senior Software Developer – EMBL

Research Software Engineer at LaminLabs | scverse Steering Council Member | Postdoc at Fabian Theis' Lab

Malte leads the integrative genomics lab at Helmholtz Munich. His lab uses machine learning and single-cell technologies to build reference atlases of human tissues and organs with the goal of using these resources for clinical applications, with a specific focus on lung disease. His lab is strongly involved in the Human Cell Atlas, where Malte leads the integration team. This team is spread across 3 continents and focuses on building integrated single-cell reference atlases for HCA Bionetwork organs and tissues.
Malte is also a co-founder of the Open Problems in Single-cell Analysis consortium, which hosts a living benchmarking platform and runs competitions in single-cell data science.

Maria Brbic is an Assistant Professor of Computer Science and Life Sciences at EPFL. She develops new machine learning methods and applies her methods to advance biology and biomedicine. Her methods have been used by global cell atlas consortia efforts aiming to create reference maps of all cell types with the potential to transform biomedicine, including the Human BioMolecular Atlas Program (HuBMAP) and Fly Cell Atlas consortium. Prior to joining EPFL in September 2022, Maria was a postdoctoral fellow at Stanford University, Department of Computer Science. Maria received her PhD from University of Zagreb in 2019 while also researching at Stanford University as a Fulbright Scholar and University of Tokyo. Among other recognitions and awards, she was named a rising star in EECS by MIT in 2021, received the Josip Loncar silver plaque for outstanding PhD thesis in 2019 and the Early Career Bioinformatics Award by SIB in 2023.

Matthias is a predoctoral fellow at the European Molecular Biology Laboratory (EMBL) in the groups of Wolfgang Huber and Sascha Dietrich. Prior to joining EMBL, he obtained a BSc and MSc in bioinformatics at the Technical University of Munich and Ludwig-Maxmilians-Universität Munich. His current research involves analyzing highly multiplexed fluorescence microscopy images of Non-Hodgkin B cell lymphoma.

Maximilian Lombardo is a Senior Product Applications Scientist at the Chan Zuckerberg Initiative, where he collaborates with the CELLxGENE team to engage the single-cell community and enhance the adoption of CELLxGENE tools. In his role, he focuses on educating users and driving the development of resources that support innovative single-cell research. Previously, Maximilian was a Data Scientist at Kallyope, contributing to the development of a gut-brain axis target discovery platform. His work involved integrating single-cell data with viral tracing techniques to identify novel therapeutic targets. Maximilian holds an MSc in Computational Science from the University of Amsterdam and an MA in Biotechnology from Columbia University.

Postdoctoral researcher at Novo Nordisk Foundation (CPR), Copenhagen, Denmark

I am a principal computational biologist at Memorial Sloan Kettering Cancer Center in New York. I received a PhD in computer science from the University of California, Irvine. Currently, I lead the cellular phenotyping team under the supervision of Dr. Sohrab Shah and I am the single cell lead in the Computational Immuno-oncology initiative under the supervision of Dr. Benjamin Greenbaum. My research interest includes single cell methods and analysis of cancer evolution and the adaptive immune response.

PostDoc in Fabian Theis‘s lab (Helmholtz Munich) and Veit Hornung‘s lab (LMU Munich)

A Molecular Biologist by training, Paul received his undergraduate degrees from the Universities of Mannheim and Aachen, where he worked on therapeutic antibody discovery and the optimization of small molecular drugs. Since 2022, he has been a PhD student in the newly established Kuppe Lab at the University Hospital RWTH in Aachen. The focus of his research is on cardiovascular and kidney diseases, which he investigates using single-cell analysis, spatial transcriptomics, and CRISPR experiments. His work aims to leverage these cutting-edge techniques to uncover new insights into disease mechanisms and potential therapeutic targets.

Pedro Aragón holds a bachelor’s and master’s degree in biochemistry from the Technical University of Munich (TUM). He developed an interest in analytical chemistry for biological applications and continued to pursue a PhD in the Cell Diversity Lab supervised by Prof. Erwin M. Schoof at the Technical University of Denmark (DTU). His current work focuses on the development and implementation of novel preparative and analytical strategies for mass spectrometry-based single-cell proteomics to understand the synergy displayed by phenotypically distinct subpopulations in the hematopoietic system.

Softwareingenieur Single Cell Biology

Pierre Bost has done a joint PhD between the Pasteur (Paris, France) and Weizmann (Rehovot, Israel) institutes from 2017 to 2020 where he developed several computational methods for the analysis of single-cell data, focusing on the analysis of viral infections.
He moved to Zürich for his postdoc where he established new statistical methods to design and analyze the results of multiplexed imaging experiments.
He has recently opened his lab in Paris within the Curie Institute where he develops new computational and experimental methods to dissect tissue spatial structures and viral infections.

PhD student at the MICS Laboratory (Paris-Saclay University) and the Gustave Roussy Institute. I'm developing deep learning tools on multi-omics data for precision medicine in oncology. I have a particular focus on spatial omics data with single-cell resolution.

Rob Patro is an associate professor of Computer Science at the University of Maryland, and a member of the University of Maryland Institute for Advanced Computer Studies (UMIACS) and the Center for Bioinformatics and Computational Biology (CBCB). His main research interests are in the design of algorithms and data structures for processing, organizing, indexing and querying high-throughput genomics data and in the intersection between efficient algorithms and statistical inference. A current research focus of his lab is the development of computational methods for accurate, efficient and uncertainty-aware transcriptome analysis using RNA-seq (both bulk and single-cell with both long and short reads) as well as on the design of scalable (often succinct) data structures for indexing and querying genomes and raw sequencing data. He is a core developer and maintainer of the salmon, alevin, alevin-fry and simpleaf software tools, and his lab develops a number of open-source tools for high-throughput genomic and transcriptomic analysis, most of which are available from GitHub at https://github.com/COMBINE-lab.

Robrecht, CTO at Data Intuitive (data-intuitive.com), is passionate about making single-cell analysis more accessible and reliable. As the lead developer of Viash, he's all about creating workflows that are easy to reproduce and reuse. He's also the lead developer of OpenProblems, a platform dedicated to establishing the best practices for single-cell analysis by rigorously testing different computational methods. These efforts drive the creation of new living best practices (sc-best-practices.org) and the development of modular single-cell workflows (openpipelines.bio).

Manager, Computational Biology at Single-cell Analytics and Innovation Lab, MSKCC

Ryan is a Staff Software Engineer at TileDB, focused on scalable scRNA-seq data processing and storage using TileDB-SOMA. He has previously built software for distributed analysis of bulk and single-cell genomic data, in industry and as part of a CZI Human Cell Atlas grant at Mount Sinai School of Medicine, and holds a BSc in Mathematical & Computational Sciences from Stanford University.

I have a solid background in applied mathematics and statistics, where I have extensively developed my programming skills with Python, R/Rcpp, Matlab, Docker, bash and pipelines scripting. I have crossed my competences with the bioinformatics field by developing efficient software and pipelines for Next Generation Sequencing and single cell RNA sequencing Data. I like to challenge myself trying new programming languages, as well as new and old machine learning techniques to solve mathematical and computational problems.

2023 - Present:
PhD course in the Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo."

Software Engineer at Theis Lab for scverse

PhD Student in the Lab of Matthias Mann at the Max Planck Institute of Biochemistry

phd student, Medical University Innsbruck

Vivek is an Assistant professor at the Institute of Biodynamics and Biocomplexity, Utrecht University (Netherlands). His work involves developing computational methods for data analysis from rapidly evolving single-cell genomics/multi-omics techniques, distributing these methods as useful tools for biologists, and training others to do so. The long-term goal of his lab is to enable technologies for in vivo epigenetic reprogramming: https://vblab.org/

I'm a Postdoctoral Fellow at CeMM, Vienna, my current research focus is on digital pathology and spatial omics. I'm an open-sourced software developer in my free time and a big fan of scientific visualization.

PhD student at Technion - Israel Institute of Technology

scverse core team