18th Berlin Summer Meeting – Sequencing Planet Earth

June 19, 2025, 9:00am - June 20, 2025, 5:00pm

The annual Berlin Summer Meeting: Computational and Experimental Molecular Biology Meet brings together scientists working at the intersection of computation and experiment and promotes cross-disciplinary exchange between early-career researchers and leading experts.

All life on earth is connected by DNA and RNA which function to determine, transmit and shape genotypes and phenotypes. Recent breakthroughs in sequencing technologies are dramatically increasing both throughput and precision, while simultaneously reducing costs. Concurrently, leaps in data science are enabling us to connect, compare, interrogate, and interpret biological data on an unprecedented scale. This synergy is powered by an exponential growth of high-resolution, digital data at the core of life.

Under the theme ‘Sequencing Planet Earth’, the 2025 Berlin Summer Meeting will explore the transformative possibilities arising from the integration of these breakthroughs in sequencing technologies and data science, with a focus on their impact on interests shared by humans across our planet. By bridging disciplines and fostering collaboration, the meeting aims to catalyze new discoveries and approaches to address global health challenges.

Registration

Early-bird Registration (until May 31, 2025): €120

Late Registration (from June 1, 2025 onwards): €150

Workshops, June 18, 2025

Accompanying workshops for early-career researchers on June 18, 2025:
These workshops are offered at no extra cost to Berlin Summer Meeting participants and will be allocated on a first-come, first-served basis via the registration.

Malva: Real-time Sequence Search across Billions of Cells
Daniel Léon Perinán (MDC)

Modern single-cell and spatial sequencing technologies create increasingly large repositories of nucleotide data from organisms across planet Earth. Current analysis methods require extensive preprocessing, limiting real-time exploration of the sequence-space by researchers and AI agents.

In this workshop, Daniel Léon Perinán will introduce and teach the use of Malva, the N. Rajewsky Lab’s new universal search index that unifies multi-terabyte repositories into an instantly queryable, dynamic resource — hundreds of millions of cells across thousands of experiments.

Malva enables immediate analysis of any nucleotide pattern with single-cell and spatial resolution, allowing researchers to, for instance, identify circular RNAs, track 3′ UTR dynamics during embryonic development, and detect alternative splicing events across cell types.

The workshop showcases various approaches for sequence analysis with Malva, including two novel analysis paradigms: discovery of cell types directly from unaligned reads, and training neural networks that predict single-cell and spatial expression patterns from primary sequence.

Participants are encouraged to bring their own data and research questions. You will be guided through running Malva from scratch and show you how to maximize the potential of this new sequence analysis framework.

Date & Time:                                                    June 18, 2025, 1 pm – 2:30 pm
Maximum number of participants:          10
Technical requirements:                              Laptop and GitHub account

Recommended preexisting skills: Basic knowledge of omics data analysis (such as: what are the data formats, what is the basic cell typing workflow, etc.)

Methodologies for nucleic acid extraction and processing, high-throughput sequencing and data analysis for environmental samples

Shuba Varshini Alampalli (BIH) & Emanuel Wyler (MDC)

Environmental samples – freshwater, wastewater, surface swabs, sediments – contain a wealth of genetic information. Accessible via high-throughput sequencing, this data can inform a broad spectrum of research and surveillance interests, from biodiversity, ecological status, water and soil quality or agriculture to spread of pathogens or anti-microbial resistances. Obtaining meaningful insights however requires broad expertise in environmental sampling, nucleic acid extraction, sequencing and data analysis. In this workshop, Shuba Varshini Alampalli and Emanuel Wyler will present their work on solid and aqueous samples, from sampling to computational analysis. The workshop is intended for people with or without work experience in the topic, and all input will be welcome for the discussion.

Date & Time: June 18, 2025, 1 pm – 2:30 pm

Maximum number of participants: 10
Technical requirements: none

Recommended preexisting skills: Basic knowledge of nucleic acid isolation and processing, sequencing library preparation high-throughput sequencing

Planning and setting up spatial transcriptomics experiments for infectious diseases
Emanuel Wyler (MDC)

Spatial transcriptomics allows the detection of hundreds to thousands of different RNAs with single cell/single molecule resolution in tissue slices. This recent technology is a major step forward for studying infectious diseases in solid tissues, as it allows to track both the spread of the pathogen and the host response at unprecedented resolution and depth. Based on ongoing spatial transcriptomics projects on virus infections in a range of tissue types, Emanuel Wyler will highlight the methodological steps from experimental design to computational data analysis.

Date & Time:                                                 June 18, 2025, 3 pm – 4:30 pmMaximum number of participants:          10
Technical requirements:                              none
Recommended preexisting skills:             Basic knowledge of the genomics of your pathogen of interest and transcriptomics in general

AI assisted genomics data analysis
Vedran Franke (MDC)

In this focused, hands-on workshop, you will engage with a conversational AI agent that guides you through a complete RNA-sequencing analysis pipeline - from processing raw count matrices to generating publication-ready figures. The AI assistant evaluates your dataset’s quality and experimental design, recommends and implements best-practice methods for normalization, differential expression, and downstream analyses such as clustering and pathway enrichment, and drafts fully reproducible R scripts.

You will learn to instruct the agent to produce and refine high-quality visualization - heatmaps, MA and volcano plots - through simple conversational prompts, empowering you to streamline your transcriptomics research with an AI-driven workflow.

Date & Time:                                                 June 18, 2025, 3 pm – 4:30 pm
Maximum number of participants:          12
Technical requirements:                             Laptop with pre-installed application (installation instructions will follow after signing up)
Recommended preexisting skills:             None or basic coding skills

Inside the Genome: A Hands-On Tour of Single-Cell Omics in Action
Ashley Sanders & team (MDC)

Step behind the scenes of cutting-edge genomics research in this immersive, hands-on workshop led by Ashley Sanders and her team in the Genome Instability and Somatic Mosaicism lab. Designed specifically for early-career PhD students, this workshop offers a unique opportunity to explore the practical side of single-cell omics through a dynamic lab tour and interactive demonstrations.

Following a brief introduction highlighting the lab's research focus on genome instability and somatic mosaicism, participants will rotate through four interactive stations showcasing key aspects of single-cell research—from sample prep and library construction to data analysis:

· Station 1: Cell Culture & Microscopy – Get hands-on experience in observing cultured cells and understanding cell-based experimental workflows.

· Station 2: Automated Library Preparation – Explore liquid handling robots like the Mantis and learn how they streamline sample prep.

· Station 3: Bioinformatics & Data Analysis – Discover how high-performance computing transforms raw sequencing data into biological insight.

Whether you're curious about the tools behind single-cell sequencing or eager to understand how big data shapes modern biology, this workshop offers an engaging, real-world introduction to the technologies and thinking that power genomic research today.

Date & Time:                                                 June 18, 2025, 3 pm – 5 pm
Maximum number of participants:          20
Technical requirements:                             none

Call for Abstracts

We invite all participants to submit an abstract for consideration for a selected short talk or poster presentation. Early career researchers are particularly encouraged to apply.

Instructions for abstract submission will be provided upon registration. Abstracts may be composed of a text with a maximum length of 2500 characters including spaces.

The abstract submission deadline has been extended to May 20, 2025.

Confirmed speakers

Detlev Arendt, EMBL, Heidelberg, Germany

Ana Rita Grosso, NOVA University of Lisbon, Portugal

Marion Koopmans, Erasmus Medical Center, Rotterdam, the Netherlands

Eugene Koonin, NCBI, Bethesda, USA

Brenda Anna Kwambana-Adams, Liverpool School of Tropical Medicine & University College London, UK

Camille Marchet, CNRS, Université de Lille, France

Tobias Marschall, Heinrich Heine University, Düsseldorf, Germany

Alfred Ngwa, MRC Unit, The Gambia, London School of Hygiene & Tropical Medicine, UK

Helder Nakaya, University of Sao Paulo, Brazil

Ulf Landegren, Uppsala University, Sweden