Testbed

Basic formatting

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

External link

Internal link

italic text

bold text

strike-through text

Text with extra blank lines above and below

• list item a
• list item b
• list item c

1. ordered list item 1
2. ordered list item 2
3. ordered list item 3

1. top level list item
   • nested list item
     1. even deeper nested list item

Plain image:

Heading 1

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Heading 2

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Heading 3

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Heading 4

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Heading 5

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Heading 6

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

It was the best of times it was the worst of times. It was the age of wisdom, it was the age of foolishness. It was the spring of hope, it was the winter of despair.

// some code with syntax highlighting
const popup = document.querySelector("#popup");
popup.style.width = "100%";
popup.innerText =
  "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.";

This sentence has inline code, useful for making references to variables, packages, versions, etc. within a sentence.

Lorem ipsum dolor sit amet.

Consectetur adipiscing elit.

Sed do eiusmod tempor incididunt.

Jekyll Spaceship

$ a * b = c ^ b $

$ 2^{\frac{n-1}{3}} $

$ \int_a^b f(x)\,dx. $

Components

Section

Section, background

Section, dark=true

Section, background dark=true

Section, size=wide

Section, size=full w/ figure

Figure

Button

Icon

Lorem Ipsum Dolor

Feature

Title

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Title

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

List

List citations

2024

2023

2022

2021

2020

2019

2018

2017

List projects

Cool Dataset a subtitle

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

resource

Cool Package a subtitle

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

resource

Cool Tutorial a subtitle

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

resource publication

Cool Web App a subtitle

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

software

Cool Web Server a subtitle

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

software

List team members

Britta Velten
Principal Investigator

Fabian Linsenmeier
MSc Student

Francisca Gaspar Vieira
PhD Student

Jan Sprengel
MSc Student

Jana Braunger
PhD Student

Nikolai Köhler
Postdoctoral Researcher

Purusharth Saxena
PhD Student

Stijn Hawinkel
Visiting Postdoc

Thomas Greulich
System Admin

Wangjun Hu
MSc Student

Yen-Hsi Beyer
Admin

Zehua Zhang
PhD Student

List blog posts

2023

Example post 3

john-doe February 23, 2023 April 16, 2025

biology medicine

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

2021

2019

Citation

[no title info]

[no publisher info]  ·  [no date info]  ·  [no id info]

Card

A Large Card A cool card

A cool description

manual-tag

A Small Card A cool card

Lorem ipsum

manual-tag

Portrait

Manual name

Post Excerpt

Alert

Tags

Float

Figures

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.

Code

const test = "Lorem ipsum dolor sit amet, consectetur adipiscing elit.";

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Nulla facilisi etiam dignissim diam quis. Id aliquet lectus proin nibh nisl condimentum id venenatis a. Tristique magna sit amet purus gravida quis blandit turpis cursus. Ultrices eros in cursus turpis massa tincidunt dui ut ornare. A cras semper auctor neque vitae tempus quam pellentesque nec. At tellus at urna condimentum mattis pellentesque. Ipsum consequat nisl vel pretium. Ultrices mi tempus imperdiet nulla malesuada pellentesque elit eget gravida. Integer vitae justo eget magna fermentum iaculis eu non diam. Mus mauris vitae ultricies leo integer malesuada nunc vel. Leo integer malesuada nunc vel risus. Ornare arcu odio ut sem nulla pharetra. Purus semper eget duis at tellus at urna condimentum. Enim neque volutpat ac tincidunt vitae semper quis lectus.

Grid

Regular

With Markdown images

Square

With figure components

Grid of citations

2024

A genome-scale single cell CRISPRi map oftransgene regulation across human pluripotent stem cell lines

Claudia Feng, Elin Madli Peets, Yan Zhou, Luca Crepaldi, Sunay Usluer, …, Bo Fussing, David Burke, Leopold Parts, Oliver Stegle, Britta Velten

Cold Spring Harbor Laboratory  ·  28 Nov 2024  ·  doi:10.1101/2024.11.28.625833

Guide assignment in single-cell CRISPR screens using crispat

Jana M Braunger, Britta Velten

Bioinformatics  ·  01 Sep 2024  ·  doi:10.1093/bioinformatics/btae535

crispat is a Python framework for assigning cells to guides in pooled single cell CRISPR assays

crispr guide-assignment

In situ analysis of osmolyte mechanisms of proteome thermal stabilization

Monika Pepelnjak, Britta Velten, Nicolas Näpflin, Tatjana von Rosen, Umberto Capasso Palmiero, …, Paolo Arosio, Eilika Weber-Ban, Natalie de Souza, Wolfgang Huber, Paola Picotti

Nature Chemical Biology  ·  29 Feb 2024  ·  doi:10.1038/s41589-024-01568-7

2023

The changing career paths of PhDs and postdocs trained at EMBL

Junyan Lu, Britta Velten, Bernd Klaus, Mauricio Ramm, Wolfgang Huber, Rachel Coulthard-Graf

eLife  ·  23 Nov 2023  ·  doi:10.7554/elife.78706

Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease

Ricardo Omar Ramirez Flores, Jan David Lanzer, Daniel Dimitrov, Britta Velten, Julio Saez-Rodriguez

eLife  ·  22 Nov 2023  ·  doi:10.7554/elife.93161

Principles and challenges of modeling temporal and spatial omics data

Britta Velten, Oliver Stegle

Nature Methods  ·  14 Sep 2023  ·  doi:10.1038/s41592-023-01992-y

FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution

Florin C Walter, Oliver Stegle, Britta Velten

Bioinformatics  ·  11 Apr 2023  ·  doi:10.1093/bioinformatics/btad183

FISHFactor identifies spatial gene expression patterns at subcellular resolution

probabilistic-factor-models spatial-omics

Spatial multiomics map of trophoblast development in early pregnancy

Anna Arutyunyan, Kenny Roberts, Kevin Troulé, Frederick C. K. Wong, Megan A. Sheridan, …, Omer Ali Bayraktar, Ashley Moffett, Oliver Stegle, Margherita Y. Turco, Roser Vento-Tormo

Nature  ·  29 Mar 2023  ·  doi:10.1038/s41586-023-05869-0

2022

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Britta Velten, Jana M. Braunger, Ricard Argelaguet, Damien Arnol, Jakob Wirbel, Danila Bredikhin, Georg Zeller, Oliver Stegle

Nature Methods  ·  13 Jan 2022  ·  doi:10.1038/s41592-021-01343-9

MEFISTO is a unsupervised method to integrate multi-modal data with continuous structures among the samples, e.g. in spatial or temporal data.

multi-modal-data-integration probabilistic-factor-models spatio-temporal-omics

2021

Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes.

Britta Velten, Wolfgang Huber

Biostatistics (Oxford, England)  ·  10 Apr 2021  ·  pmid:31596468

2020

Developmental Gene Expression Differences between Humans and Mammalian Models.

Margarida Cardoso-Moreira, Ioannis Sarropoulos, Britta Velten, Matthew Mort, David N Cooper, Wolfgang Huber, Henrik Kaessmann

Cell reports  ·  27 Oct 2020  ·  pmid:33113372

Survey of ex vivo drug combination effects in chronic lymphocytic leukemia reveals synergistic drug effects and genetic dependencies.

Marina Lukas, Britta Velten, Leopold Sellner, Katarzyna Tomska, Jennifer Hüellein, …, Alexander Jethwa, Hanibal Bohnenberger, Junyan Lu, Wolfgang Huber, Thorsten Zenz

Leukemia  ·  13 May 2020  ·  pmid:32404973

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.

Ricard Argelaguet, Damien Arnol, Danila Bredikhin, Yonatan Deloro, Britta Velten, John C Marioni, Oliver Stegle

Genome biology  ·  11 May 2020  ·  pmid:32393329

Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions.

Ignacio L Ibarra, Nele M Hollmann, Bernd Klaus, Sandra Augsten, Britta Velten, Janosch Hennig, Judith B Zaugg

Nature communications  ·  08 Jan 2020  ·  pmid:31913281

2019

Gene expression across mammalian organ development.

Margarida Cardoso-Moreira, Jean Halbert, Delphine Valloton, Britta Velten, Chunyan Chen, …, Wolfgang Huber, Julie Baker, Simon Anders, Yong E Zhang, Henrik Kaessmann

Nature  ·  26 Jun 2019  ·  pmid:31243369

2018

Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets

Ricard Argelaguet, Britta Velten, Damien Arnol, Sascha Dietrich, Thorsten Zenz, John C Marioni, Florian Buettner, Wolfgang Huber, Oliver Stegle

Molecular Systems Biology  ·  18 Jun 2018  ·  doi:10.15252/msb.20178124

MOFA is a factor analysis model that provides a general framework for the integration of multi-omic data sets in an unsupervised fashion

multi-modal-data-integration probabilistic-factor-models multi-omics

2017

Drug-perturbation-based stratification of blood cancer.

Sascha Dietrich, Małgorzata Oleś, Junyan Lu, Leopold Sellner, Simon Anders, …, Jan Dürig, Ingo Ringshausen, Marc Zapatka, Wolfgang Huber, Thorsten Zenz

The Journal of clinical investigation  ·  11 Dec 2017  ·  pmid:29227286

Grid of blog posts

2023

Example post 3

john-doe February 23, 2023 April 16, 2025

biology medicine

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

2021

Example post 2

jane-smith September 30, 2021 April 16, 2025

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

2019

Example post 1

sarah-johnson January 07, 2019 April 16, 2025

biology medicine big-data

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Cols

Text

Images

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

Code

const test = "Lorem ipsum dolor sit amet";

const test = "Lorem ipsum dolor sit amet";

const test = "Lorem ipsum dolor sit amet";

Search

Site Search