genome biology Archives

18 October 2024 Ensembl logo in white circle on blue and green background

Ensembl 113 and Ensembl Genomes 60 have been released

Ensembl 113 brings major gene and regulatory feature annotation updates in Homo sapiens (human) and Mus musculus (mouse).

2024

updates-from-data-resources

11 March 2024

Casting new light on gene regulation in development

Science & Technology New research from EMBL Heidelberg shows how cells in developing embryos undergo a major shift in the way they regulate gene expression as they mature and differentiate.

2024

sciencescience-technology

22 November 2023 Oliver Stegle passionately drawing work-related content with a green pen on a whiteboard. On the whiteboard, there are coordinates and equations, such as “n=2”.

Oliver Stegle passionately drawing work-related content with a green pen on a whiteboard. On the whiteboard, there are coordinates and equations, such as “n=2”.

How AI shapes the life sciences: an interview with Oliver Stegle

Lab MattersPeople & Perspectives EMBL scientist Oliver Stegle explains how AI-based tools have the potential to transform our ability to better understand the complexity of life and how these tools will shape the future of life science exploration.

2023

lab-matterspeople-perspectives

25 July 2023 Ensembl logo in white circle on blue and green background

Ensembl Bacteria releases new annotation for all its genomes

Ensembl 110 and Ensembl Genomes 57 have introduced in-house prokaryotic gene annotation across genomes available in Ensembl Bacteria. Since its inception, Ensembl Bacteria has imported user-submitted annotations from the International Nucleotide Sequence Database Collaboration (INSDC) for…

2023

updates-from-data-resources

24 July 2023 A stylised heart rhythm created using a DNA strand is superimposed on the image of a human heart. Two inset images show an artistic illustration of gene editing and a fluorescent microscopy image of cardiomyocytes, respectively.

A stylised heart rhythm created using a DNA strand is superimposed on the image of a human heart. Two inset images show an artistic illustration of gene editing and a fluorescent microscopy image of cardiomyocytes, respectively.

New therapies to improve cardiovascular health

Science & Technology EMBL researchers have made new strides into understanding and reversing genetic defects that underlie familial heart disease.

2023

sciencescience-technology

18 July 2023

refget v2.0 links the hidden dictionaries of DNA

The GA4GH standard refget quietly helps decipher millions of genomes sequenced worldwide, and it just got better.

2023

technology-and-innovation

14 July 2023 A close-up of the flow chamber of an ICS machine, with a scientist’s hand in the foreground.

The power of cell sorting: understanding heart disease, phase separation, plankton, and more

Science & Technology EMBL researchers use a new cell sorting technology to gain new insights into cellular function in health and disease, as well as for other innovative applications.

2023

sciencescience-technology

22 March 2023 Artistic representation that features a long, winding helix joining together a doughnut-figure to a small shaggy ball to indicate the connections long-read sequencing can make about DNA mutations.

Artistic representation that features a long, winding helix joining together a doughnut-figure to a small shaggy ball to indicate the connections long-read sequencing can make about DNA mutations.

The ‘long read’ for cancer

Using Oxford Nanopore long-read sequencing, EMBL scientists sequenced a primary childhood brain tumour known as a medulloblastoma, uncovering a novel complex mutation pattern.

2023

science

6 March 2023 Graphic on blue background showing lots of species icons and graphic representations of genomic data

Open data for biodiversity: an EMBL-EBI 2022 round-up

As major biodiversity projects ramp up, EMBL-EBI enables genomic data sharing for all species.

2023

perspectivesscience

17 November 2022 A graphic showing the logos of EMBL and the University of Malta

EMBL builds on links with Malta

EMBL deepens scientific collaboration, opening the door for greater engagement and opportunities for Malta’s life science community

2022

events

4 August 2022 An illustration provides representation of fingers hovering over a cell phone

Zooming in to get the full picture

Science & Technology EMBL and UW researchers plus additional collaborators have constructed a complete map of fruit fly embryonic development using machine learning. This research is foundational to better understanding overall embryo development in other species, including humans.

2022

sciencescience-technology

8 June 2022 The AfricaBP logo and EMBL logo on a banner with memorandum of understanding written underneath

Supporting the African BioGenome Project to build bioinformatics capacity

ConnectionsLab Matters The African BioGenome Project and EMBL have signed a Memorandum of Understanding to support each other in building genomics and bioinformatics capacity across Africa

2022

announcementsconnectionslab-matters

31 May 2022 DNA sequencing data in the background with waves to indicate neural networks. Chromosomes are found in various parts of the image and in circles are different gene symbols.

DNA sequencing data in the background with waves to indicate neural networks. Chromosomes are found in various parts of the image and in circles are different gene symbols.

A machine learning approach for allocating gene function

Science & Technology Researchers in the Ensembl team are making the most of machine learning methods to speed up genome annotation pipelines

2022

sciencescience-technologytechnology-and-innovation

25 February 2022 Three colourful overlapping circles arranged in a row, a fruit-fly embryo being visible within each. Small circles within the embryos represent cell lineages.

Three colourful overlapping circles arranged in a row, a fruit-fly embryo being visible within each. Small circles within the embryos represent cell lineages.

Converging lenses on embryo development

Science & Technology Researchers from the Furlong group at EMBL have come up with a way to observe the development of fruit-fly embryos simultaneously at the genetic and cellular levels, generating a high-resolution and integrated view of how different cell lineages form.

2022

sciencescience-technology

21 January 2022 The cross-section of a cell expressing a green fluorescently tagged protein and illuminated by a blue laser is visible in the foreground, surrounded by a vortex of cells

The cross-section of a cell expressing a green fluorescently tagged protein and illuminated by a blue laser is visible in the foreground, surrounded by a vortex of cells

Cell sorting enters a new dimension

Science & Technology EMBL researchers, in collaboration with BD Biosciences, have demonstrated a new technology that allows rapid image-based sorting of cells. The new technology represents a major upgrade to flow cytometry and has applications in diverse life science fields.

2022

sciencescience-technology

21 January 2022 The Earth with a DNA structure and sequencing information in the background

The Earth Biogenome Project: on track and ready to ramp up

Science & Technology On track to reach an ambitious goal of 3,000 genomes sequenced by the end of 2022, what’s next for the Earth Biogenome Project?

2022

announcementssciencescience-technology

9 December 2021 Portrait photo of Eileen Furlong against blue-green background.

Eileen Furlong honoured with Leibniz Prize

EMBL AnnouncementsLab Matters EMBL Senior Scientist and Head of the Genome Biology Unit is among the researchers honoured for outstanding work by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG).

2021

embl-announcementslab-matters

25 November 2021 Female scientist in front of a background of green plants

Welcome: Maria Zimmermann-Kogadeeva

Lab MattersPeople & Perspectives Maria Zimmermann-Kogadeeva is one of EMBL’s newest group leaders and a computational biologist whose research group applies computational modelling to better understand the metabolism of gut bacteria and their potential to have far-reaching impacts on other organs.

2021

lab-matterspeople-perspectives

13 October 2021 Illustration of a community of bacteria. Pills represent an antibiotic that can be used to treat an infection, and a second drug that could protect many gut bacteria from antibiotics.

Illustration of a community of bacteria. Pills represent an antibiotic that can be used to treat an infection, and a second drug that could protect many gut bacteria from antibiotics.

Tackling the collateral damage from antibiotics

Science & Technology Researchers from EMBL’s Typas group and collaborators have analysed the effects of 144 antibiotics on the wellbeing of gut microbes. The study improves our understanding of antibiotics’ side effects and suggests a new approach to mitigating the adverse effects of antibiotics therapy on gut…

2021

sciencescience-technology

7 July 2021 Fluorescence microscopy image of a cell and symbolic representation of a protein network.

New insights into Salmonella’s survival strategies

Science & Technology Research in the Typas group uncovers new details of the strategies Salmonella uses to survive in infected cells.

2021

sciencescience-technology

5 July 2021

Welcome: Sarah Dyer

Lab MattersPeople & Perspectives EMBL welcomes Sarah Dyer, the new Non-Vertebrate Genomics Team Leader at EMBL-EBI.

2021

lab-matterspeople-perspectives

18 June 2021 woman with long brown hair is smiling in front of shrubbery outside

Food safety, antibiotics, and a shrinking planet

People & Perspectives After work in antimicrobial resistance, EMBL postdoc Laura Carroll is using machine learning for next-gen antibiotic development.

2021

people-perspectivesscience

28 April 2021 Genome assemblies

Piecing together the best reference genome

Science & Technology Researchers reveal the best technology for assembling reference genomes.

2021

sciencescience-technology

26 February 2021 Woman with long brown hair stands in front of snow scene with arms crossed in front of her.

Welcome: Sinem Saka

Lab MattersPeople & Perspectives As one of EMBL’s newest group leaders, Sinem Saka will combine multiple technologies, such as microscopy and single-cell omics, to solve biological puzzles.

2021

lab-matterspeople-perspectives

16 February 2021 Microscopy images of coronavirus-infected cells in blue and red, arranged on a clockface. Illustrations of virus particles.

Finding coronavirus’s helper proteins

Science & Technology A team of EMBL scientists and colleagues have analysed how the novel coronavirus affects proteins in human cells. They identified several human proteins as potential drug targets to prevent viral replication.

2021

sciencescience-technology

9 December 2020 Illustration of a rod-shaped bacterial cell, superimposed on a red and blue background.

Heating proteins to understand how genes work

Science & Technology A new paper from EMBL’s Savitski team and Typas group describes their work on E. coli and how it brings a greater understanding of the way genes function and interact.

2020

sciencescience-technology

19 August 2020 An embryo of the fruit fly Drosophila.

Predicting how gene expression varies

Science & Technology Discoveries at EMBL will help researchers to interpret one of the most common types of experiments in genomics and medical studies.

2020

sciencescience-technology

1 June 2020 An illustration of single-cell RNA sequencing (scRNA-seq)

Enabling functional genomics studies in individual cells

Science & Technology Scientists at EMBL Heidelberg have developed a new method, called Targeted Perturb-seq (TAP-seq), which increases the scale and precision of functional genomics CRISPR–Cas9 screens by orders of magnitude. Their method overcomes limitations in previous applications of single-cell RNA sequencing,…

2020

sciencescience-technology

23 April 2020 Key visual for the EMBO | EMBL symposium ‘The Four-Dimensional Genome’

EMBL hosts its first virtual conference

Lab Matters The virtual EMBO | EMBL symposium ‘The Four-Dimensional Genome’ brought together 470 participants. Here, Jürgen Deka, Head of External Scientific Training, discusses how he and his team overcame the organisational challenges.

2020

eventslab-matters

5 March 2020

New insights into gene regulation

Science & Technology EMBL researchers investigate the role of a histone protein in regulating gene expression

2020

sciencescience-technology

11 March 2019 A visualisation of a membraneless organelle in the green-yellow style of the data presented in the Nature Communications paper

ATP affects proteome-wide solubility

Science & Technology Scientists develop technology to measure how ATP concentration affects protein solubility in cells

2019

sciencescience-technology

23 May 2018 As a cell prepares to divide, the chromosomes (shown here in pink) condense, becoming more tightly coiled and easier to observe under the microscope. The faint structure in the centre is a cell nucleus in which the chromosomes are in their usual decondensed state.

As a cell prepares to divide, the chromosomes (shown here in pink) condense, becoming more tightly coiled and easier to observe under the microscope. The faint structure in the centre is a cell nucleus in which the chromosomes are in their usual decondensed state.

Exploring genetic variation

Science & Technology EMBL group leader Jan Korbel reflects on his scientific origins and current research

2018

sciencescience-technology

15 March 2018

How drugs affect the life and death of proteins

Science & Technology Scientists at EMBL and Cellzome develop technology to monitor the effects of drug treatments on protein degradation and synthesis

2018

sciencescience-technology

15 February 2018 Architecture dependent turnover of the nuclear pore subunits. Top row shows the nuclear pore subunits seen from top, bottom row shows subunits of the nuclear pore cut in half.

Architecture dependent turnover of the nuclear pore subunits. Top row shows the nuclear pore subunits seen from top, bottom row shows subunits of the nuclear pore cut in half.

Life and death of proteins

Science & Technology EMBL scientists create a turnover catalogue of almost 10.000 proteins from primary cells

2018

sciencescience-technology

9 February 2018 Arnaud Krebs, EMBL’s new group leader studies how gene expression is controlled

Welcome: Arnaud Krebs

People & Perspectives EMBL’s new group leader studies how gene expression is controlled

2018

people-perspectivesscience

30 January 2018 Enhancer activity (green) and promoter activity (purple) in the same regulatory element. IMAGE: EMBL / Eileen Furlong

Multipurpose enhancers and promoters in embryonic development

Science & Technology EMBL scientists show that some promoters can act as enhancers and vice versa

2018

sciencescience-technology

20 December 2017 The most curious genomes in Ensebl. Credit: Spencer Phillips/EMBL-EBI

Curious genomes

Science & Technology What are the strangest genomes in EMBL-EBI's Ensembl?

2017

sciencescience-technology

28 August 2017

Bridging excellence: EMBL and Stanford’s Alliance

Connections Lars Steinmetz. Director of the Life Science Alliance, reflects on the EMBL|Stanford initiative

2017

connectionsevents

25 April 2017

Embryos use ancient viral DNA

Science & Technology EMBL scientists detect important function of genetic sequence our ancestors assimilated from a virus

2017

sciencescience-technology

6 April 2017

Blood stem cell differentiation is continuous

Science & Technology Study by EMBL and DKFZ researchers means origins of myeloid leukaemias may need rethinking

2017

sciencescience-technology

2 February 2011

The human genome’s breaking points

A detailed analysis of data from 185 human genomes sequenced in the course of the 1000 Genomes Project, by scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, in collaboration with researchers at the Wellcome Trust Sanger Institute in Cambridge, UK, as well as the…

2011

science

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genome biology

EMBLetc.

Issue 101 Winter 2023

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