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Currently available Ensembl schema balls. What is Schemaball?

anopheles gambiae

core 20.2b 21.2b
estgene 20.2b 21.2b
lite 20.2b 21.2b
snp 20.2b 21.2b

caenorhabditis briggsae

core 20.25 21.25
estgene 20.25 21.25

caenorhabditis elegans

core 20.116a 21.116a

danio rerio

core 20.3b 21.3b
est 20.3b 21.3b
estgene 20.3b 21.3b
lite 20.3b 21.3b
snp 20.3b 21.3b

drosophila melanogaster

core 20.3a 21.3a

ensembl

compara 19.2 20.1 21.1
go 20.1 21.1
mart 19.3 20.1 21.1

fugu rubripes

core 20.2b 21.2c
est 21.2c
estgene 21.2c

homo sapiens

core 19.34b 20.34c 21.34d
disease 19.34b 20.34c 21.34d
est 19.34b 20.34c 21.34d
estgene 19.34b 20.34c 21.34d
haplotype 19.34b 20.34c 21.34d
lite 19.34b 20.34c 21.34d
snp 19.34b 20.34c 21.34d
vega 19.34b 20.34c 21.34d

mus musculus

core 19.30 19.32a 20.32b 21.32b
est 19.30 20.32b 21.32b
estgene 19.30 20.32b 21.32b
lite 19.30 19.32a 20.32b 21.32b
snp 19.30 19.32a 20.32b 21.32b

pan troglodytes

core 21.1

rattus norvegicus

core 20.3b 21.3b
est 20.3b 21.3b
estgene 20.3b 21.3b
lite 20.3b 21.3b
snp 20.3b 21.3b

Schema balls for genomic databases hosted by the Ensembl public server (kaka.sanger.ac.uk).

news + thoughts

Annals of Oncology cover

Wed 14-09-2022

My cover design on the 1 September 2022 Annals of Oncology issue shows 570 individual cases of difficult-to-treat cancers. Each case shows the number and type of actionable genomic alterations that were detected and the length of therapies that resulted from the analysis.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
An organic arrangement of 570 individual cases of difficult-to-treat cancers showing genomic changes and therapies. Apperas on Annals of Oncology cover (volume 33, issue 9, 1 September 2022).

Pleasance E et al. Whole-genome and transcriptome analysis enhances precision cancer treatment options (2022) Annals of Oncology 33:939–949.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My Annals of Oncology 570 cancer cohort cover (volume 33, issue 9, 1 September 2022). (more)

Browse my gallery of cover designs.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)

Survival analysis—time-to-event data and censoring

Fri 05-08-2022

Love's the only engine of survival. —L. Cohen

We begin a series on survival analysis in the context of its two key complications: skew (which calls for the use of probability distributions, such as the Weibull, that can accomodate skew) and censoring (required because we almost always fail to observe the event in question for all subjects).

We discuss right, left and interval censoring and how mishandling censoring can lead to bias and loss of sensitivity in tests that probe for differences in survival times.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Nature Methods Points of Significance column: Survival analysis—time-to-event data and censoring. (read)

Dey, T., Lipsitz, S.R., Cooper, Z., Trinh, Q., Krzywinski, M & Altman, N. (2022) Points of significance: Survival analysis—time-to-event data and censoring. Nature Methods 19:906–908.

3,117,275,501 Bases, 0 Gaps

Sun 21-08-2022

See How Scientists Put Together the Complete Human Genome.

My graphic in Scientific American's Graphic Science section in the August 2022 issue shows the full history of the human genome assembly — from its humble shotgun beginnings to the gapless telomere-to-telomere assembly.

Read about the process and methods behind the creation of the graphic.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
3,117,275,501 Bases, 0 Gaps. Text by Clara Moskowitz (Senior Editor), art direction by Jen Christiansen (Senior Graphics Editor), source: UCSC Genome Browser.

See all my Scientific American Graphic Science visualizations.

Anatomy of SARS-Cov-2

Tue 31-05-2022

My poster showing the genome structure and position of mutations on all SARS-CoV-2 variants appears in the March/April 2022 issue of American Scientist.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

An accompanying piece breaks down the anatomy of each genome — by gene and ORF, oriented to emphasize relative differences that are caused by mutations.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
Deadly Genomes: Genome Structure and Size of Harmful Bacteria and Viruses (zoom)

Cancer Cell cover

Sat 23-04-2022

My cover design on the 11 April 2022 Cancer Cell issue depicts depicts cellular heterogeneity as a kaleidoscope generated from immunofluorescence staining of the glial and neuronal markers MBP and NeuN (respectively) in a GBM patient-derived explant.

LeBlanc VG et al. Single-cell landscapes of primary glioblastomas and matched explants and cell lines show variable retention of inter- and intratumor heterogeneity (2022) Cancer Cell 40:379–392.E9.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My Cancer Cell kaleidoscope cover (volume 40, issue 4, 11 April 2022). (more)

Browse my gallery of cover designs.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)

Nature Biotechnology cover

Sat 23-04-2022

My cover design on the 4 April 2022 Nature Biotechnology issue is an impression of a phylogenetic tree of over 200 million sequences.

Konno N et al. Deep distributed computing to reconstruct extremely large lineage trees (2022) Nature Biotechnology 40:566–575.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
My Nature Biotechnology phylogenetic tree cover (volume 40, issue 4, 4 April 2022). (more)

Browse my gallery of cover designs.

Martin Krzywinski @MKrzywinski mkweb.bcgsc.ca
A catalogue of my journal and magazine cover designs. (more)

© 1999–2022 Martin Krzywinski | contact | Canada's Michael Smith Genome Sciences CentreBC Cancer Research CenterBC CancerPHSA