Science Advances Cover
6 January 2023, Issue 9, Volume 1
contents
Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9
The cover depicts three sets of 672 bases of barcode sequences, which are encoded onto 7-dimensional cubes. Three overlapping cubes are shown, one for each of the three sequencing platforms: 10X Chromium v3 scRNA-seq, Quartz-seq2, and Drop-seq.
Individual bases are encoded by oriented triangles on each of the 2-dimensional faces of the cube (of which there are 672). I created various designs and in the one chosen by Science Advances, the triangles are 7.5% of their full size (more details).
Science Advances caption: DNA sequencing read translation in high-dimensional space. The cover image was created when 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms were encoded as oriented triangles on the faces of three 7-dimensional cubes. Kijima et al. have developed a software tool that interprets DNA sequences to extract encoded information for additional biological analysis. The tool called, INTERSTELLAR, will facilitate development of sequencing-based experiments and sharing of data analysis pipelines.
We wanted to create some kind of high-dimensional encoding of sequences. For this, I looked back to my collaboration with Max Cooper's for his Ascent video from his Unspoken Words album.
In ascent, we animated multiple 5-dimensional cubes to create a flurries of lines and shapes — a promising direction for encoding sequences.
Browse my gallery of cover designs.
Cell Genomics cover
Our cover on the 11 January 2023 Cell Genomics issue depicts the process of determining the parent-of-origin using differential methylation of alleles at imprinted regions (iDMRs) is imagined as a circuit.
Designed in collaboration with with Carlos Urzua.
Akbari, V. et al. Parent-of-origin detection and chromosome-scale haplotyping using long-read DNA methylation sequencing and Strand-seq (2023) Cell Genomics 3(1).
Browse my gallery of cover designs.
Science Advances cover
My cover design on the 6 January 2023 Science Advances issue depicts DNA sequencing read translation in high-dimensional space. The image showss 672 bases of sequencing barcodes generated by three different single-cell RNA sequencing platforms were encoded as oriented triangles on the faces of three 7-dimensional cubes.
More details about the design.
Kijima, Y. et al. A universal sequencing read interpreter (2023) Science Advances 9
Browse my gallery of cover designs.
Regression modeling of time-to-event data with censoring
If you sit on the sofa for your entire life, you’re running a higher risk of getting heart disease and cancer. —Alex Honnold, American rock climber
In a follow-up to our Survival analysis — time-to-event data and censoring article, we look at how regression can be used to account for additional risk factors in survival analysis.
We explore accelerated failure time regression (AFTR) and the Cox Proportional Hazards model (Cox PH).
Dey, T., Lipsitz, S.R., Cooper, Z., Trinh, Q., Krzywinski, M & Altman, N. (2022) Points of significance: Regression modeling of time-to-event data with censoring. Nature Methods 19.
Music video for Max Cooper's Ascent
My 5-dimensional animation sets the visual stage for Max Cooper's Ascent from the album Unspoken Words. I have previously collaborated with Max on telling a story about infinity for his Yearning for the Infinite album.
I provide a walkthrough the video, describe the animation system I created to generate the frames, and show you all the keyframes
The video recently premiered on YouTube.
Renders of the full scene are available as NFTs.
Gene Cultures exhibit — art at the MIT Museum
I am more than my genome and my genome is more than me.
The MIT Museum reopened at its new location on 2nd October 2022. The new Gene Cultures exhibit featured my visualization of the human genome, which walks through the size and organization of the genome and some of the important structures.
