Lior Pachter
@lpachter.bsky.social
Bren Professor of Computational Biology @Caltech.edu. Blog at http://liorpachter.wordpress.com. Posts represent my views, not my employer's. #methodsmatter
Report from 1992 in Nature on the cDNA controversy:
www.nature.com/articles/356...
www.nature.com/articles/356...
www.nature.com
November 9, 2025 at 9:41 PM
Report from 1992 in Nature on the cDNA controversy:
www.nature.com/articles/356...
www.nature.com/articles/356...
Worth reading Baltimore's report at the time: genome.gov/sites/defaul...
"Consideration should be given to... cDNA maps. The Committee recognizes the many challenges... it is not yet known to what extent eukaryotic cells rely on control at the transcriptional level."
"Consideration should be given to... cDNA maps. The Committee recognizes the many challenges... it is not yet known to what extent eukaryotic cells rely on control at the transcriptional level."
www.genome.gov
November 9, 2025 at 9:41 PM
Worth reading Baltimore's report at the time: genome.gov/sites/defaul...
"Consideration should be given to... cDNA maps. The Committee recognizes the many challenges... it is not yet known to what extent eukaryotic cells rely on control at the transcriptional level."
"Consideration should be given to... cDNA maps. The Committee recognizes the many challenges... it is not yet known to what extent eukaryotic cells rely on control at the transcriptional level."
Watson's objection to cDNA sequencing was that the function of the genes was not yet known 👀
A strange take considering he did not have that objection to working on the structure of DNA when the function of DNA was not known.
Venter's paper on ESTs: www.science.org/doi/10.1126/...
A strange take considering he did not have that objection to working on the structure of DNA when the function of DNA was not known.
Venter's paper on ESTs: www.science.org/doi/10.1126/...
November 9, 2025 at 9:41 PM
Watson's objection to cDNA sequencing was that the function of the genes was not yet known 👀
A strange take considering he did not have that objection to working on the structure of DNA when the function of DNA was not known.
Venter's paper on ESTs: www.science.org/doi/10.1126/...
A strange take considering he did not have that objection to working on the structure of DNA when the function of DNA was not known.
Venter's paper on ESTs: www.science.org/doi/10.1126/...
Brilliant work by Joseph Rich and Conrad Oakes working out the math and implementing wompwomp. It has been submitted to @bioconductor.bsky.social and in the future we may also implement it in Python to facilitate usage with single-cell genomics packages. Any feedback will be appreciated. Thx!
September 5, 2025 at 12:20 PM
Brilliant work by Joseph Rich and Conrad Oakes working out the math and implementing wompwomp. It has been submitted to @bioconductor.bsky.social and in the future we may also implement it in Python to facilitate usage with single-cell genomics packages. Any feedback will be appreciated. Thx!
he underlying optimization problems are NP-hard, but for many visualization tasks can probably be solved optimally. It was fun returning to Bryant and Huson's NeighborNet as a good heuristic, but there is certainly room for improvement.
September 5, 2025 at 12:20 PM
he underlying optimization problems are NP-hard, but for many visualization tasks can probably be solved optimally. It was fun returning to Bryant and Huson's NeighborNet as a good heuristic, but there is certainly room for improvement.
The advantage of organizing with wompwomp is evident in the clarity one sees when tracing, say, the Lannisters vs. Westeros
September 5, 2025 at 12:20 PM
The advantage of organizing with wompwomp is evident in the clarity one sees when tracing, say, the Lannisters vs. Westeros
The improvements produced by wompwomp are evident in the Game of Thrones dataset displayed at the opening of this thread. To the left is the alluvial plot without wompwomp, to the right with wompwomp.
September 5, 2025 at 12:20 PM
The improvements produced by wompwomp are evident in the Game of Thrones dataset displayed at the opening of this thread. To the left is the alluvial plot without wompwomp, to the right with wompwomp.
The underlying optimization questions turned out to be really interesting. The methods underlying wompwomp are described in the accompanying preprint on @cscg-bot.bsky.social. arxiv.org/abs/2509.03761
Optimizing alluvial plots
Alluvial plots can be effective for visualization of multivariate data, but rely on ordering of alluvia that can be non-trivial to arrange. We formulate two optimization problems that formalize the ch...
arxiv.org
September 5, 2025 at 12:20 PM
The underlying optimization questions turned out to be really interesting. The methods underlying wompwomp are described in the accompanying preprint on @cscg-bot.bsky.social. arxiv.org/abs/2509.03761
Work on wompwomp was motivated by plots made for this paper, where we first implemented a naïve approach to optimizing an alluvial plot (Fig. 1 panel D)
bsky.app/profile/alii...
bsky.app/profile/alii...
Required reading by @lpachter.bsky.social. Seurat vs Scanpy processing, and how package versions affect your analysis 👀 www.biorxiv.org/content/10.1...
The impact of package selection and versioning on single-cell RNA-seq analysis
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
www.biorxiv.org
September 5, 2025 at 12:20 PM
Work on wompwomp was motivated by plots made for this paper, where we first implemented a naïve approach to optimizing an alluvial plot (Fig. 1 panel D)
bsky.app/profile/alii...
bsky.app/profile/alii...
wompwomp sorts columns and blocks within columns to best reveal structure in data. For instance, this is a comparison of clustering algorithms viewed in a randomly organized alluvial plot, fixed columns (only blocks sorted), and fully optimized with wompwomp.
September 5, 2025 at 12:20 PM
wompwomp sorts columns and blocks within columns to best reveal structure in data. For instance, this is a comparison of clustering algorithms viewed in a randomly organized alluvial plot, fixed columns (only blocks sorted), and fully optimized with wompwomp.