Divij Mathew

Nov 26, 2024 | nature.com | Zhaojun Zhang |Divij Mathew |Tristan L. Lim |Kaishu Mason |Sijia Huang |E. John Wherry | +5 more

Data integration to align cells across batches has become a cornerstone of single-cell data analysis, critically affecting downstream results. Currently, there are no guidelines for when the biological differences between samples are separable from batch effects. Here we show that current paradigms for single-cell data integration remove biologically meaningful variation and introduce distortion. We present a statistical model and computationally scalable algorithm, CellANOVA (cell state space analysis of variance), that harnesses experimental design to explicitly recover biological signals that are erased during single-cell data integration. CellANOVA uses a ‘pool-of-controls’ design concept, applicable across diverse settings, to separate unwanted variation from biological variation of interest and allow the recovery of subtle biological signals. We apply CellANOVA to diverse contexts and validate the recovered biological signals by orthogonal assays. In particular, we show that CellANOVA is effective in the challenging case of single-cell and single-nucleus data integration, where it recovers subtle biological signals that can be validated and replicated by external data. A statistical framework quantifies single-cell batch variation and recovers meaningful biological signals.

Jun 20, 2024 | science.org | Jaroslav Zak |Divij Mathew |Andrew E. Whiteley

In the Perspective “Phylogenies of Methylomes” (14 May 2010, p. 837), the figure incorrectly noted evidence of Dnmt3 in Volvox carteri (green alga). This error was introduced at the production stage; it has now been corrected and does not alter the text or conclusions of the Perspective. Information & AuthorsInformationPublished In ScienceVolume 384 | Issue 670221 June 2024CopyrightCopyright ©, American Association for the Advancement of Science.

Jun 20, 2024 | science.org | Jaroslav Zak |Divij Mathew |Andrew E. Whiteley |Rana Hussein

Editor’s summaryThe protein complex photosystem II brings together a large number of cofactors and pigments within a scaffold that allows for movement of water and protons, which are key to the water oxidation chemistry performed at the oxygen-evolving center during photosynthesis. However, it is often challenging to identify water molecules, especially protons, in x-ray crystal structures. Hussein et al.

Jun 20, 2024 | science.org | Jaroslav Zak |Divij Mathew |Andrew E. Whiteley |Hui Wang

InformationPublished In ScienceVolume 384 | Issue 670221 June 2024CopyrightCopyright © 2024 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Article versionsSubmission historyPublished in print: 21 June 2024PermissionsRequest permissions for this article. AuthorsAffiliationsHui WangState Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China.

Jun 20, 2024 | science.org | Jaroslav Zak |Divij Mathew |Andrew E. Whiteley |Wei Li

Editor’s summaryBoth engineered and natural structures can exhibit directional liquid transport that is driven by the specific patterning of the surface. Yang et al. drew inspiration from the Crassula muscosa plant, in which the direction of fluid flow is determined by the shape and orientation of the structured fins, which can vary from stem to stem, and by the surface tension of the fluid.