Anindita Basu

Bio: Anindita Basu is an academic researcher from University of Chicago. The author has contributed to research in topics: Medicine & Biology. The author has an hindex of 17, co-authored 41 publications receiving 9259 citations. Previous affiliations of Anindita Basu include University of Pennsylvania & Broad Institute.

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Abstract: Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. VIDEO ABSTRACT.

Massively-parallel single nucleus RNA-seq with DroNc-seq

Abstract: Single-nucleus RNA sequencing (sNuc-seq) profiles RNA from tissues that are preserved or cannot be dissociated, but it does not provide high throughput. Here, we develop DroNc-seq: massively parallel sNuc-seq with droplet technology. We profile 39,111 nuclei from mouse and human archived brain samples to demonstrate sensitive, efficient, and unbiased classification of cell types, paving the way for systematic charting of cell atlases.

Structure-property relationships from universal signatures of plasticity in disordered solids

Abstract: When deformed beyond their elastic limits, crystalline solids flow plastically via particle rearrangements localized around structural defects. Disordered solids also flow, but without obvious structural defects. We link structure to plasticity in disordered solids via a microscopic structural quantity, “softness,” designed by machine learning to be maximally predictive of rearrangements. Experimental results and computations enabled us to measure the spatial correlations and strain response of softness, as well as two measures of plasticity: the size of rearrangements and the yield strain. All four quantities maintained remarkable commonality in their values for disordered packings of objects ranging from atoms to grains, spanning seven orders of magnitude in diameter and 13 orders of magnitude in elastic modulus. These commonalities link the spatial correlations and strain response of softness to rearrangement size and yield strain, respectively.

Microfluidic rheology of soft colloids above and below jamming.

Abstract: The rheology near jamming of a suspension of soft colloidal spheres is studied using a custom microfluidic rheometer that provides the stress versus strain rate over many decades. We find non-Newtonian behavior below the jamming concentration and yield-stress behavior above it. The data may be collapsed onto two branches with critical scaling exponents that agree with expectations based on Hertzian contacts and viscous drag. These results support the conclusion that jamming is similar to a critical phase transition, but with interaction-dependent exponents.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Integrating single-cell transcriptomic data across different conditions, technologies, and species.

Abstract: Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments representing a single condition, technology, or species to discover and define cellular phenotypes. However, identifying subpopulations of cells that are present across multiple data sets remains challenging. Here, we introduce an analytical strategy for integrating scRNA-seq data sets based on common sources of variation, enabling the identification of shared populations across data sets and downstream comparative analysis. We apply this approach, implemented in our R toolkit Seurat (http://satijalab.org/seurat/), to align scRNA-seq data sets of peripheral blood mononuclear cells under resting and stimulated conditions, hematopoietic progenitors sequenced using two profiling technologies, and pancreatic cell 'atlases' generated from human and mouse islets. In each case, we learn distinct or transitional cell states jointly across data sets, while boosting statistical power through integrated analysis. Our approach facilitates general comparisons of scRNA-seq data sets, potentially deepening our understanding of how distinct cell states respond to perturbation, disease, and evolution.

스크린 위의 삶 = Life on the screen : identity in the age of the internet

Abstract: From the Publisher: A Question of Identity Life on the Screen is a fascinating and wide-ranging investigation of the impact of computers and networking on society, peoples' perceptions of themselves, and the individual's relationship to machines. Sherry Turkle, a Professor of the Sociology of Science at MIT and a licensed psychologist, uses Internet MUDs (multi-user domains, or in older gaming parlance multi-user dungeons) as a launching pad for explorations of software design, user interfaces, simulation, artificial intelligence, artificial life, agents, "bots," virtual reality, and "the on-line way of life." Turkle's discussion of postmodernism is particularly enlightening. She shows how postmodern concepts in art, architecture, and ethics are related to concrete topics much closer to home, for example AI research (Minsky's "Society of Mind") and even MUDs (exemplified by students with X-window terminals who are doing homework in one window and simultaneously playing out several different roles in the same MUD in other windows). Those of you who have (like me) been turned off by the shallow, pretentious, meaningless paintings and sculptures that litter our museums of modern art may have a different perspective after hearing what Turkle has to say. This is a psychoanalytical book, not a technical one. However, software developers and engineers will find it highly accessible because of the depth of the author's technical understanding and credibility. Unlike most other authors in this genre, Turkle does not constantly jar the technically-literate reader with blatant errors or bogus assertions about how things work. Although I personally don't have time or patience for MUDs,view most of AI as snake-oil, and abhor postmodern architecture, I thought the time spent reading this book was an extremely good investment.

Massively parallel digital transcriptional profiling of single cells

Abstract: Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3′ mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system’s technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system’s ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients. Single-cell gene expression analysis is challenging. This work describes a new droplet-based single cell RNA-seq platform capable of processing tens of thousands of cells across 8 independent samples in minutes, and demonstrates cellular subtypes and host–donor chimerism in transplant patients.