Reading Queue

Overview

A list of papers, blog posts, etc. that I plan to read. I also track a reading list using notion, but I would like to eventually manage them here on my website.

On-deck

• massively parallel… profiling of single cells
• Albis
• Gene Set Enrichment Analysis
• Technology and Biology of Single-Cell RNA Sequencing

The Structured Queue

First Author	Research Lab	Title (maybe shortened)
Roy Fielding	Taylor Lab	Network-based Software Architectures
Reza Nasirigerdeh	UCSC SRL (Dr. Maltzahn)	Data Access Policies for Science
Niki Vazou	UCSD ProgSys (Dr. Jhala)	Liquid Haskell
Muthian Sivathanu	ADSL (Drs. Arpaci-Dusseau)	Database-Aware Storage
Kimberly Keeton		A case for intelligent disks

The Unstructured Queue

Prioritized

• Nectar: Automatic Management of Data and Computation in Datacenters
• Rethinking the application-database interface
• A Trace Query Language for Rule-Based Models
• Storage Systems and I/O for scientific discovery

Model Theory

• Semiring Provenance for First-Order Model Checking
• Finite-Model Theory - A Personal Perspective
• Reflections on Finite Model Theory

Symbolic and solver-aided execution

• Growing Solver-Aided Languages with ROSETTE
• A Lightweight Symbolic Virtual Machine for Solver-Aided Host Languages

Sequencing

• Next-Generation Sequencing Platforms
• DNA Sequencing with chain-terminating inhibitors
• Efficient storage of high-throughput dna sequencing

Gene expression

• highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
• massively parallel single-cell rna-seq for marker-free decomposition of tissues into cell types

Content and Annotation

• Is it time to change the reference genome?

Storage

• ARCHIE
• ArrayBridge
• Proactive Data Containers

Programming Languages

• What is PL Research and how is it useful?
• LiquidTypes