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Pachter Lab

Research themes and selected papers

  • Transcriptional dynamics with the chemical master equation: Approximate steady-state joint distribution solutions for a chemical master equation two-species model of the life cycle of RNA using neural networks (preprint).
  • Software tools for genomics: gget for efficient querying of genomic reference databases (preprint) and ffq for metadata retrieval from sequence databases (preprint).
  • Cell type and state: Isoform cell-type specificity in the mouse primary motor cortex (paper); Cell types and states in the jellyfish Clytia hemisphaerica (paper).
  • Single-cell genomics technology: ClickTag multiplexing of single-cell RNA-seq samples using a one-pot, two-step chemical cross-linking reaction to barcode samples (paper).
  • Single-cell genomics analysis: Examination of the foundations of RNA velocity (preprint); Benchmarking of count normalization methods (preprint); Mechanistic models for count normalization (preprint).
  • Spatial transcriptomics: Review and analysis of the origins of the field (paper / supplemental book).
  • Open-source bioinstrumentation: Low-cost hardware for biomedical applications, including the poseidon syringe pump system (paper) and the colosseum fraction collector (paper).
  • Reference-free genomics: Genome-wide association studies using k-mers (paper).
  • Pseudoalignment: Introduction of a new paradigm for quantification of targets from short read sequencing using read assignment instead of read alignment (kallisto paper).
  • Differential expression methods: Methods for differential analysis of genes and isoforms (sleuth paper, Cuffdiff).
  • RNA structure: Sequencing based characterization of RNA structure with SHAPE-seq (assay development, methods paper).
  • Transcript assembly and quantification of bulk RNA-seq data: Software for spliced short read alignment (Tophat paper),processing of bulk RNA-seq data (Cufflinks paper, eXpress paper), and a framework for studying isoform switching during cell differentiation (paper).
  • Phylogenetics: Insights into the neighbor-joining algorithm (paper); Theory of the neighbor-net algorithm (paper); A unifying framework for tree metric theorems (paper).
  • Algebraic statistics: Book on algebraic statistics for computational biology; Tropical geometry of statistical models (paper).
  • Microbial genomics and metagenomics: Bioinformatics for whole-genome shotgun sequencing of communities (paper); the asthmatic microbiome (paper).
  • Genome alignment: genomic sequence alignment (AVID paper) and multiple alignment (MAVID paper, FSA paper).
  • Genome sequencing and annotation: Mouse genome (paper), rat genome (paper), chicken genome (paper), human genome (ENCODE pilot paper), fly genome (paper); De novo annotation (SLAM paper).
  • Combinatorics: Pebbling graphs (paper); Counting tilings (paper).