742 citations · 1.5k across the 10 of their papers we have counts for
11 papers
DP-CGAN: Differentially Private Synthetic Data and Label Generation
Reihaneh Torkzadehmahani, Peter Kairouz, Benedict Paten
Generative Adversarial Networks (GANs) are one of the well-known models to generate synthetic data including images, especially for research communities that cannot use original se…
Mapping the Human Body at Cellular Resolution -- The NIH Common Fund Human BioMolecular Atlas Program
Michael P Snyder, Shin Lin, Amanda Posgai +22
Transformative technologies are enabling the construction of three dimensional (3D) maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years,…
The Human Cell Atlas White Paper
Aviv Regev, Sarah Teichmann, Orit Rozenblatt-Rosen +78
The Human Cell Atlas (HCA) will be made up of comprehensive reference maps of all human cells - the fundamental units of life - as a basis for understanding fundamental human biolo…
Canonical, Stable, General Mapping using Context Schemes
Adam Novak, Yohei Rosen, David Haussler +1
Motivation: Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. Results: We introduce context sch…
Mapping to a Reference Genome Structure
Benedict Paten, Adam Novak, David Haussler
To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to…
Comparative Assembly Hubs: Web Accessible Browsers for Comparative Genomics
Ngan Nguyen, Glenn Hickey, Brian J. Raney +6
We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment i…
Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs
Daniel R. Zerbino, Tracy Ballinger, Benedict Paten +2
The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are r…
A Unifying Model of Genome Evolution Under Parsimony
Benedict Paten, Daniel R. Zerbino, Glenn Hickey +1
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutio…
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov +88
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished g…
Accurate reconstruction of insertion-deletion histories by statistical phylogenetics
Oscar Westesson, Gerton Lunter, Benedict Paten +1
The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view…
Phylogenetic automata, pruning, and multiple alignment
Oscar Westesson, Gerton Lunter, Benedict Paten +1
We present an extension of Felsenstein's algorithm to indel models defined on entire sequences, without the need to condition on one multiple alignment. The algorithm makes use of…