Selected Scientific Papers Featuring NGX Bio Collaboration

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

  • High-throughput method to survey adaptive mutations in laboratory evolution
  • Isolation of thousands of independent single adaptive events genome-wide
  • Bulk fitness measurements and genotyping generates a genotype-to-fitness map
  • Large sample size allows sensitive detection of fitness differences even within genes

Sandeep Venkataram Barbara Dunn Yuping Li Atish Agarwala JessicaChang Emily R.Ebel Kerry Geiler-Samerotte Lucas Hérissant Jamie R.Blundell Sasha F.Levy Daniel S.Fisher Gavin Sherlock Dmitri A.Petrov
Cell Volume 166, Issue 6, 8 September 2016, Pages 1585-1596.e22

Mapping DNA sequence to transcription factor binding energy in vivo

In this work, we present a strategy for interpreting transcriptional regulatory sequences using in vivo methods (i.e. the massively parallel reporter assay Sort-Seq) to formulate quantitative models that map a transcription factor binding site’s DNA sequence to transcription factor-DNA binding energy. We use these models to predict the binding energies of transcription factor binding sites to within 1 kBT of their measured values.

Stephanie L. Barnes1 Nathan M. Belliveau1 William T. Ireland Justin B. Kinney Rob Phillips
BioRxiv May. 25, 2018, Paper

Whole-genome assembly of the coral reef Pearlscale Pygmy Angelfish (Centropyge vrolikii)

We construct and compare eight candidate assemblies combining overlapping shotgun read data, mate-pair and Chicago libraries and four different genome assemblers to produce a high-quality draft genome of the iconic coral reef Pearlscale Pygmy Angelfish, Centropyge vrolikii (family Pomacanthidae). The best candidate assembly combined all four data types and had a scaffold N50 127.5 times higher than the candidate assembly obtained from shotgun data only.

Iria Fernandez-Silva, James B. Henderson, Luiz A. Rocha & W. Brian Simison
BioRxiv 24 January 2018 Cientific Reports volume 8, Article number: 1498 (2018)

Idiosyncratic Genome Degradation in a Bacterial Endosymbiont of Periodical Cicadas

  • The Hodgkinia genome in all Magicicada exist as complexes of ≥20 circular molecules
  • Together, these circles contain most of the ancestral Hodgkinia gene set
  • The gene dosage of Hodgkinia genes is wildly different in different cicada species
  • The genomic complexity of Hodgkinia is most likely nonadaptive for the host cicada
Matthew A.Campbell Piotr Łukasik Chris Simon John P.McCutcheon
Current Biology November 9, 2017 Volume 27, Issue 22, Pages 3568-3575.e3