Evidence map›Paper›PMID 28545559›Full record

ArticleGenome biology2017

Millstone: software for multiplex microbial genome analysis and engineering.

Daniel B Goodman, Gleb Kuznetsov, Marc J Lajoie, Brian W Ahern, Michael G Napolitano, Kevin Y Chen, Changping Chen, George M Church

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. High-throughput functional variant screens via in vivo production of single-stranded DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021
    Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Daniel B GoodmanDepartment of Genetics, Harvard Medical School, Boston, MA, USA.
Gleb KuznetsovDepartment of Genetics, Harvard Medical School, Boston, MA, USA.
Marc J LajoieDepartment of Genetics, Harvard Medical School, Boston, MA, USA.
Brian W AhernMassachusetts Institute of Technology, Cambridge, MA, USA.
Michael G NapolitanoDepartment of Genetics, Harvard Medical School, Boston, MA, USA.
Kevin Y ChenMassachusetts Institute of Technology, Cambridge, MA, USA.
Changping ChenMassachusetts Institute of Technology, Cambridge, MA, USA.
George M ChurchDepartment of Genetics, Harvard Medical School, Boston, MA, USA. gchurch@genetics.med.harvard.edu.

Funding

MOLECULAR BIOPHYSICS TRAINING GRANTT32GM008313 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI MURTHY, VENKATESH N · 1989 to 2023
$14.6M
NIGMS NIH HHS T32 GM008313
6 · The paper itself

Abstract

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Indexed as

GenomicsSoftwareComputational BiologyGenomeGenome, MicrobialGenotypeHigh-Throughput Nucleotide SequencingInternetOligonucleotidesOligonucleotidesBioinformaticsExperimental evolutionGenome engineeringLaboratory evolutionMicrobial evolutionSynthetic biologySynthetic genomicsWhole-genome sequencing

Identifiers

PMID28545559
PMCPMC5445467

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.