Application of a systems approach to study developmental gene regulation.

Joshua W K Ho

Abstract readReview

In one paragraph

Review in Biophysical reviews, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it

0cells of the map it votes in

2citing papers in PubMed

0.1field-weighted citation impact, top 49% of its field

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

2 citing papers in PubMed, 2 citations in OpenAlex.

The evolution of Biophysical Reviews.Biophysical reviews · 2016
Article
How difficult is inference of mammalian causal gene regulatory networks?PloS one · 2014
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

1 author at 1 institution in 1 country.

Joshua W K HoDivision of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA. jwho@rics.bwh.harvard.edu.

Harvard University · US

Funding

SysCODE Interdisciplinary postdoctoral Training Grant (8 of 10)RL9RL9EB008539 · NIBIB · BRIGHAM AND WOMEN'S HOSPITAL · PI BONVENTRE, JOSEPH VINCENT · 2007 to 2011

$1.2M

NIBIB NIH HHS RL9 EB008539

6 · The paper itself

Abstract

All cells in a multicellular organism contain the same genome, yet different cell types express different sets of genes. Recent advances in high throughput genomic technologies have opened up new opportunities to understand the gene regulatory network in diverse cell types in a genome-wide manner. Here, I discuss recent advances in experimental and computational approaches for the study of gene regulation in embryonic development from a systems perspective. This review is written for computational biologists who have an interest in studying developmental gene regulation through integrative analysis of gene expression, chromatin landscape, and signaling pathways. I highlight the utility of publicly available data and tools, as well as some common analysis approaches.

Indexed as

ChIP-seqComputational biophysicsDevelopmental signalingEpigenomicsGene regulatory networkHistone modification

Identifiers

PMID28510076

DOI10.1007/s12551-012-0092-9

PMCPMC5418408

OpenAlexW1986795175

What OpenQuestion holds

Textmetadata

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.