NetExplore: a web server for modeling small network motifs.

Dmitri Papatsenko, Ihor R Lemischka

Abstract read

In one paragraph

Article in Bioinformatics (Oxford, England), 2015. 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

–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

2 citing papers in PubMed.

Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches.Briefings in bioinformatics · 2019
Review
Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal.Stem cell reports · 2015
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

2 authors.

Dmitri PapatsenkoDepartment of Regenerative and Developmental Biology, Black Family Stem Cell Institute andDepartment of Pharmacology and System Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York, One Gustave L. Levy Place, New York, NY 10029, USA Department of Regenerative and Developmental Biology, Black Family Stem Cell Institute andDepartment of Pharmacology and System Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York, One Gustave L. Levy Place, New York, NY 10029, USA.

Ihor R LemischkaDepartment of Regenerative and Developmental Biology, Black Family Stem Cell Institute andDepartment of Pharmacology and System Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York, One Gustave L. Levy Place, New York, NY 10029, USA Department of Regenerative and Developmental Biology, Black Family Stem Cell Institute andDepartment of Pharmacology and System Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York, One Gustave L. Levy Place, New York, NY 10029, USA Department of Regenerative and Developmental Biology, Black Family Stem Cell Institute andDepartment of Pharmacology and System Therapeutics, Icahn School of Medicine at Mount Sinai, Systems Biology Center New York, One Gustave L. Levy Place, New York, NY 10029, USA.

Funding

Global & Systems Level Analyses of Cell Fate RegulationR01GM078465 · NIGMS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI LEMISCHKA, IHOR R · 2007 to 2015

$3.7M

NIGMS NIH HHS R01 GM078465

6 · The paper itself

Abstract

motivationQuantitative and qualitative assessment of biological data often produces small essential recurrent networks, containing 3-5 components called network motifs. In this context, model solutions for small network motifs represent very high interest.

resultsSoftware package NetExplore has been created in order to generate, classify and analyze solutions for network motifs including up to six network components. NetExplore allows plotting and visualization of the solution's phase spaces and bifurcation diagrams. AVAILABILITY AND IMPLEMENTATION: The current version of NetExplore has been implemented in Perl-CGI and is accessible at the following locations: http://line.bioinfolab.net/nex/NetExplore.htm and http://nex.autosome.ru/nex/NetExplore.htm.

Indexed as

Gene Regulatory NetworksSoftwareAlgorithmsInternetModels, Genetic

Identifiers

PMID25637559

DOI10.1093/bioinformatics/btv058

PMCPMC4462664

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.