Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla (Q28552694)

12

object named as

Alexandra Z Worden

0 references

Stephen J Callister

10

object named as

Stephen J Callister

0 references

Emily Nahas Reistetter

3

object named as

Emily Nahas Reistetter

0 references

author name string

Peter H Waltman

1

0 references

Jian Guo

2

0 references

Charles K Ansong

5

0 references

Marijke J van Baren

6

0 references

Chee-Hong Wong

7

0 references

Chia-Lin Wei

8

0 references

Richard D Smith

9

0 references

Joshua M Stuart

Creative Commons CC0 License

11

0 references

language of work or name

English

0 references

publication date

2016

0 references

published in

PLOS One

0 references

volume

11

0 references

issue

7

0 references

page(s)

e0155839

0 references

copyright license

start time

19 July 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

describes a project that uses

SQL

1 reference

Europe PubMed Central

26 June 2022

https://europepmc.org/article/PMC/PMC4951065

based on heuristic

inferred from PubMed Central ID database lookup

cites work

Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Transcriptome and proteome dynamics of a light-dark synchronized bacterial cell cycle

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Green algae and the origin of land plants

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Global quantification of mammalian gene expression control

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

AREsite: a database for the comprehensive investigation of AU-rich elements

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Structure and function of sphingosine-1-phosphate lyase, a key enzyme of sphingolipid metabolism

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

The nuclear pore complex protein ALADIN is anchored via NDC1 but not via POM121 and GP210 in the nuclear envelope

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

TopHat: discovering splice junctions with RNA-Seq

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for L-lysine biosynthesis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

VIPER: an advanced software package to support high-throughput LC-MS peptide identification

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

19 March 2017

Plant circadian rhythms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

AU-rich elements and associated factors: are there unifying principles?

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

InterProScan: protein domains identifier

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

The Pathway Tools software

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Role of HuD and other RNA-binding proteins in neural development and plasticity

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Predicting subcellular localization of proteins based on their N-terminal amino acid sequence

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Gene ontology: tool for the unification of biology

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

The ENZYME database in 2000

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

The WD repeat: a common architecture for diverse functions

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Correlation between protein and mRNA abundance in yeast

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Cell cycle regulated expression of nucleolar antigen P120 in normal and transformed human fibroblasts

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

A conserved AU sequence from the 3' untranslated region of GM-CSF mRNA mediates selective mRNA degradation

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Cloning of the cDNA and sequence of the human proliferating-cell nucleolar protein P120

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

KEGG for integration and interpretation of large-scale molecular data sets

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Galaxy: a platform for interactive large-scale genome analysis

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

InterProScan--an integration platform for the signature-recognition methods in InterPro

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

AU-rich elements: characterization and importance in mRNA degradation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Regularization Paths for Generalized Linear Models via Coordinate Descent

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

A multi-omic analysis of human naïve CD4 T cells

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Marine algae and land plants share conserved phytochrome signaling systems.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Proteome-wide analysis and diel proteomic profiling of the cyanobacterium Arthrospira platensis PCC 8005

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

System wide analyses have underestimated protein abundances and the importance of transcription in mammals

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Glycerolipids in photosynthesis: composition, synthesis and trafficking

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Post-transcriptional regulation of iron homeostasis in Saccharomyces cerevisiae.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Large-scale gene function analysis with the PANTHER classification system

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Protein Expression Regulation under Oxidative Stress

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Analysis of biostimulated microbial communities from two field experiments reveals temporal and spatial differences in proteome profiles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Plant sphingolipids: decoding the enigma of the Sphinx

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Correlation of mRNA and protein in complex biological samples.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

The nucleolar RNA methyltransferase Misu (NSun2) is required for mitotic spindle stability

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Integrative analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: a non-linear model to predict abundance of undetected proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Ecological niche partitioning in the picoplanktonic green alga Micromonas pusilla: evidence from environmental surveys using phylogenetic probes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

DAnTE: a statistical tool for quantitative analysis of -omics data.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Integrative analyses of posttranscriptional regulation in the yeast Saccharomyces cerevisiae using transcriptomic and proteomic data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

The anatomy of microbial cell state transitions in response to oxygen

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Posttranscriptional expression regulation: what determines translation rates?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

An introduction to multivariate adaptive regression splines

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Translational efficiency is regulated by the length of the 3' untranslated region

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4951065

Characterizing microbial community and geochemical dynamics at hydrothermal vents using osmotically driven continuous fluid samplers

3 June 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0155839

A user's guide to support vector machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0155839

Mapping the dynamic organization of the nuclear pore complex inside single living cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0155839

Circadian rhythms confer a higher level of fitness to Arabidopsis plants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0155839

Photosynthetic Genes of Petunia (Mitchell) Are Differentially Expressed during the Diurnal Cycle.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0155839

Purification and characterization of class-I and class-II fructose-1,6-bisphosphate aldolases from the cyanobacterium Synechocystis sp. PCC 6803.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0155839

Smallest Algae Thrive As the Arctic Ocean Freshens

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0155839

Open-source machine learning: R meets Weka

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0155839

Change in flagellar beat frequency of Chlamydomonas in response to light

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27434306

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0155839

1 reference

ADS bibcode

2016PLoSO..1155839W

0 references

1 reference

1 reference

PubMed publication ID

27434306

1 reference