Published in Plant Cell on May 25, 2012
Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant. Plant Cell (2013) 1.27
Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. Plant Cell (2012) 1.14
An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii. Plant Cell (2016) 1.06
Introducing an algal carbon-concentrating mechanism into higher plants: location and incorporation of key components. Plant Biotechnol J (2015) 0.94
Acclimation to very low CO2: contribution of limiting CO2 inducible proteins, LCIB and LCIA, to inorganic carbon uptake in Chlamydomonas reinhardtii. Plant Physiol (2014) 0.89
Identification of AGO3-associated miRNAs and computational prediction of their targets in the green alga Chlamydomonas reinhardtii. Genetics (2015) 0.85
Characterization of cooperative bicarbonate uptake into chloroplast stroma in the green alga Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A (2015) 0.84
The interplay of light and oxygen in the reactive oxygen stress response of Chlamydomonas reinhardtii dissected by quantitative mass spectrometry. Mol Cell Proteomics (2014) 0.84
Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation. PLoS One (2013) 0.79
Using natural selection to explore the adaptive potential of Chlamydomonas reinhardtii. PLoS One (2014) 0.78
Growth rate evolution in improved environments under Prodigal Son dynamics. Evol Appl (2016) 0.77
Dynamics of carbon-concentrating mechanism induction and protein relocalization during the dark-to-light transition in synchronized Chlamydomonas reinhardtii. Plant Physiol (2014) 0.77
Pluralistic and stochastic gene regulation: examples, models and consistent theory. Nucleic Acids Res (2016) 0.75
Analysis of Sensitive CO2 Pathways and Genes Related to Carbon Uptake and Accumulation in Chlamydomonas reinhardtii through Genomic Scale Modeling and Experimental Validation. Front Plant Sci (2016) 0.75
Contemporary reliance on bicarbonate acquisition predicts increased growth of seagrass Amphibolis antarctica in a high-CO2 world. Conserv Physiol (2014) 0.75
Structural insights into the LCIB protein family reveals a new group of β-carbonic anhydrases. Proc Natl Acad Sci U S A (2016) 0.75
A mutant of Chlamydomonas without LHCSR maintains high rates of photosynthesis, but has reduced cell division rates in sinusoidal light conditions. PLoS One (2017) 0.75
Regulatory components of carbon concentrating mechanisms in aquatic unicellular photosynthetic organisms. Plant Cell Rep (2017) 0.75
A Spatial Interactome Reveals the Protein Organization of the Algal CO2-Concentrating Mechanism. Cell (2017) 0.75
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) 150.21
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (2009) 67.17
Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
The Pfam protein families database. Nucleic Acids Res (2011) 33.46
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res (2008) 26.36
MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res (2009) 23.27
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res (2006) 22.20
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15
RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics (2009) 10.74
Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics (2003) 8.92
baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics (2010) 8.01
TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res (2010) 6.65
An abundance of bidirectional promoters in the human genome. Genome Res (2004) 5.90
On the sequencing of the human genome. Proc Natl Acad Sci U S A (2002) 5.59
Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res (2011) 4.75
Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics (2010) 4.48
KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res (2008) 4.14
An ancient light-harvesting protein is critical for the regulation of algal photosynthesis. Nature (2009) 2.47
PLAZA: a comparative genomics resource to study gene and genome evolution in plants. Plant Cell (2009) 2.43
Intronic CA-repeat and CA-rich elements: a new class of regulators of mammalian alternative splicing. EMBO J (2005) 2.30
A single nucleotide polymorphism in the first intron of the human IFN-gamma gene: absolute correlation with a polymorphic CA microsatellite marker of high IFN-gamma production. Hum Immunol (2000) 2.21
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Nucleic Acids Res (2010) 1.95
RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. Plant Cell (2010) 1.83
Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps. Plant Cell (2011) 1.74
Expression profiling-based identification of CO2-responsive genes regulated by CCM1 controlling a carbon-concentrating mechanism in Chlamydomonas reinhardtii. Plant Physiol (2004) 1.49
The Arabidopsis bZIP transcription factor HY5 regulates expression of the PFG1/MYB12 gene in response to light and ultraviolet-B radiation. Plant Cell Environ (2009) 1.47
Direct interaction of a divergent CaM isoform and the transcription factor, MYB2, enhances salt tolerance in arabidopsis. J Biol Chem (2004) 1.47
Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Res (2007) 1.41
The LxxLL motif: a multifunctional binding sequence in transcriptional regulation. Trends Biochem Sci (2005) 1.41
Structure and differential expression of two genes encoding carbonic anhydrase in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A (1990) 1.38
A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii. Plant J (2011) 1.29
Proposed carbon dioxide concentrating mechanism in Chlamydomonas reinhardtii. Eukaryot Cell (2007) 1.25
Internal architecture of mitochondrial complex I from Arabidopsis thaliana. Plant Cell (2010) 1.24
Carbon dioxide concentrating mechanism in Chlamydomonas reinhardtii: inorganic carbon transport and CO2 recapture. Photosynth Res (2011) 1.20
The CRR1 nutritional copper sensor in Chlamydomonas contains two distinct metal-responsive domains. Plant Cell (2010) 1.18
The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles. Photosynth Res (2011) 1.17
The novel Myb transcription factor LCR1 regulates the CO2-responsive gene Cah1, encoding a periplasmic carbonic anhydrase in Chlamydomonas reinhardtii. Plant Cell (2004) 1.15
Partial characterization of a new isoenzyme of carbonic anhydrase isolated from Chlamydomonas reinhardtii. J Biol Chem (1991) 1.15
Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. Plant Cell (2012) 1.14
The GreenCut2 resource, a phylogenomically derived inventory of proteins specific to the plant lineage. J Biol Chem (2011) 1.14
Subtelomeric repetitive elements determine TERRA regulation by Rap1/Rif and Rap1/Sir complexes in yeast. EMBO Rep (2011) 1.13
Analysis of PRODUCTION OF FLAVONOL GLYCOSIDES-dependent flavonol glycoside accumulation in Arabidopsis thaliana plants reveals MYB11-, MYB12- and MYB111-independent flavonol glycoside accumulation. New Phytol (2010) 1.13
Identification and regulation of high light-induced genes in Chlamydomonas reinhardtii. Plant J (2002) 1.12
Expression analysis of genes associated with the induction of the carbon-concentrating mechanism in Chlamydomonas reinhardtii. Plant Physiol (2008) 1.09
Analysis of light and CO(2) regulation in Chlamydomonas reinhardtii using genome-wide approaches. Photosynth Res (2003) 1.09
Light and low-CO2-dependent LCIB-LCIC complex localization in the chloroplast supports the carbon-concentrating mechanism in Chlamydomonas reinhardtii. Plant Cell Physiol (2010) 1.09
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. BMC Bioinformatics (2011) 1.06
Carbon dioxide and light regulation of promoters controlling the expression of mitochondrial carbonic anhydrase in Chlamydomonas reinhardtii. Biochem J (1997) 1.06
Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics (2010) 1.05
Diversification of the core RNA interference machinery in Chlamydomonas reinhardtii and the role of DCL1 in transposon silencing. Genetics (2008) 1.04
RNA-mediated silencing in Algae: biological roles and tools for analysis of gene function. Eukaryot Cell (2011) 1.02
Knockdown of limiting-CO2-induced gene HLA3 decreases HCO3- transport and photosynthetic Ci affinity in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A (2009) 1.02
Expression of a low CO₂-inducible protein, LCI1, increases inorganic carbon uptake in the green alga Chlamydomonas reinhardtii. Plant Cell (2010) 0.98
An inorganic carbon transport system responsible for acclimation specific to air levels of CO2 in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A (2006) 0.98
The Chlamydomonas reinhardtii proteins Ccp1 and Ccp2 are required for long-term growth, but are not necessary for efficient photosynthesis, in a low-CO2 environment. Plant Mol Biol (2004) 0.97
Cis-acting elements and DNA-binding proteins involved in CO2-responsive transcriptional activation of Cah1 encoding a periplasmic carbonic anhydrase in Chlamydomonas reinhardtii. Plant Physiol (2003) 0.97
Gbp1p, a protein with RNA recognition motifs, binds single-stranded telomeric DNA and changes its binding specificity upon dimerization. Mol Cell Biol (1999) 0.96
An improved retroviral vector for assaying promoter activity. Analysis of promoter interference in pIP211 vector. FEBS Lett (1993) 0.87
Insertional mutants of Chlamydomonas reinhardtii that require elevated CO(2) for survival. Plant Physiol (2001) 0.86
Carbon-concentrating mechanism in a green alga, Chlamydomonas reinhardtii, revealed by transcriptome analyses. J Basic Microbiol (2009) 0.85
Isolation and characterisation of chemotactic mutants of Chlamydomonas reinhardtii obtained by insertional mutagenesis. Protist (2000) 0.83
Enhanced binding of poly(ADP-ribose)polymerase-1 and Ku80/70 to the ITGA2 promoter via an extended cytosine-adenosine repeat. PLoS One (2010) 0.82
Identification and characterization of two closely related beta-carbonic anhydrases from Chlamydomonas reinhardtii. Physiol Plant (2008) 0.82
Significance of zinc in a regulatory protein, CCM1, which regulates the carbon-concentrating mechanism in Chlamydomonas reinhardtii. Plant Cell Physiol (2008) 0.81
A whole genome analysis of 5' regulatory regions of human genes for putative cis-acting modulators of nucleosome positioning. Gene (2007) 0.78
Photosynthetic characteristics of a multicellular green alga Volvox carteri in response to external CO2 levels possibly regulated by CCM1/CIA5 ortholog. Photosynth Res (2011) 0.77
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res (2003) 7.21
TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain. Nucleic Acids Res (2010) 6.65
Relationship between nucleosome positioning and DNA methylation. Nature (2010) 5.27
Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res (2011) 4.75
High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol (2012) 3.61
Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res (2013) 2.99
Dicamba resistance: enlarging and preserving biotechnology-based weed management strategies. Science (2007) 2.19
Selenoproteins and selenocysteine insertion system in the model plant cell system, Chlamydomonas reinhardtii. EMBO J (2002) 2.13
Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas. J Biol Chem (2012) 2.03
RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival. Plant Cell (2010) 1.83
Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol (2013) 1.81
Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps. Plant Cell (2011) 1.74
Evolution of an expanded sex-determining locus in Volvox. Science (2010) 1.55
The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. Genome Biol (2012) 1.49
A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome Res (2013) 1.48
Transcriptome sequencing identifies SPL7-regulated copper acquisition genes FRO4/FRO5 and the copper dependence of iron homeostasis in Arabidopsis. Plant Cell (2012) 1.40
Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage. Plant Cell (2012) 1.38
The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical functions. Plant Cell (2008) 1.35
A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii. Plant J (2011) 1.29
Dynamic changes in genome-wide histone H3 lysine 4 methylation patterns in response to dehydration stress in Arabidopsis thaliana. BMC Plant Biol (2010) 1.28
Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant. Plant Cell (2013) 1.27
RNAi screening reveals requirement for host cell secretory pathway in infection by diverse families of negative-strand RNA viruses. Proc Natl Acad Sci U S A (2011) 1.19
The sigma-1 receptor enhances brain plasticity and functional recovery after experimental stroke. Brain (2011) 1.18
Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO2-concentrating mechanism regulator CIA5/CCM1. Plant Cell (2012) 1.14
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. BMC Bioinformatics (2011) 1.06
Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival. Proc Natl Acad Sci U S A (2013) 1.06
The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii. Eukaryot Cell (2014) 1.05
A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: gene isolation, characterization, and heterologous expression. J Biol Chem (2005) 1.04
Knockdown of limiting-CO2-induced gene HLA3 decreases HCO3- transport and photosynthetic Ci affinity in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A (2009) 1.02
Remodeling of membrane lipids in iron-starved Chlamydomonas. J Biol Chem (2013) 0.99
The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii. Mol Cell Proteomics (2012) 0.97
Impact of oxidative stress on ascorbate biosynthesis in Chlamydomonas via regulation of the VTC2 gene encoding a GDP-L-galactose phosphorylase. J Biol Chem (2012) 0.96
Expanding the spectral palette of fluorescent proteins for the green microalga Chlamydomonas reinhardtii. Plant J (2013) 0.95
Copper response regulator1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia. Plant Cell (2013) 0.94
The small ubiquitin-like modifier (SUMO) and SUMO-conjugating system of Chlamydomonas reinhardtii. Genetics (2008) 0.93
Hypoxic survival requires a 2-on-2 hemoglobin in a process involving nitric oxide. Proc Natl Acad Sci U S A (2013) 0.92
SINGLET OXYGEN RESISTANT 1 links reactive electrophile signaling to singlet oxygen acclimation in Chlamydomonas reinhardtii. Proc Natl Acad Sci U S A (2012) 0.92
Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii. J Biol Chem (2013) 0.91
Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation. J Mol Biol (2009) 0.88
Chlamydomonas reinhardtii selenocysteine tRNA[Ser]Sec. RNA (2003) 0.87
Lethal iron deprivation induced by non-neutralizing antibodies targeting transferrin receptor 1 in malignant B cells. Leuk Lymphoma (2011) 0.86
Insights into the mechanism of cell death induced by saporin delivered into cancer cells by an antibody fusion protein targeting the transferrin receptor 1. Toxicol In Vitro (2012) 0.84
Defining a relationship between dietary fatty acids and the cytochrome P450 system in a mouse model of fatty liver disease. Physiol Genomics (2010) 0.81
A three-component dicamba O-demethylase from Pseudomonas maltophilia, strain DI-6: purification and characterization. Arch Biochem Biophys (2005) 0.81
Probabilistic peak calling and controlling false discovery rate estimations in transcription factor binding site mapping from ChIP-seq. Methods Mol Biol (2010) 0.81
Genetic engineering of maize (Zea mays) for high-level tolerance to treatment with the herbicide dicamba. J Agric Food Chem (2010) 0.80
Position-dependent expression of GADD45alpha in rat brain tumours. Med Oncol (2007) 0.79
Weakly positioned nucleosomes enhance the transcriptional competency of chromatin. PLoS One (2010) 0.79
Evaluation of three herbicide resistance genes for use in genetic transformations and for potential crop protection in algae production. Plant Biotechnol J (2014) 0.78
O-Demethylations catalyzed by Rieske nonheme iron monooxygenases involve the difficult oxidation of a saturated C-H bond. ACS Chem Biol (2013) 0.77
A rapid live-cell ELISA for characterizing antibodies against cell surface antigens of Chlamydomonas reinhardtii and its use in isolating algae from natural environments with related cell wall components. BMC Plant Biol (2014) 0.75
A small-scale, inexpensive method for detecting formaldehyde or methanol in biochemical reactions containing interfering substances. Anal Biochem (2013) 0.75