Identifying spatially similar gene expression patterns in early stage fruit fly embryo images: binary feature versus invariant moment digital representations.

PubWeight™: 1.64‹?› | Rank: Top 3%

🔗 View Article (PMC 545963)

Published in BMC Bioinformatics on December 16, 2004

Authors

Rajalakshmi Gurunathan1, Bernard Van Emden, Sethuraman Panchanathan, Sudhir Kumar

Author Affiliations

1: Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA. Rajalakshmi.Gurunathan@asu.edu <Rajalakshmi.Gurunathan@asu.edu>

Articles citing this

Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol (2007) 6.27

Bioimage informatics: a new area of engineering biology. Bioinformatics (2008) 6.26

Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics (2008) 1.50

Automatic image analysis for gene expression patterns of fly embryos. BMC Cell Biol (2007) 1.47

Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-Term Interactions. KDD (2009) 1.45

A bag-of-words approach for Drosophila gene expression pattern annotation. BMC Bioinformatics (2009) 1.34

A combinatorial code for pattern formation in Drosophila oogenesis. Dev Cell (2008) 1.33

Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence. Dev Dyn (2011) 1.27

Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape. Mol Syst Biol (2010) 1.26

Developmental Stage Annotation of Drosophila Gene Expression Pattern Images via an Entire Solution Path for LDA. ACM Trans Knowl Discov Data (2008) 1.02

Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. IJCAI (U S) (2009) 0.99

Medium-throughput processing of whole mount in situ hybridisation experiments into gene expression domains. PLoS One (2012) 0.96

Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval. BMC Bioinformatics (2012) 0.86

Association of orthodenticle with natural variation for early embryonic patterning in Drosophila melanogaster. J Exp Zool B Mol Dev Evol (2009) 0.82

Articles cited by this

Basic local alignment search tool. J Mol Biol (1990) 659.07

The FlyBase database of the Drosophila Genome Projects and community literature. Nucleic Acids Res (1999) 26.10

Gene expression during the life cycle of Drosophila melanogaster. Science (2002) 11.36

Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol (2002) 8.89

Expression cloning of 2-5A-dependent RNAase: a uniquely regulated mediator of interferon action. Cell (1993) 4.10

Local inhibition and long-range enhancement of Dpp signal transduction by Sog. Nature (1999) 2.56

BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics (2002) 2.43

Control of developmental timing in animals. Nat Rev Genet (2001) 2.13

Joint action of two RNA degradation pathways controls the timing of maternal transcript elimination at the midblastula transition in Drosophila melanogaster. EMBO J (1999) 2.02

A morphogenetic gradient of hunchback protein organizes the expression of the gap genes Krüppel and knirps in the early Drosophila embryo. Nature (1990) 1.84

A logical analysis of the Drosophila gap-gene system. J Theor Biol (2001) 1.82

Groucho and dCtBP mediate separate pathways of transcriptional repression in the Drosophila embryo. Proc Natl Acad Sci U S A (1999) 1.72

Pole region-dependent repression of the Drosophila gap gene Krüppel by maternal gene products. Cell (1987) 1.70

The gap protein knirps mediates both quenching and direct repression in the Drosophila embryo. EMBO J (1996) 1.65

Targeting gene expression to the head: the Drosophila orthodenticle gene is a direct target of the Bicoid morphogen. Development (1998) 1.61

Spatial control of the gap gene knirps in the Drosophila embryo by posterior morphogen system. Science (1992) 1.59

Disperse versus compact elements for the regulation of runt stripes in Drosophila. Dev Biol (1996) 1.48

Complex regulation of early paired expression: initial activation by gap genes and pattern modulation by pair-rule genes. Development (1993) 1.39

Retracted TAF(II)s mediate activation of transcription in the Drosophila embryo. Cell (1996) 1.39

A Drosophila APC tumour suppressor homologue functions in cellular adhesion. Nat Cell Biol (2002) 1.36

Developmental and molecular characterization of mutations in the Drosophila-raf serine/threonine protein kinase. Development (1993) 1.34

Serotonin synchronises convergent extension of ectoderm with morphogenetic gastrulation movements in Drosophila. Mech Dev (1999) 1.33

The even-skipped locus is contained in a 16-kb chromatin domain. Dev Biol (1999) 1.32

Autonomous concentration-dependent activation and repression of Krüppel by hunchback in the Drosophila embryo. Development (1994) 1.31

Molecular analysis of even-skipped mutants in Drosophila development. Genes Dev (1988) 1.30

The relationship between the functional complexity and the molecular organization of the Antennapedia locus of Drosophila melanogaster. Genetics (1986) 1.30

Dual role of the Drosophila pattern gene tailless in embryonic termini. Science (1991) 1.29

Localized expression of sloppy paired protein maintains the polarity of Drosophila parasegments. Genes Dev (1994) 1.26

Huckebein repressor activity in Drosophila terminal patterning is mediated by Groucho. Development (1999) 1.25

FlyView, a Drosophila image database, and other Drosophila databases Semin Cell Dev Biol (1997) 1.24

Gap gene properties of the pair-rule gene runt during Drosophila segmentation. Development (1994) 1.23

Sequence interval within the PEST motif of Bicoid is important for translational repression of caudal mRNA in the anterior region of the Drosophila embryo. EMBO J (1999) 1.20

Three maternal coordinate systems cooperate in the patterning of the Drosophila head. Development (1994) 1.19

Establishment of dorsal-ventral polarity of the Drosophila egg requires capicua action in ovarian follicle cells. Development (2001) 1.17

Linear signaling in the Toll-Dorsal pathway of Drosophila: activated Pelle kinase specifies all threshold outputs of gene expression while the bHLH protein Twist specifies a subset. Development (2002) 1.16

Regulation of the infraabdominal regions of the bithorax complex of Drosophila by gap genes. Development (1995) 1.14

Differential regulation of target genes by different alleles of the segmentation gene hunchback in Drosophila. Genetics (1994) 1.14

Control of cell fates and segmentation in the Drosophila mesoderm. Development (1997) 1.13

The activity of the Drosophila morphogenetic protein Bicoid is inhibited by a domain located outside its homeodomain. Development (2002) 1.11

hairy stripe 7 element mediates activation and repression in response to different domains and levels of Krüppel in the Drosophila embryo. Mech Dev (1999) 1.08

Quantitative variations in the level of MAPK activity control patterning of the embryonic termini in Drosophila. Dev Biol (1999) 1.07

Gap genes and gradients--the logic behind the gaps. Bioessays (1991) 1.06

The Snail repressor positions Notch signaling in the Drosophila embryo. Development (2002) 1.06

achaete-scute feminizing activities and Drosophila sex determination. Development (1993) 1.06

The tissue polarity gene nemo carries out multiple roles in patterning during Drosophila development. Mech Dev (2001) 1.05

Regulation of a dpp target gene in the Drosophila embryo. Development (1997) 1.05

Zygotic caudal regulation by hunchback and its role in abdominal segment formation of the Drosophila embryo. Development (1995) 1.04

Sloppy paired acts as the downstream target of wingless in the Drosophila CNS and interaction between sloppy paired and gooseberry inhibits sloppy paired during neurogenesis. Development (2000) 1.03

buttonhead does not contribute to a combinatorial code proposed for Drosophila head development. Development (1997) 1.01

Thoracic patterning by the Drosophila gap gene hunchback. Dev Biol (2001) 1.01

Role of CtBP in transcriptional repression by the Drosophila giant protein. Dev Biol (2001) 0.99

DWnt4 and wingless elicit similar cellular responses during imaginal development. Dev Biol (2001) 0.97

Regulation of the Tribolium homologues of caudal and hunchback in Drosophila: evidence for maternal gradient systems in a short germ embryo. Development (1998) 0.97

Pattern formation in Drosophila head development: the role of the orthodenticle homeobox gene. Development (1995) 0.96

The Drosophila wispy gene is required for RNA localization and other microtubule-based events of meiosis and early embryogenesis. Genetics (2000) 0.96

A two-step mode of stripe formation in the Drosophila blastoderm requires interactions among primary pair rule genes. Mech Dev (1994) 0.96

Interaction between Drosophila EGF receptor and vnd determines three dorsoventral domains of the neuroectoderm. Development (1998) 0.91

Role of gap genes in early Drosophila development. Adv Genet (1990) 0.91

Persistence of Hunchback in the terminal region of the Drosophila blastoderm embryo impairs anterior development. Development (2000) 0.90

Impressive expressions: developing a systematic database of gene-expression patterns in Drosophila embryogenesis. Genome Biol (2003) 0.90

Combinatorial signaling by an unconventional Wg pathway and the Dpp pathway requires Nejire (CBP/p300) to regulate dpp expression in posterior tracheal branches. Dev Biol (2002) 0.88

Both the paired domain and homeodomain are required for in vivo function of Drosophila Paired. Development (1996) 0.88

Introduction: Making and filling gene-expression developmental databases Semin Cell Dev Biol (1997) 0.77

Articles by these authors

MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol (2011) 220.97

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol (2007) 168.76

MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol (2013) 112.81

Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci U S A (2004) 20.53

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

Precision of molecular time estimates. Trends Genet (2004) 15.94

Estimating divergence times in large molecular phylogenies. Proc Natl Acad Sci U S A (2012) 13.49

TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (2006) 10.24

Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference. Mol Biol Evol (2003) 7.78

Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times. Mol Biol Evol (2011) 6.93

Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol (2003) 5.30

Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Mol Biol Evol (2010) 5.13

Evolutionary diagnosis method for variants in personal exomes. Nat Methods (2012) 3.32

Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature (2007) 3.04

Genomic clocks and evolutionary timescales. Trends Genet (2003) 2.83

Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics (2004) 2.63

BEST: a novel computational approach for comparing gene expression patterns from early stages of Drosophila melanogaster development. Genetics (2002) 2.43

Evolutionary distance estimation under heterogeneous substitution pattern among lineages. Mol Biol Evol (2002) 2.23

Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. J Exp Zool B Mol Dev Evol (2005) 2.22

Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res (2003) 1.94

Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome. BMC Genomics (2006) 1.87

Bone and Joint day - India. Indian J Orthop (2013) 1.84

Nullomers: really a matter of natural selection? PLoS One (2007) 1.67

Clinical and laboratory features and response to treatment in patients presenting with vitamin B12 deficiency-related neurological syndromes. Neurol India (2005) 1.66

Genomics. Vertebrate genomes compared. Science (2002) 1.57

Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders. Mol Biol Evol (2011) 1.55

Zinc oxide nanoparticles selectively induce apoptosis in human cancer cells through reactive oxygen species. Int J Nanomedicine (2012) 1.54

Automated annotation of Drosophila gene expression patterns using a controlled vocabulary. Bioinformatics (2008) 1.50

Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations. Bioinformatics (2012) 1.46

Decompressive surgery for severe cerebral venous sinus thrombosis. Neurol India (2010) 1.46

Drosophila Gene Expression Pattern Annotation Using Sparse Features and Term-Term Interactions. KDD (2009) 1.45

Taxon sampling, bioinformatics, and phylogenomics. Syst Biol (2003) 1.44

Improved lignocellulose conversion to biofuels with thermophilic bacteria and thermostable enzymes. Bioresour Technol (2012) 1.40

Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol (2010) 1.40

Bilateral anterior shoulder dislocation: a case report. Eur J Emerg Med (2005) 1.35

A bag-of-words approach for Drosophila gene expression pattern annotation. BMC Bioinformatics (2009) 1.34

Classification of Drosophila embryonic developmental stage range based on gene expression pattern images. Comput Syst Bioinformatics Conf (2006) 1.33

Effect of fatigue on psychomotor and cognitive skills. Am J Surg (2008) 1.33

FlyExpress: visual mining of spatiotemporal patterns for genes and publications in Drosophila embryogenesis. Bioinformatics (2011) 1.33

Comparison of embryonic expression within multigene families using the FlyExpress discovery platform reveals more spatial than temporal divergence. Dev Dyn (2011) 1.27

Genomic sequence of a ranavirus (family Iridoviridae) associated with salamander mortalities in North America. Virology (2003) 1.27

Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Res Notes (2012) 1.24

Local or general anesthesia for open hernia repair: a randomized trial. Ann Surg (2003) 1.20

The origin of Metazoa: a transition from temporal to spatial cell differentiation. Bioessays (2009) 1.16

Patterns of transitional mutation biases within and among mammalian genomes. Mol Biol Evol (2003) 1.13

Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous. Mol Biol Evol (2005) 1.12

Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Mol Biol Evol (2006) 1.12

Signatures of ecological resource availability in the animal and plant proteomes. Mol Biol Evol (2006) 1.10

Outcome of laparoscopic cholecystectomy in patients 80 years and older. World J Surg (2004) 1.09

Branding: a harmful practice. Indian Pediatr (2005) 1.07

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure. Philos Trans R Soc Lond B Biol Sci (2010) 1.05

Nanotoxicity of pure silica mediated through oxidant generation rather than glutathione depletion in human lung epithelial cells. Toxicology (2010) 1.05

Contamination levels and spatial distribution of organochlorine pesticides in soils from India. Ecotoxicol Environ Saf (2011) 1.04

The spectrum of human rhodopsin disease mutations through the lens of interspecific variation. Gene (2004) 1.04

Human genomic disease variants: a neutral evolutionary explanation. Genome Res (2012) 1.02

Isolated dorsal dislocation of the intermediate cunieform: a case report and review of the literature. Arch Orthop Trauma Surg (2003) 1.02

Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. Bioinformatics (2009) 1.02

Developmental Stage Annotation of Drosophila Gene Expression Pattern Images via an Entire Solution Path for LDA. ACM Trans Knowl Discov Data (2008) 1.02

Magnetic resonance evaluation of tubercular lesion in spine. Int Orthop (2011) 1.01

Isolated bilateral ptosis as the presentation of midbrain tuberculoma. Neurol India (2008) 1.01

The role of simultaneous gap arthroplasty and distraction osteogenesis in the management of temporo-mandibular joint ankylosis with mandibular deformity in children. J Craniomaxillofac Surg (2004) 1.01

DNA vaccines encoding viral envelope proteins confer protective immunity against WSSV in black tiger shrimp. Vaccine (2007) 1.01

Ecological nitrogen limitation shapes the DNA composition of plant genomes. Mol Biol Evol (2009) 1.00

Drosophila Gene Expression Pattern Annotation through Multi-Instance Multi-Label Learning. IJCAI (U S) (2009) 0.99

Evolutionary balancing is critical for correctly forecasting disease-associated amino acid variants. Mol Biol Evol (2013) 0.99

Multifocal skeletal tuberculosis in children: a retrospective study of 18 cases. Scand J Infect Dis (2003) 0.97

Structural dynamics flexibility informs function and evolution at a proteome scale. Evol Appl (2013) 0.95

Reversible electrophysiological abnormalities in hypokalemic periodic paralysis. Indian Pediatr (2008) 0.95

Kaempferol has osteogenic effect in ovariectomized adult Sprague-Dawley rats. Mol Cell Endocrinol (2008) 0.95

Drosophila gene expression pattern annotation through multi-instance multi-label learning. IEEE/ACM Trans Comput Biol Bioinform (2011) 0.95

Stoichiogenomics: the evolutionary ecology of macromolecular elemental composition. Trends Ecol Evol (2010) 0.94

Effects of Egb 761 on bone mineral density, bone microstructure, and osteoblast function: Possible roles of quercetin and kaempferol. Mol Cell Endocrinol (2009) 0.92

Evolutionary meta-analysis of association studies reveals ancient constraints affecting disease marker discovery. Mol Biol Evol (2012) 0.92

Behaviour problems in children and adolescents with seizure disorder: associations and risk factors. Seizure (2005) 0.91

Rampant purifying selection conserves positions with posttranslational modifications in human proteins. Mol Biol Evol (2011) 0.91

IPS multicentric study: Antidepressant prescription patterns. Indian J Psychiatry (2013) 0.90

A survey of prescribing pattern for osteoarticular tuberculosis: orthopaedic surgeons' and infectious disease experts' perspective. Indian J Tuberc (2009) 0.90

Gsdma3(I359N) is a novel ENU-induced mutant mouse line for studying the function of Gasdermin A3 in the hair follicle and epidermis. J Dermatol Sci (2012) 0.90

Snake venom: a potent anticancer agent. Asian Pac J Cancer Prev (2012) 0.90

Efficacy of extended DOTS category I chemotherapy in spinal tuberculosis based on MRI-based healed status. Indian J Orthop (2012) 0.89

Differential diagnosis of scrub typhus meningitis from bacterial meningitis using clinical and laboratory features. Neurol India (2013) 0.89

Genotoxicity assessment of acute exposure of chlorpyrifos to freshwater fish Channa punctatus (Bloch) using micronucleus assay and alkaline single-cell gel electrophoresis. Chemosphere (2008) 0.88

Laparoscopic totally extraperitoneal mesh repair for femoral hernia. J Laparoendosc Adv Surg Tech A (2004) 0.88

Purifying selection modulates the estimates of population differentiation and confounds genome-wide comparisons across single-nucleotide polymorphisms. Mol Biol Evol (2012) 0.88

Assessment of health risks with reference to oxidative stress and DNA damage in chromium exposed population. Sci Total Environ (2012) 0.88

Y Chromosome microdeletion and altered sperm quality in human males with high concentration of seminal hexachlorocyclohexane (HCH). Chemosphere (2010) 0.88

POSSUM scoring for laparoscopic cholecystectomy in the elderly. ANZ J Surg (2005) 0.88

Macrophage migration inhibitory factor: a potential marker for cancer diagnosis and therapy. Asian Pac J Cancer Prev (2012) 0.87

MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. Bioinformatics (2014) 0.87

Effect of dust aerosol in patients with asthma. J Asthma (2012) 0.87

Awake fibreoptic intubation in the sitting position in a patient with a huge goitre. Case Rep Anesthesiol (2011) 0.87

Interlaminar discectomy and selective foraminotomy in lumbar disc herniation. J Orthop Surg (Hong Kong) (2001) 0.87

Learning sparse representations for fruit-fly gene expression pattern image annotation and retrieval. BMC Bioinformatics (2012) 0.86

Constraining fossil calibrations for molecular clocks. Bioessays (2006) 0.85

Genome-wide profiling of human cap-independent translation-enhancing elements. Nat Methods (2013) 0.84

A case study: biomedical waste management practices at city hospital in Himachal Pradesh. Waste Manag Res (2011) 0.84

Guillain-Barre syndrome occurring in the course of dengue fever. Neurol India (2005) 0.84

Phylogenetic placement of metagenomic reads using the minimum evolution principle. BMC Genomics (2015) 0.83

Cytotoxicity and apoptosis induction by nanoscale talc particles from two different geographical regions in human lung epithelial cells. Environ Toxicol (2012) 0.83