Published in IEEE/ACM Trans Comput Biol Bioinform on November 11, 2011
Principal-oscillation-pattern analysis of gene expression. PLoS One (2012) 0.84
DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks. PLoS Comput Biol (2016) 0.75
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell (2008) 6.91
Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A (2005) 6.19
A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol (2005) 4.85
Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci U S A (2005) 3.30
The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet (2009) 3.11
A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol (2010) 2.57
The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation. Theor Popul Biol (2007) 2.07
Quasispecies theory in the context of population genetics. BMC Evol Biol (2005) 2.02
Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol (2009) 1.96
T cell dynamics and the response to HAART in a cohort of HIV-1-infected elite suppressors. Clin Infect Dis (2009) 1.94
Analysis of human immunodeficiency virus type 1 viremia and provirus in resting CD4+ T cells reveals a novel source of residual viremia in patients on antiretroviral therapy. J Virol (2009) 1.89
Adaptive radiation from resource competition in digital organisms. Science (2004) 1.86
Thermodynamics of neutral protein evolution. Genetics (2006) 1.83
Limits on replenishment of the resting CD4+ T cell reservoir for HIV in patients on HAART. PLoS Pathog (2007) 1.81
Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol (2006) 1.75
Decay dynamics of HIV-1 depend on the inhibited stages of the viral life cycle. Proc Natl Acad Sci U S A (2008) 1.72
A machine learning perspective on the development of clinical decision support systems utilizing mass spectra of blood samples. J Biomed Inform (2006) 1.68
Avida: a software platform for research in computational evolutionary biology. Artif Life (2004) 1.62
Objective assessment of aesthetic outcomes of breast cancer treatment: measuring ptosis from clinical photographs. Comput Biol Med (2006) 1.47
3D Symmetry Measure Invariant to Subject Pose During Image Acquisition. Breast Cancer (Auckl) (2011) 1.45
On the conservative nature of intragenic recombination. Proc Natl Acad Sci U S A (2005) 1.37
Density-dependent selection in vesicular stomatitis virus. J Virol (2004) 1.37
Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics (2004) 1.31
The stochastic edge in adaptive evolution. Genetics (2008) 1.30
Differentiating tumor recurrence from treatment necrosis: a review of neuro-oncologic imaging strategies. Neuro Oncol (2013) 1.30
The look-ahead effect of phenotypic mutations. Biol Direct (2008) 1.28
The relationship between relative solvent accessibility and evolutionary rate in protein evolution. Genetics (2011) 1.25
Assessment of breast aesthetics. Plast Reconstr Surg (2008) 1.23
Stability and the evolvability of function in a model protein. Biophys J (2004) 1.21
Maximum allowed solvent accessibilites of residues in proteins. PLoS One (2013) 1.18
Low-level HIV-1 replication and the dynamics of the resting CD4+ T cell reservoir for HIV-1 in the setting of HAART. BMC Infect Dis (2008) 1.15
Integrating sequence variation and protein structure to identify sites under selection. Mol Biol Evol (2012) 1.15
The relationship between retinal ganglion cell axon constituents and retinal nerve fiber layer birefringence in the primate. Invest Ophthalmol Vis Sci (2009) 1.10
Contact density affects protein evolutionary rate from bacteria to animals. J Mol Evol (2008) 1.10
Probing local tissue changes in the oral cavity for early detection of cancer using oblique polarized reflectance spectroscopy: a pilot clinical trial. J Biomed Opt (2008) 1.09
Contact heterogeneity and phylodynamics: how contact networks shape parasite evolutionary trees. Interdiscip Perspect Infect Dis (2010) 1.07
Lethal mutagenesis of bacteria. Genetics (2008) 1.05
Complex wavelet structural similarity: a new image similarity index. IEEE Trans Image Process (2009) 1.03
Effects of population size and mutation rate on the evolution of mutational robustness. Evolution (2007) 1.03
The phenotype-fitness map in experimental evolution of phages. PLoS One (2011) 1.03
Experiments on the role of deleterious mutations as stepping stones in adaptive evolution. Proc Natl Acad Sci U S A (2013) 1.03
Thickness, phase retardation, birefringence, and reflectance of the retinal nerve fiber layer in normal and glaucomatous non-human primates. Invest Ophthalmol Vis Sci (2012) 1.03
Modeling coding-sequence evolution within the context of residue solvent accessibility. BMC Evol Biol (2012) 1.02
Constraints on the dominant mechanism for HIV viral dynamics in patients on raltegravir. Antivir Ther (2009) 1.02
Towards quantifying the aesthetic outcomes of breast cancer treatment: comparison of clinical photography and colorimetry. J Eval Clin Pract (2009) 1.00
Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol Biol Evol (2010) 1.00
Selection for mutational robustness in finite populations. J Theor Biol (2006) 0.99
Breaking proteins with mutations: threads and thresholds in evolution. Mol Syst Biol (2007) 0.98
Monte Carlo lookup table-based inverse model for extracting optical properties from tissue-simulating phantoms using diffuse reflectance spectroscopy. J Biomed Opt (2013) 0.97
Sinonasal anatomic variants and asthma are associated with faster development of chronic rhinosinusitis in patients with allergic rhinitis. Int Forum Allergy Rhinol (2013) 0.97
Automated image analysis of digital colposcopy for the detection of cervical neoplasia. J Biomed Opt (2008) 0.96
Translationally optimal codons associate with aggregation-prone sites in proteins. Proteomics (2010) 0.96
Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design. J Mol Evol (2014) 0.95
Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin. Philos Trans R Soc Lond B Biol Sci (2013) 0.95
Correspondence in texture features between two mammographic views. Med Phys (2005) 0.95
Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biol Evol (2011) 0.95
Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses. BMC Evol Biol (2011) 0.94
PeptideBuilder: A simple Python library to generate model peptides. PeerJ (2013) 0.93
Rapid adaptive amplification of preexisting variation in an RNA virus. J Virol (2008) 0.93
Automated calculation of symmetry measure on clinical photographs. J Eval Clin Pract (2010) 0.93
Risk factors for development of chronic rhinosinusitis in patients with allergic rhinitis. Int Forum Allergy Rhinol (2012) 0.92
A model-based framework for the detection of spiculated masses on mammography. Med Phys (2008) 0.92
Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites. Phys Biol (2015) 0.92
Short communication: dynamic constraints on the second phase compartment of HIV-infected cells. AIDS Res Hum Retroviruses (2011) 0.90
Incongruent fitness landscapes, not tradeoffs, dominate the adaptation of vesicular stomatitis virus to novel host types. J Gen Virol (2010) 0.90
A research agenda for appearance changes due to breast cancer treatment. Breast Cancer (Auckl) (2008) 0.90
Retinal nerve fiber layer reflectance for early glaucoma diagnosis. J Glaucoma (2014) 0.89
Validation of stereophotogrammetry of the human torso. Breast Cancer (Auckl) (2011) 0.89
Parametric power spectral density analysis of noise from instrumentation in MALDI TOF mass spectrometry. Cancer Inform (2007) 0.88
Model-driven, probabilistic level set based segmentation of magnetic resonance images of the brain. Conf Proc IEEE Eng Med Biol Soc (2011) 0.87
Methods of modelling viral disease dynamics across the within- and between-host scales: the impact of virus dose on host population immunity. Philos Trans R Soc Lond B Biol Sci (2010) 0.86
Cross-institutional evaluation of BI-RADS predictive model for mammographic diagnosis of breast cancer. AJR Am J Roentgenol (2002) 0.86
Breast cancer CADx based on BI-RAds descriptors from two mammographic views. Med Phys (2006) 0.86
Membrane environment imposes unique selection pressures on transmembrane domains of G protein-coupled receptors. J Mol Evol (2013) 0.85
Principal-oscillation-pattern analysis of gene expression. PLoS One (2012) 0.84
Detecting clusters of mutations. PLoS One (2008) 0.84
Does mutational robustness inhibit extinction by lethal mutagenesis in viral populations? PLoS Comput Biol (2010) 0.83
Socioeconomic disparities in the presentation of acute bacterial sinusitis complications in children. Laryngoscope (2013) 0.82
Amino-acid site variability among natural and designed proteins. PeerJ (2013) 0.82
Quantifying the aesthetic outcomes of breast cancer treatment: assessment of surgical scars from clinical photographs. J Eval Clin Pract (2010) 0.82
Guilt-by-association feature selection: identifying biomarkers from proteomic profiles. J Biomed Inform (2007) 0.82
Biomedical imaging informatics in the era of precision medicine: progress, challenges, and opportunities. J Am Med Inform Assoc (2013) 0.82
Lethal mutagenesis in a structured environment. J Theor Biol (2009) 0.82
Genomic evolution of vesicular stomatitis virus strains with differences in adaptability. J Virol (2010) 0.81
Specific and nonspecific host adaptation during arboviral experimental evolution. J Mol Microbiol Biotechnol (2012) 0.81
Path-length-multiplexed scattering-angle-diverse optical coherence tomography for retinal imaging. Opt Lett (2013) 0.81
A novel quantitative measure of breast curvature based on catenary. IEEE Trans Biomed Eng (2012) 0.81
Stereoscopic interpretation of low-dose breast tomosynthesis projection images. J Digit Imaging (2014) 0.81
Toward decision support for breast reconstruction: automated calculation of symmetry measure on clinical photographs. AMIA Annu Symp Proc (2008) 0.80
Snakules: a model-based active contour algorithm for the annotation of spicules on mammography. IEEE Trans Med Imaging (2010) 0.80
Helping patients make choices about breast reconstruction: a decision analysis approach. Plast Reconstr Surg (2014) 0.80
RNaseIII and T4 polynucleotide Kinase sequence biases and solutions during RNA-seq library construction. Biol Direct (2013) 0.80
Comparison of linear and non-linear classifiers for oral cancer screening by optical spectroscopy. AMIA Annu Symp Proc (2007) 0.79
A shape constrained parametric active contour model for breast contour detection. Conf Proc IEEE Eng Med Biol Soc (2012) 0.79
Empirical comparison of tests for differential expression on simulated time series microarray experiments. AMIA Annu Symp Proc (2006) 0.79
Indexes for three-class classification performance assessment--an empirical comparison. IEEE Trans Inf Technol Biomed (2009) 0.79
Analysis of Breast Contour using Rotated Catenary. AMIA Annu Symp Proc (2010) 0.78