Abe Pressman
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View article: Precision engineering of biological function with large-scale measurements and machine learning
Precision engineering of biological function with large-scale measurements and machine learning Open
As synthetic biology expands and accelerates into real-world applications, methods for quantitatively and precisely engineering biological function become increasingly relevant. This is particularly true for applications that require progr…
View article: Precision engineering of biological function with large-scale measurements and machine learning
Precision engineering of biological function with large-scale measurements and machine learning Open
As synthetic biology expands and accelerates into real-world applications, methods for quantitatively and precisely engineering biological function become increasingly relevant. This is particularly true for applications that require progr…
View article: Interpretable modeling of genotype–phenotype landscapes with state-of-the-art predictive power
Interpretable modeling of genotype–phenotype landscapes with state-of-the-art predictive power Open
Large-scale measurements linking genetic background to biological function have driven a need for models that can incorporate these data for reliable predictions and insight into the underlying biophysical system. Recent modeling efforts, …
View article: Kinetic sequencing ( <i>k</i> -Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters
Kinetic sequencing ( <i>k</i> -Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters Open
Characterizing genotype-phenotype relationships of biomolecules (e.g. ribozymes) requires accurate ways to measure activity for a large set of molecules. Kinetic measurement using high-throughput sequencing (e.g. k-Seq) is an emerging assa…
View article: The genotype‐phenotype landscape of an allosteric protein
The genotype‐phenotype landscape of an allosteric protein Open
Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale m…
View article: Kinetic sequencing (<i>k</i>-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters
Kinetic sequencing (<i>k</i>-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters Open
Characterization of genotype-phenotype relationships of genetically encoded molecules (e.g., ribozymes) requires accurate quantification of activity for a large set of molecules. Kinetic measurement using high-throughput sequencing (e.g., …
View article: The genotype-phenotype landscape of an allosteric protein
The genotype-phenotype landscape of an allosteric protein Open
Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here we report the large-scale me…
View article: The genotype-phenotype landscape of an allosteric protein
The genotype-phenotype landscape of an allosteric protein Open
Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Quantitative methods to characterize the genotype-phenotype relationships for allosteric proteins would provide data needed to imp…
View article: Mapping a Systematic Ribozyme Fitness Landscape Reveals a Frustrated Evolutionary Network for Self-Aminoacylating RNA
Mapping a Systematic Ribozyme Fitness Landscape Reveals a Frustrated Evolutionary Network for Self-Aminoacylating RNA Open
Molecular evolution can be conceptualized as a walk over a "fitness landscape", or the function of fitness (e.g., catalytic activity) over the space of all possible sequences. Understanding evolution requires knowing the structure of the f…
View article: Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences
Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences Open
The emergence of catalytic RNA is believed to have been a key event during the origin of life. Understanding how catalytic activity is distributed across random sequences is fundamental to estimating the probability that catalytic sequence…
View article: Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences
Analysis of in vitro evolution reveals the underlying distribution of catalytic activity among random sequences Open
The emergence of catalytic RNA is believed to have been a key event during the origin of life. Understanding how catalytic activity is distributed across random sequences is fundamental to estimating the probability that catalytic sequence…
View article: Additional file 4: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation
Additional file 4: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Open
Predicted Membrane Proteins. (XLSX 206 kb)
View article: Additional file 2: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation
Additional file 2: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Open
Genes in Msph. cuniculi not in other Methanosphaera. (XLSX 13 kb)
View article: Additional file 3: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation
Additional file 3: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Open
Genes in Mcor. parvum not in other Methanocorpusculum. (XLSX 16 kb)
View article: Additional file 5: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation
Additional file 5: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Open
Predicted Transporter Proteins. (XLSX 39 kb)