Faculty

Institution

Unit

Venue

Daniel P. Aalberts

Williams College

Affiliations

Williams College

Department of Physics

NoneDaniel P. Aalberts is currently serving as a Physics faculty at Williams College.

Honors

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Experiences

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Education

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Daniel P. Aalberts

Williams College

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molecular biology nucleic acids rna biology biophysics rna structure prediction molecular biophysics gene expression transcription (biology) molecular cell biology biomolecular structure protein science rna processing protein folding bioinformatics structural molecular biology splicing variant microbiology biophysical chemistry protein biosynthesis protein synthesis biochemistry ultrafast laser spectroscopy photonics microbial cell factory molecular science genome biology protein expression biophysical modeling free energies ultrafast photoisomerization e. coli dna beacon kinetics thermodynamic modeling biophysical review metals molecular structure molecular physics quantum chemistry quantum science biological chemistry light science single molecule biophysics polymer modeling biological network visualization quantum dynamics coherent process quantum photonics electronic excited states long non-coding rna computational genomics sequence analysis optical physics transient grating sequence design loop space sequence alignment directed evolution monte carlo molecular research molecular computing protein modeling biological computation codon influence mrna levels rna pseudoknots oxidative stress homeostasis queuosine trna modification helix stacking two-length-scale polymer theory rnabow diagrams protein production quantum coherent dynamics simple scenario

Notable Scholarly Works

Notable Federal Grants

Collaborators

Base Composition at the Start of the Coding Sequence Controls the Balance Between Translation Initiation and Mrna Degradation in E. Coli. Nucleic Acids Research (2025)

molecular researchbase compositionmicrobial cell factorydna replicationprotein biosynthesismrna degradationtranscription factorsmolecular cell biologybiomolecular structureprotein sciencenucleic acidsrna processingtranscription (biology)molecular and cellular biologyprotein synthesismutagenesis (molecular biology technique)coding sequencetranscriptomegene expressionmolecular biologyrna biologymicrobiology

OPT: Codon Optimize Gene Sequences for E. Coli Protein Overexpression. Journal of Molecular Biology (2025)

genomicsgenome biologyfunctional genomicssequence alignmentdirected evolutiongeneticsnucleic acidsmolecular biologye. colibioinformatics

The Absence of the Queuosine Trna Modification Leads to Pleiotropic Phenotypes Revealing Perturbations of Metal and Oxidative Stress Homeostasis in Escherichia Coli K12. Metallomics (2022)

Leticia Pollo-OliveiraNick K DavisIntekhab HossainPeiying HoYifeng YuanPedro Salguero GarcíaCécile PereiraShane R ByrneJiapeng LengMelody SzeCrysten E Blaby-HaasAgnieszka SekowskaAlvaro MontoyaThomas BegleyAntoine DanchinDaniel P AalbertsAlexander AngerhoferJohn HuntAna ConesaPeter C DedonValérie de Crécy-Lagard

oxidative stress homeostasisqueuosine trna modificationmolecular biologyoxidative stressmetalsbiochemistry

The Four Mrna Bases Have Quite Different (Un)Folding Free Energies, Applications to Rna Splicing and Translation Initiation With Bindoligonet. Journal of Molecular Biology (2022)

rna structure predictionsplicing variantbiological chemistryfour mrna basesfree energiesbiochemistrymolecular sciencetranscription factorsmolecular cell biologyprotein foldingnucleic acidsrna processingtranscription (biology)protein synthesistranscriptomegene expressionmolecular biologyrna biologytranslation initiation

Optimizing Recombinant Protein Expression With Synonymous Codons. Biophysical Journal (2020)

Daniel WongKam-Ho WongGregory BoëlJohn F. HuntDaniel P. Aalberts

biophysical chemistrybiophysicsrecombinant protein expressionmolecular biologyprotein expressionprotein sciencesynonymous codonsbiophysical modeling

The New Strategies to Overcome Challenges in Protein Production in Bacteria. Microbial Biotechnology (2018)

Anna LipońskaFarès OusalemDaniel P. AalbertsJohn F. HuntGrégory Boël

biomanufacturingbiotechnologymicrobial cell factoryprotein biosynthesisprotein productionmicrobiologybiosynthesis

Codon Clarity or Conundrum?. Cell Systems (2017)

Daniel P. AalbertsGregory BoëlJohn F. Hunt

systems biologycell biology

Codon Influence on Protein Expression in E. Coli Correlates With Mrna Levels. Nature (2016)

Grégory BoëlReka LetsoHelen NeelyW. Nicholson PriceKam-Ho WongMin SuJon D. LuffMayank ValechaJohn K. EverettThomas B. ActonRong XiaoGaetano T. MontelioneDaniel P. AalbertsJohn F. Hunt

gene expressionmrna levelstranscription (biology)e. colimolecular cell biologyprotein synthesiscodon influencemolecular biologyprotein expressionprotein biosynthesisprotein sciencemicrobiologynucleic acids

Modeling Unpairing Costs for Fast Computation of the Net Binding Free Energy of an Oligo to an Mrna Target. Biophysical Journal (2014)

mrna targetprotein modelingbiological computationsystems biologymolecular sciencemolecular modellingmolecular computingfast computationmolecular biologytheoretical biologycomputational biologyprotein sciencemolecular informaticsnucleic acids

Free Energy Cost of Stretching Mrna Hairpin Loops Inhibits Small Rna Binding. Biophysical Journal (2013)

transcriptomerna structure predictionmolecular biophysicsbiophysicsgene expressionfree energy costtranscription (biology)molecular cell biologylong non-coding rnamolecular biologystructural molecular biologyrna biologynucleic acids

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Daniel P. Aalberts

Williams College

Affiliations

Williams College

Department of Physics

NoneDaniel P. Aalberts is currently serving as a Physics faculty at Williams College.

Honors

Create free account to unlock more features

Experiences

Create free account to unlock more features

Education

Create free account to unlock more features

Daniel P. Aalberts

Williams College

You can click a keyword to filter the displayed items

Notable Scholarly Works

Notable Federal Grants

Collaborators

Base Composition at the Start of the Coding Sequence Controls the Balance Between Translation Initiation and Mrna Degradation in E. Coli. Nucleic Acids Research (2025)

OPT: Codon Optimize Gene Sequences for E. Coli Protein Overexpression. Journal of Molecular Biology (2025)

genomicsgenome biologyfunctional genomicssequence alignmentdirected evolutiongeneticsnucleic acidsmolecular biologye. colibioinformatics

The Absence of the Queuosine Trna Modification Leads to Pleiotropic Phenotypes Revealing Perturbations of Metal and Oxidative Stress Homeostasis in Escherichia Coli K12. Metallomics (2022)

oxidative stress homeostasisqueuosine trna modificationmolecular biologyoxidative stressmetalsbiochemistry

The Four Mrna Bases Have Quite Different (Un)Folding Free Energies, Applications to Rna Splicing and Translation Initiation With Bindoligonet. Journal of Molecular Biology (2022)

Optimizing Recombinant Protein Expression With Synonymous Codons. Biophysical Journal (2020)

Daniel WongKam-Ho WongGregory BoëlJohn F. HuntDaniel P. Aalberts

biophysical chemistrybiophysicsrecombinant protein expressionmolecular biologyprotein expressionprotein sciencesynonymous codonsbiophysical modeling

The New Strategies to Overcome Challenges in Protein Production in Bacteria. Microbial Biotechnology (2018)

Anna LipońskaFarès OusalemDaniel P. AalbertsJohn F. HuntGrégory Boël

biomanufacturingbiotechnologymicrobial cell factoryprotein biosynthesisprotein productionmicrobiologybiosynthesis

Codon Clarity or Conundrum?. Cell Systems (2017)

Daniel P. AalbertsGregory BoëlJohn F. Hunt

systems biologycell biology

Codon Influence on Protein Expression in E. Coli Correlates With Mrna Levels. Nature (2016)

Grégory BoëlReka LetsoHelen NeelyW. Nicholson PriceKam-Ho WongMin SuJon D. LuffMayank ValechaJohn K. EverettThomas B. ActonRong XiaoGaetano T. MontelioneDaniel P. AalbertsJohn F. Hunt

Modeling Unpairing Costs for Fast Computation of the Net Binding Free Energy of an Oligo to an Mrna Target. Biophysical Journal (2014)

Free Energy Cost of Stretching Mrna Hairpin Loops Inhibits Small Rna Binding. Biophysical Journal (2013)

1
2
3
10 / page