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Published in BMC Genomics
2024
2024
Vol. 25
Issue #1
Robert A. Drewell, Daniel Klonaros, Jacqueline M. Dresch
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The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing
Published in NAR Genomics and Bioinformatics
Robert Drewell, Tayla C Cormier, Jacob L Steenwyk, James St. Denis, Javier F Tabima Restrepo, Jacqueline M. Dresch, Denis A Larochelle
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Published in G3: Genes|Genomes|Genetics
Daniel Klonaros, Jacqueline M. Dresch, Robert Drewell
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Jacqueline M. Dresch, Regan D. Conrad, Daniel Klonaros, Robert Drewell
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Improving bioinformatic tools using protein-DNA binding data
Joint Mathematics Meetings
Hynes Convention Center, Boston, MA
Jacqueline M. Dresch
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Transcriptome profile in Drosophila Kc and S2 embryonic cell lines
Published in G3 Genes|Genomes|Genetics
Daniel Klonaros, Jacqueline M Dresch, Robert A Drewell
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Published in Mathematical Biosciences
Michael Gaiewski, Robert Drewell, Jacqueline M. Dresch
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Biophysical and structural analysis of Antennapedia and Ultrabithorax homeodomain transcription factor-DNA binding affinities
Protein Science
Jeanmarie Loss, Jacqueline M. Dresch, Robert Drewell, Donald E. Spratt
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Analyzing the stability of gene expression using a simple reaction-diffusion model in an early Drosophila embryo
Published in Mathematical biosciences
Gregory D McCarthy, Robert A Drewell, Jacqueline M Dresch
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Rapid and efficient purification of Drosophila homeodomain transcription factors for biophysical characterization
Published in Protein expression and purification
Rachel Orlomoski, Aaron Bogle, Jeanmarie Loss, Rylee Simons, Jacqueline M Dresch, Robert A Drewell, Donald E Spratt
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Getting the most out of an interdisciplinary undergraduate research experience
Gryphon and Pleiades Honors Society Seminar Series
Clark University
Sponsored by Gryphon and Pleiades Honors Society
Jacqueline M. Dresch
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Biophysical and structural analysis of Drosophila transcription factors
Next-in-BIO 2018
Worcester MA
Aaron Bogle, Jacqueline M. Dresch, Robert Drewell, Donald E. Spratt
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The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies
Abdulkadir Elmas, Xiaodong Wang, Jacqueline M Dresch
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Whole genome bisulfite sequencing reveals a sparse, but robust pattern of DNA methylation in the Dictyostelium discoideum genome
Jacob Steenwyk, James St. Denis, Jacqueline M. Dresch, Denis A Larochelle, Robert Drewell
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Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks
Published in Mechanisms of development
Kade P Pettie, Jacqueline M Dresch, Robert A Drewell
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Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo
Rupinder Sayal, Jacqueline M Dresch, Irina Pushel, Benjamin R Taylor, David N Arnosti
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Nucleotide Interdependency in Transcription Factor Binding Sites in the Drosophila Genome
Published in Gene regulation and systems biology
Jacqueline M Dresch, Rowan G Zellers, Daniel K Bork, Robert A Drewell
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The Wisdom of Crowds: Can Mathematical Models Crack the cis Regulatory Code?
Published in Cell systems
Jacqueline M Dresch, David N Arnosti
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Global sensitivity analysis of a dynamic model for gene expression in Drosophila embryos
Gregory D McCarthy, Robert A Drewell, Jacqueline M Dresch
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MARZ: an algorithm to combinatorially analyze gapped n-mer models of transcription factor binding
Published in BMC bioinformatics
Rowan G Zellers, Robert A Drewell, Jacqueline M Dresch
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Deciphering the combinatorial architecture of a Drosophila homeotic gene enhancer
Published in Mechanisms of development
Robert A Drewell, Michael J Nevarez, Je S Kurata, Laure N Winkler, Lily Li, Jacqueline M Dresch
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A primer on thermodynamic-based models for deciphering transcriptional regulatory logic
Published in Biochimica et biophysica acta
Jacqueline M Dresch, Megan Richards, Ahmet Ay
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Flanking sequence context-dependent transcription factor binding in early Drosophila development
Published in BMC bioinformatics
Jessica L Stringham, Adam S Brown, Robert A Drewell, Jacqueline M Dresch
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TWO-LAYER MATHEMATICAL MODELING OF GENE EXPRESSION: INCORPORATING DNA-LEVEL INFORMATION AND SYSTEM DYNAMICS
Published in SIAM journal on applied mathematics
Jacqueline M Dresch, M A Thompson, David N Arnosti, Chichia Chiu
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Global parameter estimation for thermodynamic models of transcriptional regulation
Published in Methods (San Diego, Calif.)
Yerzhan Suleimenov, Ahmet Ay, Md A Samee, Jacqueline M Dresch, Saurabh Sinha, David N Arnosti
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Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects
Published in BMC systems biology
Jacqueline M Dresch, Xiaozhou Liu, David N Arnosti, Ahmet Ay
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Network structure, and vaccination strategy and effort interact to affect the dynamics of influenza epidemics
Published in Journal of theoretical biology
G Hartvigsen, J M Dresch, A L Zielinski, A J Macula, C C C Leary
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Two shadow enhancers regulate twin of eyeless expression during early Drosophila development
Jacqueline M. Dresch, Luke L. Nourie, Regan D. Conrad, Lindsay T. Carlson, Elizabeth Tchantouridze, Biruck Tessema, Eleanor Verhagen, Mahima Gupta, Diego Borges-Rivera, Robert Drewell
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Precise measurements of protein-DNA binding affinities support the use of PWM-based approaches in modeling transcriptional regulation
Jacqueline M. Dresch, Fadwa Mekkaoui, Eleanor Verhagen, Rachel Orlomoski, Sean Monroe, Aaron Bogle, Navid Al-Hassan, Robert Drewell, Don E. Spratt
