D. Gresham

发表

Comparing whole genomes using DNA microarrays

Maitreya J. Dunham, D. Botstein, D. Gresham, 2008, Nature Reviews Genetics.

Coordination of growth rate, cell cycle, stress response, and metabolic activity in yeast.

Matthew J. Brauer, D. Botstein, J. Matese, 2008, Molecular biology of the cell.

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

Dayanne M. Castro, Richard Bonneau, D. Gresham, 2020, eLife.

Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen

D. Gresham, Darach Miller, Nathan Brandt, 2018, PLoS genetics.

Global analysis of gene expression dynamics identifies factors required for accelerated mRNA degradation

D. Gresham, Darach Miller, Nathan Brandt, 2018, bioRxiv.

Single-cell copy number variant detection reveals the dynamics and diversity of adaptation

Sasha F. Levy, Sasha F Levy, David Gresham, 2018, bioRxiv.

Steady-state and dynamic gene expression programs in Saccharomyces cerevisiae in response to variation in environmental nitrogen

Edoardo M. Airoldi, David Gresham, Tatsu Hashimoto, 2016, Molecular biology of the cell.

The functional basis of adaptive evolution in chemostats.

D. Gresham, Jungeui Hong, 2014, FEMS microbiology reviews.

The enduring utility of continuous culturing in experimental evolution.

David Gresham, Maitreya J. Dunham, Maitreya J Dunham, 2014, Genomics.

Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

D. Gresham, Jungeui Hong, 2014, PLoS genetics.

The use of chemostats in microbial systems biology.

David Gresham, Naomi Ziv, D. Gresham, 2013, Journal of visualized experiments : JoVE.

Genetic and Nongenetic Determinants of Cell Growth Variation Assessed by High-Throughput Microscopy

M. Siegal, D. Gresham, N. Ziv, 2013, Molecular biology and evolution.

System-Level Analysis of Genes and Functions Affecting Survival During Nutrient Starvation in Saccharomyces cerevisiae

David Botstein, John D. Storey, David Gresham, 2011, Genetics.

The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

David Botstein, David Gresham, Maitreya J. Dunham, 2008, PLoS genetics.

Gene regulatory network reconstruction using single-cell RNA sequencing of barcoded genotypes in diverse environments

Dayanne M. Castro, Richard Bonneau, D. Gresham, 2019, bioRxiv.

A molecular barcoded yeast ORF library enables mode-of-action analysis of bioactive compounds

D. Botstein, G. Giaever, B. Andrews, 2009, Nature Biotechnology.

De-Novo Learning of Genome-Scale Regulatory Networks in S. cerevisiae

P. Kemmeren, A. Statnikov, Sisi Ma, 2014, PloS one.

Dissection of genetically complex traits with extremely large pools of yeast segregants

Leonid Kruglyak, Amy A. Caudy, David Gresham, 2010, Nature.

Oracle® Reference Architecture

D. Gresham, Dave Chappelle, Bob Hensle, 2010 .

Genome-Wide Analysis of Nucleotide-Level Variation in Commonly Used Saccharomyces cerevisiae Strains

Kara Dolinski, David Botstein, Leonid Kruglyak, 2007, PloS one.

N-myc downstream-regulated gene 1 is mutated in hereditary motor and sensory neuropathy-Lom.

P K Thomas, F. Baas, A. Rosenthal, 2000, American journal of human genetics.

High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly Used Candida albicans Strains

J. Berman, D. Gresham, D. Abbey, 2011, G3: Genes | Genomes | Genetics.

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0

Dayanne M. Castro, D. Gresham, Emily R. Miraldi, 2022, Bioinformatics.

Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states

A. Baryshnikova, D. Gresham, Nathan Brandt, 2020, Molecular systems biology.

Accumulation of Recessive Lethal Mutations in Saccharomyces cerevisiae mlh1 Mismatch Repair Mutants Is Not Associated With Gross Chromosomal Rearrangements

D. Botstein, D. Gresham, E. Alani, 2006, Genetics.

Human genetics: Simplifying complexity

D. Gresham, 2002, Nature Reviews Genetics.

Differential analysis of prokaryotic 1 communities from pristine mangrove tidal 2 zone sediments reveal distinct structures 3 and functional profiles 4 5

D. Gresham, P. Spealman, F. Chinalia, 2020 .

Predicting seasonal influenza vaccine response using systemic gene expression profiling

C. Forst, D. Gresham, E. Ghedin, 2022, medRxiv.

OP-MOLB210173 4362..4375

D. Tranchina, D. Gresham, Farah Abdul-Rahman, 2021 .

Neural networks enable efficient and accurate simulation-based inference of evolutionary parameters from adaptation dynamics

G. Sherlock, D. Gresham, Grace Avecilla, 2022, PLoS biology.

PLOS Biology Simulation-based inference of evolutionary parameters from adaptation dynamics using neural networks

G. Sherlock, D. Gresham, Grace Avecilla, 2022 .

N-myc downstream-regulated gene 1 is mutated in hereditary motor and sensory neuropathy-Lom.

F. Baas, A. Rosenthal, D. Gresham, 2000, American journal of human genetics.

Hereditary motor and sensory neuropathy Lom

D. Gresham, L. Kalaydjieva, R. King, 2001 .

Hereditary motor and sensory neuropathy – Lom (HMSNL): refined genetic mapping in Romani (Gypsy) families from several European countries

F. Baas, A. Starr, D. Gresham, 2000, Neuromuscular Disorders.

Influenza A virus reassortment is strain dependent

D. Gresham, E. Ghedin, Tsui-Wen Chou, 2022, bioRxiv.

Complex Genomic Rearrangements following Selection in a Glutamine-Limited Medium over Hundreds of Generations

D. Gresham, Grace Avecilla, P. Spealman, 2022, Microbiology resource announcements.

Vaccination History, Body Mass Index, Age, and Baseline Gene Expression Predict Influenza Vaccination Outcomes

C. Forst, D. Gresham, E. Ghedin, 2022, Viruses.

Hst3p, a histone deacetylase, promotes maintenance of Saccharomyces cerevisiae chromosome III lacking efficient replication origins

C. Newlon, D. Gresham, C. Irene, 2015, Molecular Genetics and Genomics.

The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time.

Giovanni Destro-Bisol, David Gresham, Marcus W Feldman, 2004, American journal of human genetics.

Design and Analysis of Bar-seq Experiments

David G. Robinson, John D. Storey, David Gresham, 2013, G3: Genes, Genomes, Genetics.

Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae

David Gresham, Benjamin Neymotin, D. Gresham, 2016, G3: Genes, Genomes, Genetics.

The Details in the Distributions: Why and How to Study Phenotypic Variability This Review Comes from a Themed Issue on Systems Biology Experimental Methods for Studying Phenotypic Variability within Genotype Variability between Genotype Variation between Plate Technical Variation between Environment

Orkun S. Soyer, M. Siegal, D. Gresham, 2022 .

Structure primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference

D. Gresham, R. Bonneau, L. Christiaen, 2023, bioRxiv.

Genetic variation and disease in the Roma (Gypsies)

D. Gresham, 2001 .

Genome-Wide Detection of Polymorphisms at Nucleotide Resolution with a Single DNA Microarray

Maitreya J. Dunham, D. Botstein, S. Pratt, 2006, Science.

Origins and divergence of the Roma (gypsies).

P. Underhill, P. Shen, P. Oefner, 2001, American journal of human genetics.

Meeting Report: Experimental and Evolutionary Approaches to Yeast and Other Organisms 2018

D. Gresham, G. Rancati, Giulia Rancati, 2019, G3: Genes, Genomes, Genetics.

Amino Acid Transporter Genes Are Essential for FLO11-Dependent and FLO11-Independent Biofilm Formation and Invasive Growth in Saccharomyces cerevisiae

E. Boles, B. Regenberg, D. Gresham, 2012, PloS one.

Genetic studies of the Roma (Gypsies): a review

D. Gresham, L. Kalaydjieva, F. Calafell, 2001, BMC Medical Genetics.

Evolution: Fitness tracking for adapting populations

D. Gresham, 2015, Nature.

Fluctuating Environments Maintain Genetic Diversity through Neutral Fitness Effects and Balancing Selection

D. Tranchina, D. Gresham, Farah Abdul-Rahman, 2021, bioRxiv.

Predicting Cellular Growth from Gene Expression Signatures

Edoardo M. Airoldi, David Botstein, Olga G. Troyanskaya, 2009, PLoS Comput. Biol..

Adaptation to diverse nitrogen-limited environments by deletion or extrachromosomal element formation of the GAP1 locus

D. Botstein, B. Regenberg, D. Gresham, 2010, Proceedings of the National Academy of Sciences.

Global Mapping of Transposon Location

David Gresham, Stephen C Pratt, Johannes Dapprich, 2006, PLoS genetics.

Inverted duplicate DNA sequences increase translocation rates through sequencing nanopores resulting in reduced base calling accuracy

D. Gresham, P. Spealman, Jaden Burrell, 2020, Nucleic acids research.

Nanopore sequencing undergoes catastrophic sequence failure at inverted duplicated DNA sequences

David Gresham, D. Gresham, P. Spealman, 2019, bioRxiv.

An evolving view of copy number variants

D. Gresham, Stephanie Lauer, 2019, Current Genetics.

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0

Dayanne M. Castro, N. Carriero, D. Gresham, 2021, bioRxiv.

Determination of in vivo RNA kinetics using RATE-seq

D. Gresham, R. Athanasiadou, Benjamin Neymotin, 2014, RNA.

Rise of the Machines

Leonid Kruglyak, David Gresham, L. Kruglyak, 2008, PLoS genetics.

Determining mRNA Decay Rates Using RNA Approach to Equilibrium Sequencing (RATE-Seq).

D. Gresham, Farah Abdul-Rahman, 2017, Methods in molecular biology.

Effects of tidal influence on the structure and function of prokaryotic communities in the sediments of a pristine Brazilian mangrove

D. Gresham, P. Spealman, F. Chinalia, 2021 .

Large-scale differences in diversity and functional adaptations of prokaryotic communities from conserved and anthropogenically impacted mangrove sediments in a tropical estuary

D. Gresham, P. Spealman, F. Chinalia, 2021, PeerJ.

Global determinants of mRNA degradation rates in Saccharomyces cerevisiae

D. Gresham, Benjamin Neymotin, Victoria M. Ettorre, 2015, bioRxiv.

Optimized quantification of intra-host viral diversity in SARS-CoV-2 and influenza virus sequence data

M. Lässig, M. Mulligan, D. Gresham, 2021, bioRxiv.

An incoherent feedforward loop facilitates adaptive tuning of gene expression

Ally Yang, D. Gresham, Nathan Brandt, 2018, eLife.

An incoherent feedforward loop facilitates adaptive tuning of gene 15 expression 16 17

Ally Yang, D. Gresham, Nathan Brandt, 2018 .

Adaptive evolution of transcription factor binding affinities

Ally Yang, D. Gresham, Nathan Brandt, 2017, bioRxiv.

Mutation history of the roma/gypsies.

Jeff P. Reeve, J. Reeve, A. Tordai, 2004, American journal of human genetics.

Simulation-based inference of evolutionary parameters from adaptation dynamics using neural networks

G. Sherlock, D. Gresham, Grace Avecilla, 2021, bioRxiv.

Optimized detection of sequence variation in heterozygous genomes using DNA microarrays with isothermal-melting probes

D. Botstein, L. Kruglyak, D. B. Gordon, 2010, Proceedings of the National Academy of Sciences.

Cellular quiescence in budding yeast

D. Gresham, Siyu Sun, 2020, Yeast.

Resolving the Complex Genetic Basis of Phenotypic Variation and Variability of Cellular Growth

David Gresham, Naomi Ziv, Mark L Siegal, 2017, Genetics.

A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory

Wei Wang, Daniel Tranchina, Lionel Christiaen, 2019, PLoS Comput. Biol..

Growth Rate-Dependent Global Amplification of Gene Expression

D. Tranchina, D. Gresham, Darach Miller, 2016, bioRxiv.

Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing.

Jungeui Hong, David Gresham, D. Gresham, 2017, BioTechniques.

Functional genomics and metabolomics advance the ethnobotany of the Samoan traditional medicine “matalafi”

Allegra T. Aron, P. Dorrestein, D. Gresham, 2021, Proceedings of the National Academy of Sciences.

Regulatory kinase genetic interaction profiles differ between environmental conditions and cellular states

A. Baryshnikova, D. Gresham, Nathan Brandt, 2019, bioRxiv.

Copy number variants alter local and global mutational tolerance

D. Gresham, Grace Avecilla, P. Spealman, 2022, bioRxiv.

A common mechanism involving the TORC1 pathway can lead to amphotericin B-persistence in biofilm and planktonic Saccharomyces cerevisiae populations

B. Regenberg, D. Gresham, A. Folkesson, 2016, Scientific Reports.

Best Practices in Microbial Experimental Evolution: Using Reporters and Long-Read Sequencing to Identify Copy Number Variation in Experimental Evolution

D. Gresham, P. Spealman, Julie N. Chuong, 2023, Journal of Molecular Evolution.

mRNA condensation fluidizes the cytoplasm

D. Gresham, L. Holt, Ying Xie, 2023, bioRxiv.

Increased mesoscale diffusivity in response to acute glucose starvation

D. Gresham, L. Holt, Ying Xie, 2023, bioRxiv.

Increased mesoscale diffusivity in response to acute glucose starvation

D. Gresham, L. Holt, Ying Xie, 2023, microPublication biology.

Metagenomes from Soils along an Agricultural Transect in Ulster County, New York

D. Gresham, P. Spealman, G. Perron, 2023, Microbiology resource announcements.

DNA microarray-based mutation discovery and genotyping.

D. Gresham, 2011, Methods in molecular biology.

“Hit-and-Run” transcription: de novo transcription initiated by a transient bZIP1 “hit” persists after the “run”

Gloria M. Coruzzi, Ying Li, David Gresham, 2016, BMC Genomics.

Parallel proteomics and phosphoproteomics defines starvation signal specific processes in cell quiescence

D. Tranchina, D. Gresham, Siyu Sun, 2023, bioRxiv.

Host obesity impacts genetic variation in influenza A viral populations

D. Gresham, E. Ghedin, Victoria A. Meliopoulos, 2023, bioRxiv.

mRNA condensation fluidizes the cytoplasm

D. Gresham, L. Holt, Ying Xie, 2023, bioRxiv.

Modifying Reference Sequence and Annotation Files Quickly and Reproducibly with ref orm

D. Gresham, P. Spealman, M. Khalfan, 2021 .

An evolving view of copy number variants

D. Gresham, Stephanie Lauer, 2019, Current Genetics.

Amino Acid Transporter Genes Are Essential for FLO11-Dependent and FLO11-Independent Biofilm Formation and Invasive Growth in Saccharomyces cerevisiae

E. Boles, B. Regenberg, D. Gresham, 2012, PloS one.

The details in the distributions: why and how to study phenotypic variability.

M. Siegal, D. Gresham, Kerry Geiler-Samerotte, 2013, Current opinion in biotechnology.

Genetic and Nongenetic Determinants of Cell Growth Variation Assessed by High-Throughput Microscopy

M. Siegal, D. Gresham, Naomi Ziv, 2013, Molecular biology and evolution.

Post-transcriptional mechanisms modulate the consequences of adaptive copy number variation

D. Gresham, P. Spealman, Titir De, 2022 .

Copy number variation alters local and global mutational tolerance

D. Gresham, Grace Avecilla, P. Spealman, 2023, Genome research.

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction

Richard Bonneau, Christopher S. Poultney, Kristin C. Gunsalus, 2011, PloS one.

System-Level Analysis of Genes and Functions Affecting Survival During Nutrient Starvation in Saccharomyces cerevisiae

John D. Storey, D. Botstein, A. Caudy, 2011, Genetics.

A common mechanism involving the TORC1 pathway can lead to amphotericin B-persistence in biofilm and planktonic Saccharomyces cerevisiae populations

D. Gresham, A. Folkesson, Rasmus K Bojsen, 2016, Scientific Reports.

Multilevel gene expression changes in lineages containing adaptive copy number variants

D. Gresham, P. Spealman, Titir De, 2023, bioRxiv.

DNA replication errors are a major source of adaptive gene amplification

D. Gresham, Grace Avecilla, Farah Abdul-Rahman, 2024, bioRxiv.

A Bright IDEA

D. Gresham, Christopher A. Jackson, 2020, Molecular systems biology.

Single-cell gene regulatory network inference at scale: The Inferelator 3.0

Dayanne M. Castro, N. Carriero, D. Gresham, 2021 .