D Gresham

Publications (23)

A Bright IDEA.

Molecular systems biology

Avec: Christopher Jackson , David Gresham

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

Nucleic acids research

Avec: Pieter Spealman , Jaden Burrell , David Gresham

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

Molecular systems biology

Avec: Siyu Sun , Anastasia Baryshnikova , Nathan Brandt , David Gresham

Evaluating the Feasibility and Effectiveness of an Australian Safety Planning Smartphone Application: A Pilot Study Within a Tertiary Mental Health Service.

Suicide & life-threatening behavior

Avec: Glenn A Melvin , Daniel Gresham , Susan Beaton , Jan Coles , Bruce J Tonge , Michael S Gordon , Barbara Stanley

An evolving view of copy number variants.

Current genetics

Avec: Stephanie Lauer , David Gresham

Cellular quiescence in budding yeast.

Yeast (Chichester, England)

Avec: Siyu Sun , David Gresham

Simultaneous estimation of gene regulatory network structure and RNA kinetics from single cell gene expression.

bioRxiv : the preprint server for biology

Avec: Christopher A Jackson , Maggie Beheler-Amass , Andreas Tjärnberg , Ina Suresh , Angela Shang-Mei Hickey , Richard Bonneau , David Gresham

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

Journal of molecular evolution

Avec: Pieter Spealman , Titir De , Julie N Chuong , David Gresham

Phenotypic Variability of LGMD 2C/R5 in a Genetically Homogenous Group of Bulgarian Muslim Roma.

Genes

Avec: Ani Taneva , David Gresham , Velina Guergueltcheva , Teodora Chamova , Veneta Bojinova , Mariana Gospodinova , Maria Katzarova , Radoslav Petkov , Thomas Voit , Lidia Aneva , Ognyan Asenov , Bilyana Georgieva , Violeta Mihaylova , Stoyan Bichev , Tihomir Todorov , Albena Todorova , Luba Kalaydjieva , Ivailo Tournev

Template switching during DNA replication is a prevalent source of adaptive gene amplification.

bioRxiv : the preprint server for biology

Avec: Julie N Chuong , Nadav Ben Nun , Ina Suresh , Julia Cano Matthews , Titir De , Grace Avecilla , Farah Abdul-Rahman , Nathan Brandt , Yoav Ram , David Gresham

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

bioRxiv : the preprint server for biology

Avec: Pieter Spealman , Carolina de Santana , Titir De , David Gresham

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

Viruses

Avec: Christian V Forst , Matthew Chung , Megan Hockman , Lauren Lashua , Emily Adney , Angela Hickey , Michael Carlock , Ted Ross , Elodie Ghedin , David Gresham

Optimized Quantification of Intrahost Viral Diversity in SARS-CoV-2 and Influenza Virus Sequence Data.

bioRxiv : the preprint server for biology

Avec: A E Roder , Kee Johnson , M Knoll , M Khalfan , B Wang , S Schultz-Cherry , S Banakis , A Kreitman , C Mederos , J-H Youn , R Mercado , W Wang , D Ruchnewitz , M I Samanovic , M J Mulligan , M Lassig , M Åuksza , S Das , D Gresham , E Ghedin

mRNA condensation fluidizes the cytoplasm.

bioRxiv : the preprint server for biology

Avec: Ying Xie , Tiewei Liu , David Gresham , Liam J Holt

Host obesity impacts genetic variation in influenza A viral populations.

bioRxiv : the preprint server for biology

Avec: Marissa Knoll , Rebekah Honce , Victoria Meliopoulos , Stacey Schultz-Cherry , Elodie Ghedin , David Gresham

Host obesity impacts genetic variation in influenza A viral populations.

Journal of virology

Avec: Marissa Knoll , Rebekah Honce , Victoria Meliopoulos , Ernesto Alejandro Segredo-Otero , Katherine E E Johnson , Stacey Schultz-Cherry , Elodie Ghedin , David Gresham

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

eLife

Avec: Christopher A Jackson , Dayanne M Castro , Giuseppe-Antonio Saldi , Richard Bonneau , David Gresham

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

Bioinformatics (Oxford, England)

Avec: Claudia Skok Gibbs , Christopher A Jackson , Giuseppe-Antonio Saldi , Andreas Tjärnberg , Aashna Shah , Aaron Watters , Nicholas De Veaux , Konstantine Tchourine , Ren Yi , Tymor Hamamsy , Dayanne M Castro , Nicholas Carriero , Bram L Gorissen , David Gresham , Emily R Miraldi , Richard Bonneau

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

Genome biology

Avec: Andreas Tjärnberg , Maggie Beheler-Amass , Christopher A Jackson , Lionel A Christiaen , David Gresham , Richard Bonneau

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

bioRxiv : the preprint server for biology

Avec: Siyu Sun , Daniel Tranchina , David Gresham

Copy number variation alters local and global mutational tolerance.

Genome research

Avec: Grace Avecilla , Pieter Spealman , Julia Matthews , Elodie Caudal , Joseph Schacherer , David Gresham

Prokaryote communities along a source-to-estuary river continuum in the Brazilian Atlantic Forest.

PeerJ

Avec: Carolina O de Santana , Pieter Spealman , Eddy Oliveira , David Gresham , Taise de Jesus , Fabio Chinalia

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

PLoS computational biology

Avec: Rodoniki Athanasiadou , Benjamin Neymotin , Nathan Brandt , Wei Wang , Lionel Christiaen , David Gresham , Daniel Tranchina

Réseau de co-auteurs

David Gresham 21 collaborations

Pieter Spealman 5 collaborations

Christopher A Jackson 4 collaborations

Richard Bonneau 4 collaborations

Siyu Sun 3 collaborations

Nathan Brandt 3 collaborations

Andreas Tjärnberg 3 collaborations

Titir De 3 collaborations

Elodie Ghedin 3 collaborations

Maggie Beheler-Amass 2 collaborations

Ina Suresh 2 collaborations

Julie N Chuong 2 collaborations

Grace Avecilla 2 collaborations

Marissa Knoll 2 collaborations

Rebekah Honce 2 collaborations

Victoria Meliopoulos 2 collaborations

Stacey Schultz-Cherry 2 collaborations

Dayanne M Castro 2 collaborations

Giuseppe-Antonio Saldi 2 collaborations

Daniel Tranchina 2 collaborations

Christopher Jackson 1 collaboration

Jaden Burrell 1 collaboration

Anastasia Baryshnikova 1 collaboration

Glenn A Melvin 1 collaboration

Daniel Gresham 1 collaboration

Susan Beaton 1 collaboration

Jan Coles 1 collaboration

Bruce J Tonge 1 collaboration

Michael S Gordon 1 collaboration

Barbara Stanley 1 collaboration

Stephanie Lauer 1 collaboration

Angela Shang-Mei Hickey 1 collaboration

Ani Taneva 1 collaboration

Velina Guergueltcheva 1 collaboration

Teodora Chamova 1 collaboration

Veneta Bojinova 1 collaboration

Mariana Gospodinova 1 collaboration

Maria Katzarova 1 collaboration

Radoslav Petkov 1 collaboration

Thomas Voit 1 collaboration

Lidia Aneva 1 collaboration

Ognyan Asenov 1 collaboration

Bilyana Georgieva 1 collaboration

Violeta Mihaylova 1 collaboration

Stoyan Bichev 1 collaboration

Tihomir Todorov 1 collaboration

Albena Todorova 1 collaboration

Luba Kalaydjieva 1 collaboration

Ivailo Tournev 1 collaboration

Nadav Ben Nun 1 collaboration

Julia Cano Matthews 1 collaboration

Farah Abdul-Rahman 1 collaboration

Yoav Ram 1 collaboration

Carolina de Santana 1 collaboration

Christian V Forst 1 collaboration

Matthew Chung 1 collaboration

Megan Hockman 1 collaboration

Lauren Lashua 1 collaboration

Emily Adney 1 collaboration

Angela Hickey 1 collaboration

Michael Carlock 1 collaboration

Ted Ross 1 collaboration

A E Roder 1 collaboration

Kee Johnson 1 collaboration

M Knoll 1 collaboration

M Khalfan 1 collaboration

B Wang 1 collaboration

S Schultz-Cherry 1 collaboration

S Banakis 1 collaboration

A Kreitman 1 collaboration

C Mederos 1 collaboration

J-H Youn 1 collaboration

R Mercado 1 collaboration

W Wang 1 collaboration

D Ruchnewitz 1 collaboration

M I Samanovic 1 collaboration

M J Mulligan 1 collaboration

M Lassig 1 collaboration

M Åuksza 1 collaboration

S Das 1 collaboration

E Ghedin 1 collaboration

Ying Xie 1 collaboration

Tiewei Liu 1 collaboration

Liam J Holt 1 collaboration

Ernesto Alejandro Segredo-Otero 1 collaboration

Katherine E E Johnson 1 collaboration

Claudia Skok Gibbs 1 collaboration

Aashna Shah 1 collaboration

Aaron Watters 1 collaboration

Nicholas De Veaux 1 collaboration

Konstantine Tchourine 1 collaboration

Ren Yi 1 collaboration

Tymor Hamamsy 1 collaboration

Nicholas Carriero 1 collaboration

Bram L Gorissen 1 collaboration

Emily R Miraldi 1 collaboration

Lionel A Christiaen 1 collaboration

Julia Matthews 1 collaboration

Elodie Caudal 1 collaboration

Joseph Schacherer 1 collaboration

Carolina O de Santana 1 collaboration

Eddy Oliveira 1 collaboration

Taise de Jesus 1 collaboration

Fabio Chinalia 1 collaboration

Rodoniki Athanasiadou 1 collaboration

Benjamin Neymotin 1 collaboration

Wei Wang 1 collaboration

Lionel Christiaen 1 collaboration