Academic research

Introduction

Dominic currently holds a MRC UKRI Fellowship at the MRC Weatherall Institute of Molecular Medicine (WIMM), University of Oxford. For more details relating to his position at the WIMM please visit his institute page. His background is diverse, spanning the fields of computer vision, machine learning, automated microscopy, bioimage analysis, image analysis, fluorescence correlation spectroscopy, cell biology, neuroscience, super resolution microscopy, high-perfomance computing and cloud computing. For details relating to his education and previous appointments please download his curriculum vitae below.

Curriculum vitae
Research affiliations
Research repositories
BioRxiv papers
Peer-reviewed research papers

Curriculum Vitae

Technical CV - click to download pdf.
Academic CV - click to download pdf.
Orcid ID - http://orcid.org/0000-0003-2685-4226

Research affiliations

Dominic is currently affiliated with the:

Wolfson Imaging Centre Oxford, WIMM. University of Oxford.
MRC Centre for Computational Biology, WIMM. University of Oxford.
The Department of Biochemical Engineering. University of Oxford.

Societies:
Between 2018-2020, Dominic was chair of the Royal Microscopical Society Image Analysis Focused Interest Group (RMS-IAFIG). Dominic is also on the UK management committee for the COST funded Neubias initiative.

Research repositories

Dominic develops and maintains a number of code repositories which support his research interests. Please refer to the main code repositories page for more details. Code repositories page

BioRxiv papers

Juban G, Sakakini N, Chagraoui H, Cheng Q, Soady K, Stoilova B, Garnett C, Waithe D, Doondeea J, Usukhbayar B, Karkoulia E, Alexiou M, Strouboulis J, Morrissey E, Roberts I, Porcher C, Vyas P. “Oncogenic Gata1 causes stage-specific megakaryocyte differentiation delay.” bioRxiv. DOI:10.1101/791079 (2019)

Waithe D, Brown JM, Reglinski K, Diez-Sevilla I, Roberts D, Eggeling C. “Object Detection Networks and Augmented Reality for Cellular Detection in Fluorescence Microscopy Acquisition and Analysis.” bioRxiv. DOI:10.1101/544833 (2019)

Urbančič a I, Brun J, Shrestha D, Waithe D, Eggeling C, Chojnacki J. “Lipid composition but not curvature is a determinant of a low molecular mobility within {HIV}-1 lipid envelope.” bioRxiv. DOI:10.1101/315168 (2018)

Martin Hailstone* , Lu Yang1, Dominic Waithe1, Tamsin J Samuels, Yoav Arava, Tomasz Dobrzycki, Richard M Parton and Ilan Davis. “Brain Development: Machine Learning Analysis Of Individual Stem Cells In Live 3D Tissue” bioRxiv. DOI:10.1101/137406 (2017)

Peer-reviewed research papers

41 Publications in peer-reviewed journals (http://orcid.org/0000-0003-2685-4226)

Martin Hailstone, Dominic Waithe, Tamsin J Samuels, Lu Yang, Ita Costello, Yoav Arava, Elizabeth Robertson, Richard M Parton, Ilan Davis “CytoCensus, mapping cell identity and division in tissues and organs using machine learning” eLife. DOI: 10.7554/eLife.51085 (2020)

Carravilla P, Chojnacki J, Rujas E, Insausti S, Largo E, Waithe D, Apellaniz B, Sicard T, Julien J, Eggeling C, Nieva JL. “Molecular recognition of the native {HIV}-1 {MPER} revealed by {STED} microscopy of single virions.” Nature Communications. DOI:10.1038/s41467-018-07962-9 (2019)

Chen Y, Gutowska-Owsiak D, Hardman CS, Westmoreland M, MacKenzie T, Cifuentes L, Waithe D, Lloyd-Lavery A, Marquette A, Londei M, Ogg G. “Proof-of-concept clinical trial of etokimab shows a key role for {IL}-33 in atopic dermatitis pathogenesis.” Science Translational Medicine. DOI:10.1126/scitranslmed.aax2945 (2019)

Sezgin E, Schneider F, Galiani S, Urbančič I, Waithe D, Lagerholm BC, Eggeling C. “Measuring nanoscale diffusion dynamics in cellular membranes with super-resolution STED-FCS.” Nature Protocols. DOI:10.1038/s41596-019-0127-9 (2019)

Brown JM, Roberts NA, Graham B, Waithe D, Lagerholm C, Telenius JM, Ornellas SD, Oudelaar AM, Scott C, Szczerbal I, Babbs C, Kassouf MT, Hughes JR, Higgs DR, Buckle VJ. “A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions.” Nature Communications. DOI:10.1038/s41467-018-06248-4 (2018)

Chagraoui H, Kristiansen MS, Ruiz JP, Serra-Barros A, Richter J, Hall-Ponselé E, Gray N, Waithe D, Clark K, Hublitz P, Repapi E, Otto G, Sopp P, Taylor S, Thongjuea S, Vyas P, Porcher C. “SCL/TAL1 cooperates with Polycomb RYBP-PRC1 to suppress alternative lineages in blood-fated cells.” Nature Communications. DOI:10.1038/s41467-018-07787-6 (2018)

Urbančič I, Brun J, Shrestha D, Waithe D, Eggeling C, Chojnacki J. “Lipid Composition but Not Curvature Is the Determinant Factor for the Low Molecular Mobility Observed on the Membrane of Virus-Like Vesicles.” Viruses. DOI:10.3390/v10080415 (2018)

Schneider F, Waithe D, BC L, Shrestha D, Sezgin E, Eggeling C, Fritzsche M. “Statistical Analysis of Scanning Fluorescence Correlation Spectroscopy Data Differentiates Free from Hindered Diffusion.” ACS nano. DOI:10.1021/acsnano.8b04080 (2018)

Spiess M, Hernandez-Varas P, Oddone A, Olofsson H, Blom H, Waithe D, Lock JG, Lakadamyali M, Strömblad S. “Active and inactive β1 integrins segregate into distinct nanoclusters in focal adhesions.” The Journal of Cell Biology. DOI:10.1083/jcb.201707075 (2018)

Schneider F, Waithe D, Galiani S, Bernardino de la Serna J, Sezgin E, Eggeling C. “Nanoscale Spatiotemporal Diffusion Modes Measured by Simultaneous Confocal and Stimulated Emission Depletion Nanoscopy Imaging..” Nano letters. DOI:10.1021/acs.nanolett.8b01190 (2018)

Hockman D, Adameyko I, Kaucka M, Barraud P, Otani T, Hunt A, AC H, Sock E, Waithe D, MCM F, Ernfors P, Ehinger S, MJ H, Brown N, Reese J, CVH B. “Striking parallels between carotid body glomus cell and adrenal chromaffin cell development..” Developmental biology. DOI:10.1016/j.ydbio.2018.05.016 (2018)

Brown JM, Roberts NA, Graham B, Waithe D, Lagerholm C, Telenius JM, Ornellas SD, Oudelaar M, Szczerbal I, Babbs C, Kassouf MT, Hughes JR, Higgs DR, Buckle VJ. “A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions.” bioxriv. DOI:10.1101/234427 (2017)

Dominic Waithe, Falk Schneider, Jakub Chojnacki, Mathias P. Clausen, Dilip Shrestha, Jorge Bernardino de la Serna, Christian Eggeling “ Optimized processing and analysis of conventional confocal microscopy generated scanning FCS data”, Methods. https://doi.org/10.1016/j.ymeth.2017.09.010

Jakub Chojnacki, Dominic Waithe, Pablo Carravilla, Nerea Huarte, Silvia Galiani, Jörg Enderlein & Christian Eggeling “Envelope glycoprotein mobility on HIV-1 particles depends on the virus maturation state” Nature Communications, pp. 8, Article number: 545 (2017)

Marco Fritzsche, Ricardo A. Fernandes, Veronica T. Chang, Huw Colin-York, Mathias P. Clausen, James H. Felce, Silvia Galiani, Christoph Erlenkämper, Ana M. Santos, John M. Heddleston, Isabela Pedroza-Pacheco, Dominic Waithe, Jorge Bernardino de la Serna, B. Christoffer Lagerholm, Tsung-li Liu, Teng-Leong Chew, Eric Betzig, Simon J. Davis, and Christian Eggeling “Cytoskeletal actin dynamics shape a ramifying actin network underpinning immunological synapse formation”, Sci Adv. June; 3(6): e1603032. (2017)

Falk Schneider, Dominic Waithe, Mathias P. Clausen, Silvia Galiani, Thomas Koller, Gunes Ozhan, Christian Eggeling, Erdinc Sezgin “Diffusion of lipids and GPI-anchored proteins in actin-free plasma membrane vesicles measured by STED-FCS”, Molecular biology of the cell, pp. 1507—1518, 28 no. 11 (2017)

Sezgin, Erdinc, Falk Schneider, Victoria Zilles, Iztok Urbančič, Esther Garcia, Dominic Waithe, Andrey S. Klymchenko, and Christian Eggeling. “Polarity-Sensitive Probes for Superresolution Stimulated Emission Depletion Microscopy.” Biophysical Journal 113, no. 6 (2017): 1321-1330.

Dominic Waithe, Martin Hailstone, Mukesh Kumar Lalwani, Richard Parton, Lu Yang, Roger Patient, Christian Eggeling, and Ilan Davis. “3-D Density Kernel Estimation for Counting in Microscopy Image Volumes Using 3-D Image Filters and Random Decision Trees.” European Conference on Computer Vision workshop, pp. 244-255. Springer International Publishing, (2016).

Silvia Galiani2, Dominic Waithe , Katharina Reglinski, Luis Daniel Cruz-Zaragoza, Esther Garcia, Mathias P. Clausen, Wolfgang Schliebs, Ralf Erdmann, and Christian Eggeling. “Super-resolution Microscopy Reveals Compartmentalization of Peroxisomal Membrane Proteins.” Journal of Biological Chemistry 291, no. 33 (2016): 16948-16962.

Huw Colin-York, Dilip Shrestha, James H. Felce, Dominic Waithe, Emad Moeendarbary, Simon J. Davis, Christian Eggeling, and Marco Fritzsche. “Super-resolved traction force microscopy (STFM).” Nano letters 16, no. 4 (2016): 2633-2638.

Erdinc Sezgin, Fatma Betul Can, Falk Schneider, Mathias P. Clausen, Silvia Galiani, Tess A. Stanly, Dominic Waithe, Alexandria Colaco , Alf Honigmann, Daniel Wüstner , Frances Platt, Christian Eggeling. “A comparative study on fluorescent cholesterol analogs as versatile cellular reporters.” Journal of lipid research 57, no. 2 (2016): 299-309.

Mario Buono, Raffaella Facchini, Sahoko Matsuoka, Supat Thongjuea, Dominic Waithe, Tiago Luis, Alice Giustacchini, Peter Besmer, Adam Mead, Sten Eirik Jacobsen, and Claus Nerlov “A dynamic niche provides Kit ligand in a stage-specific manner to the earliest thymocyte progenitors.” Nature Cell Biology (2016) 10.1038/ncb3299

Chris A. Brackley, Jill M. Brown, Dominic Waithe, Christian Babbs, James Davies, Jim R. Hughes, Veronica J. Buckle, and Davide Marenduzzo. “Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models.” Genome Biology (2016). 10.1186/s13059-016-0909-0

Dominic Waithe, Mathias P. Clausen, Erdinc Sezgin, Christian Eggeling. “FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting.” Bioinformatics (2015): btv687.

Dominic Waithe, Peter Rennert, Gabriel Brostow, and Matthew DW Piper. “QuantiFly: Robust Trainable Software for Automated Drosophila Egg Counting.” Plos One (2015): e0127659.

Erdinc Sezgin, Dominic Waithe, Jorge Bernardino de la Serna, and Christian Eggeling. “Back Cover: Spectral Imaging to Measure Heterogeneity in Membrane Lipid.” ChemPhysChem 16, no. 7 (2015): 1560-1560.

Mathias P. Clausen, Erdinc Sezgin, Jorge Bernardino de la Serna, Dominic Waithe, B. Christoffer Lagerholm, and Christian Eggeling. “A straightforward approach for gated STED-FCS to investigate lipid membrane dynamics.” Methods 88 (2015): 67-75.

Giuseppe Vicidomini, Haisen Ta, Alf Honigmann, Veronika Mueller, Mathias P. Clausen, Dominic Waithe, Silvia Galiani et al. “Sted-flcs: An advanced tool to reveal spatiotemporal heterogeneity of molecular membrane dynamics.”Nano letters 15, no. 9 (2015): 5912-5918.

Chandima Jeewandara, Laksiri Gomes, N. Wickramasinghe, Danuta Gutowska-Owsiak, Dominic Waithe, S. A. Paranavitane, N. L. A. Shyamali, Graham S. Ogg, and Gathsaurie Neelika Malavige. “Platelet Activating Factor Contributes to Vascular Leak in Acute Dengue Infection.” PLoS neglected tropical diseases 9, no. 2 (2015): e0003459-e0003459.

Katharina Reglinski, Marina Keil, Sabrina Altendorf, Dominic Waithe, Christian Eggeling, Wolfgang Schliebs, and Ralf Erdmann. “Peroxisomal Import Reduces the Proapoptotic Activity of Deubiquitinating Enzyme USP2.”PloS one 10, no. 10 (2015): e0140685.

Madeleine M. Hipp, Dawn Shepherd, Sarah Booth, Dominic Waithe, Caetano Reis e Sousa, and Vincenzo Cerundolo. “The Processed Amino-Terminal Fragment of Human TLR7 Acts as a Chaperone To Direct Human TLR7 into Endosomes.” The Journal of Immunology 194, no. 11 (2015): 5417-5425.

Dominic, Waithe, Laurent Ferron, and Annette C. Dolphin. “Stargazin-related protein γ7 is associated with signalling endosomes in superior cervical ganglion neurons and modulates neurite outgrowth.” J Cell Sci 124, no. 12 (2011): 2049-2057.

Dominic, Waithe, Laurent Ferron, Karen M. Page, Kanchan Chaggar, and Annette C. Dolphin. “β-Subunits promote the expression of CaV2.2 channels by reducing their proteasomal degradation.” Journal of Biological Chemistry 286, no. 11 (2011): 9598-9611.

Laurent Ferron, Anthony Davies, Karen M. Page, David J. Cox, Jerôme Leroy, Dominic Waithe, Adrian J. Butcher et al. “The stargazin-related protein γ7 interacts with the mRNA-binding protein heterogeneous nuclear ribonucleoprotein A2 and regulates the stability of specific mRNAs, including Cav2. 2.” The Journal of Neuroscience 28, no. 42 (2008): 10604-10617.

Adaoha EC Ihekwaba, Stephen J. Wilkinson, Dominic Waithe, David S. Broomhead, Peter Li, Rachel L. Grimley, and Neil Benson. “Bridging the gap between in silico and cell‐based analysis of the nuclear factor‐κB signaling pathway by in vitro studies of IKK2.” FEBS Journal 274, no. 7 (2007).