Publications From Our

Full-Time Bioinformaticians


Our full-time bioinformaticians understand the challenges faced by bench biologists and enjoy using their expertise to help others. Some of their published scientific contributions are listed below. Our full-timers comprise only a small part of our team, which is augmented by similarly qualified bioinformaticians who greatly expand the topics we cover.

 

Genome-wide changes in lncRNA, alternative splicing, and regional gene expression patterns in autism

Neelroop N Parikshak*, Vivek Swarup*, T Grant Belgard*, Manuel Irimia, et al. Nature (2016). 

*Co-first authors

CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting

M Münz, E Ruark, A Renwick, E Ramsay, M Clarke, S Mahamdallie, et al. Genome Medicine (2015)

A Transcriptomic Atlas of Mouse Neocortical Layers

T Grant Belgard, Ana C Marques, Peter L Oliver, Hatice Ozel Abaan, Tamara M Sirey, Anna Hoerder-Suabedissen, et al. Neuron  (2011).

CoverView: a sequence quality evaluation tool for next generation sequencing data

M Münz, S Mahamdallie, S Yost, A Rimmer, E Poyastro-Pearson, et al. Wellcome Open Research (2018)

Genome-wide, integrative analysis implicates microRNA dysregulation in autism spectrum disorder

Ye E Wu, Neelroop N Parikshak, T Grant Belgard, Daniel H Geschwind. Nature Neuroscience (2016). 

Correspondence between resting state activity and brain gene expression

Guang-Zhong Wang*, T Grant Belgard*, Deng Mao, Leslie Chen, Stefano, et al.  Neuron  (2015). 
*Co-first authors

Retooling spare parts: gene duplication and cognition

T Grant Belgard and Daniel H Geschwind. Nature Neuroscience (2012). 

Transcriptional Profiling of Layers of the Primate Cerebral Cortex

Zoltán Molnár* and T Grant Belgard*. Neuron  (2012). 

*Co-first authors

Molecularly distinct astrocyte subpopulations spatially pattern the adult mouse brain

Mykhailo BatiukAraks MartirosyanThierry VoetChris PontingT Grant BelgardMatthew G Holt. bioRxiv preprint (2018). 

Haploinsufficiency leads to neurodegeneration in C9ORF72 ALS/FTD human induced motor neurons

Yingxiao Shi, Shaoyu Lin, Kim A Staats, Yichen Li, Wen-Hsuan Chang, Shu-Ting Hung, Eric Hendricks, Gabriel R Linares, Yaoming Wang, Esther Y Son, Xinmei Wen, Kassandra Kisler, Brent Wilkinson, Louise Menendez, Tohru Sugawara, Phillip Woolwine, Mickey Huang, Michael J Cowan, Brandon Ge, Nicole Koutsodendris, Kaitlin P Sandor, Jacob Komberg, Vamshidhar R Vangoor, Ketharini Senthilkumar, Valerie Hennes, Carina Seah, Amy R Nelson, Tze-Yuan Cheng, Shih-Jong J Lee, Paul R August, Jason A Chen, Nicholas Wisniewski, Victor Hanson-Smith, T Grant Belgard, et al. Nature Medicine (2018). 

Mouse genomic variation and its effect on phenotypes and gene regulation

Thomas M Keane, Leo Goodstadt, Petr Danecek, Michael A White, Kim Wong, Binnaz Yalcin, Andreas Heger, Avigail Agam, Guy Slater, Martin Goodson, Nicholas A Furlotte, Eleazar Eskin, Christoffer Nellåker, Helen Whitley, James Cleak, Deborah Janowitz, Polinka Hernandez-Pliego, Andrew Edwards, T Grant Belgard, et al. Nature (2011). 

Adult pallium transcriptomes surprise in not reflecting predicted homologies across diverse chicken and mouse pallial sectors

T Grant Belgard*, Juan F Montiel, Wei Zhi Wang, Fernando Garcia-Moreno, Elliott H Margulies, Chris P Ponting*, Zoltán Molnár*. Proceedings of the National Academy of Sciences of the United States of America (2013).  (free PDF)

*co-corresponding authors

The role of flexibility and conformational selection in the binding promiscuity of PDZ domains

M Münz, J Hein, PC Biggin. PLoS Computational Biology (2012)

Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

M Münz, R Lyngsø, J Hein, PC Biggin. BMC Bioinformatics (2010)

JGromacs: a Java package for analyzing protein simulations

M Münz, PC Biggin. Journal of
Chemical Information and Modeling (2012)

Population structure confounds autism genetic classifier

T Grant Belgard, Ivana Jankovic, Jennifer K Lowe, Daniel H Geschwind. Molecular Psychiatry (2013).

Analysis of B cell repertoire dynamics following hepatitis B vaccination in humans, and enrichment of vaccine- specific antibody sequences

JD Galson, J Trück, A Fowler, EA Clutterbuck, M Münz, V Cerundolo, et al. EBioMedicine (2015)

In-depth assessment of within-individual and inter-individual variation in the B cell receptor repertoire

JD Galson, J Trück, A Fowler, M Münz, V Cerundolo, AJ Pollard, G Lunter, et al. Frontiers in Immunology
(2015)

Significant transcriptional changes in 15q duplication but not Angelman syndrome deletion stem cell-derived neurons

Nora Urraca, Kevin Hope, A Kaitlyn Victor, T Grant Belgard, Rawaha Memon, Sarita Goorha, Colleen Valdez, Quynh T Tran, Silvia Sanchez, Juanma Ramirez, Martin Donaldson, Dave Bridges, Lawrence T Reiter. Molecular Autism (2018). 

An Immunoaffinity-Based Method for Isolating Ultrapure Adult Astrocytes Based on ATP1B2 Targetting by the ACSA-2 Antibody 

Mykhailo Y. Batiuk, Filip de Vin, Sandra I. Duqué, Chen Li, Takashi Saito, Takaomi Saido, Mark Fiers, T. Grant Belgard, Matthew G. Holt. The Journal of Biological Chemistry (2017). 

Elevated gene expression of most microglial markers, and reduced expression of most pyramidal neuron and interneuron markers, in postmortem autism cortex

Rebeca Borges-Monroy, Chris Ponting*, T Grant Belgard*. bioRxiv preprint (2015). 

*co-corresponding authors

The Quality Sequencing Minimum (QSM): providing comprehensive, consistent, transparent next generation sequencing data quality assurance

S Mahamdallie, E Ruark, S Yost, M Münz, A Renwick, et al. Wellcome Open Research (2018)

OpEx – a validated, automated pipeline optimised for clinical exome sequence analysis

E Ruark, M Münz, M Clarke, A Renwick, E Ramsay, A Elliott, S Seal, et al. Scientific Reports (2016)

The ICR1000 UK exome series: a resource of gene variation in an outbred population

E Ruark, M Münz, A Renwick, M Clarke, E Ramsay, S Hanks, et al. F1000Research (2015)

Histone Acetylome-wide Association Study of Autism Spectrum Disorder

Wenjie Sun, Jeremie Poschmann, Ricardo Cruz-Herrera del Rosario, Neelroop N Parikshak, Hajira Shreen Hajan, Vibhor Kumar, Ramalakshmi Ramaswamy, T Grant Belgard, et al. Cell (2016). 

Water-Phase Synthesis of Cationic Silica/Polyamine Nanoparticles

Quang X Nguyen, T Grant Belgard, John J Taylor, Vinit S Murthy, Naomi J Halas, Michael S Wong. Chemistry of Materials (2012). 

Plasma cell antibody repertoire analysis following administration of meningococcal polysaccharide and protein-polysaccharide conjugate vaccines: evidence of distinct patterns of B cell activation

JD Galson, EA Clutterbuck, J Trueck, M Münz, A Fowler, V Cerundolo, et al. Immunology (2014)

Endothelium-derived extracellular vesicles promote splenic monocyte mobilisation in myocardial infarction

Naveed Akbar, Janet Digby, Thomas J Cahill, Abhijeet N Tavare, Alastair L Corbin, Sushant Saluja, Sam Dawkins, Laurienne Edgar, Nadiia Rawlings, Klemen Ziberna, Eileen McNeill, Oxford Acute Myocardial Infarction (OxAMI) Study, Errin Johnson, Alaa A Aljabali, Rebecca A Dragovic, Mala Rohling, T Grant Belgard, et al. JCI Insight (2017).

Expression profiling of mouse subplate reveals a dynamic gene network and disease association with autism and schizophrenia

Anna Hoerder-Suabedissen, Franziska M Oeschger, Michelle L Krishnan, T Grant Belgard, et al. Proceedings of the National Academy of Sciences of the United States of America (2013).

The genomic landscape shaped by selection on transposable elements across 18 mouse strains

Christoffer Nellaker, Thomas M Keane, Binnaz Yalcin, Kim Wong, Avigail Agam, T Grant Belgard, Jonathan Flint, David J Adams, Wayne N Frankel, Chris P Ponting. Genome Biology (2012).

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