Simon Andrews

Simon Andrews did his first degree in Microbiology at the University of Warwick.  After a breif period working for Sandoz pharmaceuticals he went on  to do a PhD in protein engineering a the University of Newcastle with Harry Gilbert.  During his PhD his interests moved from bench work toward the emerging field of bioinformatics, and he decided to follow this direction in his future career.

After completing his PhD Simon worked with the BBSRC IT Services where he developed and then presented a series of bioinformatics training courses in protein structure analysis to the BBSRC institutes.  At one of these courses at Babraham he met John Coadwell who establised the Babraham bioinformatics group and was then employed as the second member of the bioinformatics team.  Since joining Babraham Simon has seen the group grow from two people to nine as the field has become far more prominent in the biological research community.  He took over the running of the group in 2010.

Latest Publications

IL-7R signaling activates widespread V and D gene usage to drive antibody diversity in bone marrow B cells.
Baizan-Edge A, Stubbs BA, Stubbington MJT, Bolland DJ, Tabbada K, Andrews S, Corcoran AE

Generation of the primary antibody repertoire requires V(D)J recombination of hundreds of gene segments in the immunoglobulin heavy chain (Igh) locus. The role of interleukin-7 receptor (IL-7R) signaling in Igh recombination has been difficult to partition from its role in B cell survival and proliferation. With a detailed description of the Igh repertoire in murine IL-7Rα bone marrow B cells, we demonstrate that IL-7R signaling profoundly influences V gene selection during V-to-DJ recombination. We find skewing toward 3' V genes during de novo V-to-DJ recombination more severe than the fetal liver (FL) repertoire and uncover a role for IL-7R signaling in D-to-J recombination. Transcriptome and accessibility analyses suggest reduced expression of B lineage transcription factors (TFs) and targets and loss of D and V antisense transcription in IL-7Rα B cells. Thus, in addition to its roles in survival and proliferation, IL-7R signaling shapes the Igh repertoire by activating underpinning mechanisms.

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Cell reports, 36, 2, 13 Jul 2021

PMID: 34260907

The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle.
Furlan-Magaril M, Ando-Kuri M, Arzate-Mejía RG, Morf J, Cairns J, Román-Figueroa A, Tenorio-Hernández L, Poot-Hernández AC, Andrews S, Várnai C, Virk B, Wingett SW, Fraser P

Circadian gene expression is essential for organisms to adjust their physiology and anticipate daily changes in the environment. The molecular mechanisms controlling circadian gene transcription are still under investigation. In particular, how chromatin conformation at different genomic scales and regulatory elements impact rhythmic gene expression has been poorly characterized.

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Genome biology, 22, 1, 08 Jun 2021

PMID: 34099014

Accelerating cryoprotectant diffusion kinetics improves cryopreservation of pancreatic islets.
Dolezalova N, Gruszczyk A, Barkan K, Gamble JA, Galvin S, Moreth T, O'Holleran K, Mahbubani KT, Higgins JA, Gribble FM, Reimann F, Surmacki J, Andrews S, Casey JJ, Pampaloni F, Murphy MP, Ladds G, Slater NKH, Saeb-Parsy K

Cryopreservation offers the potential to increase the availability of pancreatic islets for treatment of diabetic patients. However, current protocols, which use dimethyl sulfoxide (DMSO), lead to poor cryosurvival of islets. We demonstrate that equilibration of mouse islets with small molecules in aqueous solutions can be accelerated from > 24 to 6 h by increasing incubation temperature to 37 °C. We utilize this finding to demonstrate that current viability staining protocols are inaccurate and to develop a novel cryopreservation method combining DMSO with trehalose pre-incubation to achieve improved cryosurvival. This protocol resulted in improved ATP/ADP ratios and peptide secretion from β-cells, preserved cAMP response, and a gene expression profile consistent with improved cryoprotection. Our findings have potential to increase the availability of islets for transplantation and to inform the design of cryopreservation protocols for other multicellular aggregates, including organoids and bioengineered tissues.

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Scientific reports, 11, 1, 17 May 2021

PMID: 34001961

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