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Gene expression is the vital path that converts DNA information into functional proteins. Our group studies mechanisms and machines of gene expression using single-molecule biophysical methods and biochemistry. We observe single biomachines in real time, both "in vitro" and inside living cells. We also develop single-molecule fluorescence methods, instruments, assays and DNA-based biosensors.

Our team is a Biological Physics research group within Condensed Matter Physics. We are also linked to many of the Oxford Doctoral Training Centres (DTCs) programmes (including the Interdisciplinary Bioscience DTP), and the Computational Discovery interdisciplinary DPhil programme.

July 2021:

- Finally moved to our new space in the Kavli Institute for Nanoscience Discovery. Sad to say goodbye to our home in the Department of Physics, but excited for the future ahead!

- We're helping to organise a single-molecule bacteriology symposium for the Biochemical Society, featuring exciting work ranging from DNA repair to membrane organisaation!

June 2021:

- New pre-print further advancing our work on rapid detection of the novel coronvirus by single-molecule FISH! Well done to Christof Hepp and all those involved! Preprint

- We ran the Oxford Town and Gown 2021! Big congrats to all those who ran, and supported the lab!

- Lab day out in the Cotswolds! Great to welcome our new starters and say hello to some old friends as coronavirus restrictions ease!

Charlbury trip group photo

May 2021:

- Team Rapinidis is running again, with a team entered in the Oxford Town and Gown 2021! We are raising funds for Muscular Dystrophy UK! If you are interested, please visit our donation page.

- We are recruiting for a Machine Learning specialist to join our Oxford Martin School funded project on rapid detection of antimicrobial resistance. More information here and here.

- We are gearing up for our move to the Kavli Institute for Nanoscience Discovery, in the recently completed Oxford Biochemistry building. Stay tuned for further updates!

April 2021:

- Mirjam Kummerlin has won a prestigious Boehringer Ingelheim Fonds fellowship to join us for her PhD/DPhil. Congratulations, and welcome to the group!

- Stelios Chatzimichail has joined our group as a postdoc, to work on single-molecule studies of single-cell bacterial isolates for rapid testing of antimicrobial resistance. Welcome!

- A new rotation student, Alison Farrar has joined our group. Welcome to the group!

- Big congratulations to Rebecca Andrews for passing her viva!

January 2021:

- Maabur Sow passes his viva with flying colours and moves to Ulm to start a post-doctoral position. Congratulations, and best of luck in the new position!

- A new rotation student, Emma Lalande has joined our group. Welcome to the group!

October 2020:

- Breakthrough! A team from our lab has developed a new rapid test for the novel coronavirus, using single-molecule microscopy and advanced machine learning. Well done Nic, Andrew, Christof, Achilles and Nicole! Press release Preprint

- Rasched Haidari from the Computational Discovery DTC has joined our group to work on computational projects involving tracking proteins in bacteria. A warm welcome to Rasched!

- Barak Gilboa leaves us to continue his imaging work at the Novo Nordisk Research Center Oxford. Farewell, and best of luck!

- We are recruiting! Looking for 3 Postdoctoral Fellows to work on developing single-cell imaging assays related to antibiotic resistance (see https://www.oxfordmartin.ox.ac.uk/antimicrobial-resistance-testing/). The work will also be relevant to understand chromosome organisation in bacteria and the mode-of-action of antibiotics. Two positions (microscopist, image-analyst) will be based in our lab, and the third in the Medical School. Email us for questions and to express interest!

September 2020:

- Maabur's paper on single-molecule imaging of nanodiamonds will appear in Nanoscale! Congrats Maabur!

July 2020:

- Back into the lab! In line with government and University regulations, we can finally return to regular experimental work in the lab!

- New paper! Abhishek has just published some of his latest work on using single molecule imaging to study the opening and closing of the RNA polymerase trigger loop, a crucial step of the polymerase mechanism. Well done Abhishek! Mazumder et al 2020 PNAS

April 2020:

- Good news! We have received a generous grant from the Oxford Martin School to establish a programme in rapid detection of antibiotic resistance (see https://www.oxfordmartin.ox.ac.uk/antimicrobial-resistance-testing/). This is a great collaboration with clinicians Nicole Stoesser, Derrick Crook and Monique Andersson (all at John Radcliffe Hospital) and image analysis expert Chris Nellaker (Big Data Institute).

OMS programme on Antimicrobial Resistance Testing

March 2020:

- We have initiated work on the novel coronavirus, aiming to expand our previous work on rapid labeling and detection of viruses to the novel pathogen, led by Nicole and Achilles. We wish them the best of luck in these unprecedented times!

- Following the advice of the UK government in response to COVID-19, we have switched to remote working.

January 2020:

- Jun Fan leaves us to take up a professorship position at the University of Electronic Science and Technology of China, in Chengdu. We wish him the best of luck with this exciting opportunity!

December 2019:

- Xiaojuan Li from Beijing Forestry University joins us as an Academic Visitor, to work with us on single-molecule imaging.

November 2019:

- Abhishek and Achilles present work on conformational changes of RNAP at Transcription in Health and Disease in London.

- The Single Molecule Bacteriology meeting will be returning in the third week of September 2020.

- New paper: Robb et al 2019 Sci Rep. Our first report of a super-fast labeling and detection method for viruses. Well done Nicole and the team!

- New paper: Gilboa et al 2019 Biophys J. Solution WiFi offers a simple approach to study the diffusion of single molecules. Congratulations Barak!

October 2019:

- It's the start of a new academic year!

- Anna Wang joins the lab to work on project that develops methods to look at coupled conformational changes using advanced single-molecule fluorescence methods.

- Aleksander Zagajewski joins the lab to work on projects that explore the organisation of the chromosome and the effect of forces on gene expression; the project is a collaboration with Physics colleague Professor Sonia Contera.

- We also welcome MPhys students Alex and Kieran who will be with us for 6 months working on projects related to flu and bacterial imaging.

September 2019:

- New paper: Craggs et al 2019 NAR. An in vitro - in vivo and in silico tour-de-force! And the FIRST FRET-derived structure from our lab! Well done Tim and Marko, and thanks to our collaborators.

- Our first Nanodiamond paper is now on Arxiv. Well done Maabur!

- A photo of what will be our new “home” in 15 months: the brand new interdisciplinary institute Dorothy Hodgkin Centre.

May 2019:

- Achilles received the BBSRC Innovator of the Year award jointly with Bo Jing for developing the Nanoimager. Congratulations!

April 2019:

- The 31st annual RNAP workshop in Oxford. Well done! Nicole, Abhishek and Achilles. You can find a Flyer and a Program here.

March 2019:

- New postdoc Heesoo Uhm is here, welcome to the group!

February 2019:

- Welcome to our new website! This is now live! Modern look and a Twitter feed. The old website is now archived.

- We are looking for two postdocs to work on in vivo single-molecule DNA repair. This is an exciting BBSRC-funded collaboration of our lab with Meriem El Karoui (Edinburgh) and Mark Dillingham (Bristol). The advert for the Oxford job is here. DEADLINE extended to March 15.

October 2018:

- It's the start of a new academic year!

- We bid goodbye to our favourite computer scientist Horst Steuer, and wish him good luck with his new job in Heidelberg!

- A big welcome to Richard Ludescher, Professor of Food Science, who is visiting from Rutgers University in New Jersey.

- We have been busy, check out our publications page for the latest manuscripts from the lab!

April 2018:

- It has been a busy month for papers, check out our exciting new work on the E.coli RNA polymerase, published in Mol. Cell Link and Nature Communications Link.

- We also have two new papers uploaded on BioRxiv! Link and Link.

- Congratulations to Maabur for winning the Arthur H Cooke Memorial Prize, which is awarded for distinguished work by a first year research student in Condensed Matter Physics. Well done!!!

- We say goodbye to our two MPhys students Amy Kent and Joseph Dolphin and wish them the best of luck with their exams!

- Team Rapinidis is running the Oxford Town and Gown 10K, in aid of Muscular Dystrophy UK, on the 13th of May. Our team has grown since last year and we are all training hard. If you would like to donate to this great cause please see our Justgiving page below: Link.

February 2018:

- Nicole, Becky and Barak have just been to the 2018 Biophysical Society Meeting in San Francisco! We heard some great science, caught up with old friends and made some new ones.

December 2017:

- We all had a great time at the annual Kapanidis Christmas lunch! Merry Christmas everyone!!!

October 2017:

- Hello to our brand new DPhil student Jingwen Xiao, welcome to the group!

September 2017:

- Congratulations to Nicole Robb on being awarded a Royal Society Dorothy Hodgkin Fellowship! Link.

- We had a great time chatting to the public about our research at the Curiosity Carnival, thanks to everyone that helped out on the night!

August 2017:

- We bid farewell to Jonny Taylor, and wish him good luck with his PhD!

- A big welcome to our new post-docs Oliver Pambos and Abhishek Mazumder, to our rotation student Jingwen Xiao and to our new summer student Amy Kent.

- In other news Team Rapidnidis is busy preparing for our next challenge - the Oxford Half Marathon on the 8th of October!

July 2017:

- Farewell to Sophie Schuman, and good luck with your next rotation project. To say goodbye we went on a lab punting trip!

May 2017:

- Team Rapidnidis successfully completed the Oxford Town and Gown 10k! We raised over £300 for Muscular Dystrophy UK, thank you so much to everyone who donated money and supported us on the day, we had a great time and couldn't have done it without you!!

April 2017:

- Congratulations to Fede on the publication of his work in Biophys Journal: Link.

- On the 14th of May the Rapidnidis group will be running the Oxford Town and Gown 10k, in order to raise money for Muscular Dystrophy UK. If you would like to support this excellent cause please use the link below.

Link.

- We are all (mostly) training hard and looking forward to the race!!

March 2017:

- We have a new arrival - welcome to Hafez El Sayyed, who has joined the group as a post-doctoral researcher to work on tracking of RNAP in vivo.

- At the same time, we bid farewell to Mathew Stracy, and wish him the best of luck for his new position in the Biochemistry department, University of Oxford.

- And finally, photo of the month goes to Becky, pictured here using the Nanoimager!! (thanks to Micron, Oxford).

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