LAPTI members.

Where do they come from? I can't say.
But I bet they have come
a long, long way.

We see them come
We see them go.

Dr. Seuss

Current

Pavel Baranov aka Pasha or Pól Ó Reithe (Gaeilge).

Jack Tierney.

Phil O'Brien.

Fabio Boiocchi.

Anmol Kiran.

GionMattia Carancini (JM).

Maiken Hemme Bro-Jørgensen.

Elizaveta Siling.

Associates

Dmitry Andreev (aka Antibiotic) is a regular visitor scientist from Moscow State University. Dmitry is interested in regulation of translation initiation in eukaryotes.

John Atkins was Pasha's postdoctoral advisor at U of U. LAPTI closely collaborates with John on the topics of Recoding.

Maria Bozko is a PhD student at the University of Warsaw and a regular visitor of LAPTI.

Michal Swirski is a visitor from the University of Warsaw with very broad interests .

Martina Yordanova was beyond the discovery of ribosome stalling at the end of extended AMD1 coding region. She started her own lab next door to LAPTI and continues to work closely with us.

Former

Cashel Slevin was a Bioinformatcis Master student who developed a pipeline for single cell ribosome profiling data analysis .

While working on his PhD focusing on an elusive topic of lncRNA translation Oza Zaheed Maheswaran was apartial member of LAPTI . He now moved to EIRNABio .

Arnau Garciìa I Salmeroìn worked as a research assistant on CRISPR-Cas editing of AMD1 tail.

Hobbes Ingels was an intern from Belgium, he was working on developing a stand alone tool for translon detection using Trips-Viz algorithm.

Håkon Tjeldnes was a postdoc working on Ribocrypt , he also played a key role in solving the mistery of highly unusual footprints in one of the published studies.

Gary Loughran was a legendery figure, describing his contributions in a single sentence would be an insult. Gary moved to EIRNABio that he had cofounded.

Darren Fenton completed his PhD in collaboration with John Morrisey carrying out ribosome profiling in K. marxianus. Then he contuned as postdoc trying to solve misteries of AMD1 tail and studying ribosomal frameshifting in S. cerevisiae before moving to NIH.

Artur Fartukh worked in LAPTI for one year as a research assistant trying to help us to elucidate mysterious function of AMD1 tail.

Oscar Ting obtaied his MSc degree while working in LAPTI, he also worked as a research assistant with us before moving to a company.

Asuman Inan made an attempt to identify novel cases of ribosomal frameshifting in CrAssphages.

During her PhD Alla Fedorova discovered many new human proteoforms generated via translation initiation at codons other than AUG, she also ressurected RiboGalaxy .

Conor Toomey searched for new cases of ribosomal frameshifting in the human genes during his MSc project. Like most his predecessors he didnt find any.

Patrick O'Connor While in LAPTI, Patrick discovered that mRNA moves through the bacterial ribosome like a caterpillar and developed an elegant approach for assessing sequence properties that affect local ribosome footprints distribution on mRNAs globally. He is now at Eirna Bio .

Stephen Kiniry developed Trips-Viz while working on his PhD in LAPTI. After a short postdoc with Kellie Dean he moved to Eirna Bio .

While in LAPTI, Audrey Michel started RiboSeq.Org and Eirna Bio . The latter took her away from us.

During his MSc project, Luke Power carried out ribosome profiling in an amazing yeast species, Yarrowia lipolytica. His appreciation for yeast grew to the proportions that explain his move to industry.

James Mullan (Paddy). Paddy was our SysAdmin. He used to make sure that all servers work in LAPTI before moving to APC.

Ciara Judge worked in LAPTI on her final year project at UCC Genetics programme and also during the Summer 2020. She has developed a script for mining proteomics dtata to be displayed in Trips-Viz.

Lode Van Dijcker was an intern from Belgium, he was working on an automation of GWIPS-viz data processing.

Sara Dufour was an intern from Belgium, she worked on adoptation of RUST for bacterial data.

Stephen Heaphy was a Ph.D. student who found a genetic code with all codons coding for amino acids.

Romika Kumari was a Ph.D. student, she studied the role of G-quadruplexes in translation.

James Keane was a M.Sc. student who developed a scoring system for the quality of ribosome profiling datasets..

Marisol Benitez-Cantos was a summer research student supported by Erasmus program. She was looking for hidden information in protein coding regions of mRNA.

Xiangwu Lu (a.k.a. Chris) was a Ph.D. student from CIT/NSilico working with us on a collaborative project.

Anjali Pai was a Cancer Biology Ph.D. Scholar.

Matthias Claes made GWIPS-viz upgrade which now provides the latest ucsc genome browser functionality such as multi-region view.

Zena Abbas was working on a collaborative project supported by NCRC that focuses on transcriptomic analysis of whole blood in febrile infants.

Svetlana Koroteeva valunteered to process several data tracks for GWIPS-viz GWIPS-viz tracks.

Sándor Dedeyne created strand functionality in GWIPS-viz browser and made a number of additional important improvements

Emily Power was developing the ribo-seq transcriptome viewer

Elizaveta Sokolova was a visitor from the Institute of Molecular Biology in Moscow. She was probing the nucleotide context of translation termination in mammals.

Vimalkumar Velayudhan developed a number of usefool tools for RiboSeq.ORG resources. He is now at APC Microbiome Institute.

Kevin O'Riordan worked on his Master project in LAPTI. During the project he upgraded GWIPS-viz to a newer version and made a number of improvements to it.

Paul Korir worked in LAPTI for a short period as a postdoctoral researcher. He moved to EBI to work on processing EM imaging data.

Claire Donohue. After completing her Master degree in Bioinformatics in LAPTI, Claire worked on GWIPS-viz. Many GWIPS datasets were processed by Claire. She also was a key person behind RiboGalaxy development.

Sharon O'Sullivan. Sharon was a research assistant in LAPTI for two years and is still involved in our work. We hope she will come back soon.

Shauna O'Donovan studied intransitive relationship between codons in the genetic code while working on he MSc project in Bioinformatics.

Siobhan Cleary was a partial member of our lab in academic year 2013/2014 when she was working on a collaborative project with Prof. Rosemary O'Connor. Siobhan moved to a Bioinformatician position at the West Midlands Regional Genetics Laboratory in the Birmingham Women's NHS Foundation Trust.

Carmen Ferrara was a visitor to our lab from Naples. She is interested in an incredible extremophile Sulfolobus Solfataricus

Anmol Kiran (अनमोल किरण) was the mighty hero behind DARNED database. After obtaining his Ph.D. he left to sunny Malawi to fight infectious diseases at theWellcome Trust Campus, but now is back.

Christof De Bo was an itern from Belgium, he helped us to populate GWIPS-viz with data.

While doing his Ph.D. with us Virag Sharma had a chance to be entered into Guinness World Records for the discovery of the largest set of evolutionary conserved recoded genes in a single study. Irish connections didn't help. Now he is doing his first postdoc at MPI-CBG with Michael Hiller. We wish him strength in his resistance to German temptations.

Gearóid Fox was a MSc student who helped us to bring GWIPS-viz to life. He went to the capital of Not Cork to work on his Ph.D with Not Darwin.

Nicole Vaughan was a MSc student who was exploring transcriptional landscape of the pregnancy specific glycoprotein genes cluster.

Oleksandr Nychyk was a summer student supported by a vocational fellowship from Wellcome Trust. After completing his BS in Genetics he went to do his Ph.D. at University College London..

Komal Sanjeev was a remote intern whose magic spells can be found in DARNED database source. She went to do a master in computer science at Stony Brook.

Ioanna Tzani was a rotation Cancer Biology Ph.D. Scholar. Ioanna tried her grit on BAD gene, very BAD gene. She continues her work on Cancer with John Atkins.

David Murphy (aka Dave the Builder) was working in LAPTI in 2011/2012. Dave developed CodonLogo. Dave moved to Titian Software as a software developer.

John O'Mahony (aka the wiki man) started community based annotation of RNA editing while working on his final project in UCC Biochemistry programme.

Kathy Barriscale was a rotation student from PhD Programme in Cancer Biology in 2009/2010. By means of comparative sequence analysis Kathy discovered an important Recoding event (programmed ribosomal frameshifting) in expression of a nematode homolog of one of the most important human tumour suppressor gene, adenomatous polyposis coli (APC). After completing her Ph.D. in Tommie McCarthy lab she started her postdoctoral reseacrh at Tom Moore lab.

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