Methods papers
2022
ClustAssess: tools for assessing the robustness of single-cell clustering
Arash Shahsavari, Andi Munteanu, Irina Mohorianu
doi: https://doi.org/10.1101/2022.01.31.478592
bulkAnalyseR: An accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data
Ilias Moutsopoulos*, Eleanor C Williams*, Irina Mohorianu (2022)
https://doi.org/10.1101/2021.12.23.473982;
https://doi.org/10.1093/bib/bbac591 Briefings in Bioinformatics
2021
The sum of two halves may be different from the whole. Effects of splitting sequencing samples across lanes.
Eleanor C Williams*, Ruben Chazarra-Gil*, Arash Shahsavari*, Irina Mohorianu (2022)
https://doi.org/10.3390/genes13122265 Genes
noisyR: Enhancing biological signal in sequencing datasets by characterising random technical noise
I. Moutsopoulos, L. Maischak, E. Lauzikaite, S. A. Vasquez Urbina, E. C. Williams, H. G. Drost, I. Mohorianu
https://doi.org/10.1101/2021.01.17.427026
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab433/629...
2020
feamiR: Feature selection based on Genetic Algorithms for predicting miRNA-mRNA interactions
Eleanor C. Williams, Anisoara Calinescu, Irina Mohorianu
https://doi.org/10.1101/2020.12.23.424130
Publications in collaboration with CSCI PIs
2022
Myeloid cell interferon secretion restricts Zika flavivirus infection of developing and malignant human neural progenitor cells
H Bulstrode, G C. Girdler, T Gracia, A Aivazidis, I Moutsopoulos, A M.H. Young, J Hancock, X He, K Ridley, Z Xu, J H. Stockley, J Finlay, C Hallou, T Fajardo, D M.Fountain, S Dongen, A Joannides, R Morris, R Mair, C Watts, T Santarius, SJ. Price, P J.A. Hutchinson, E J. Hodson, S M. Pollard, I Mohorianu, R A.Barker, T R. Sweeney, O Bayraktar, F Gergely, D H.Rowitch
https://www.sciencedirect.com/science/article/pii/S0896627322008078
Host Respiratory Transcriptome Signature Associated with Poor Outcome in Children with Influenza–Staphylococcus aureus Pneumonia
Carl Britto*, Irina Mohorianu*, ... Adrienne G Randolph, Kristin L Moffitt
https://academic.oup.com/jid/article/226/7/1286/6650994
Chronic injury induces plasticity between cholangiocytes and hepatocytes in the human liver
Vasileios Galanakis, Christopher Gribben, Alexander Calderwood, Ilias Moutsopoulos,... , Irina Mohorianu*, Ludovic Vallier*
RBPMS promotes contractile smooth muscle splicing and alters phenotypic behaviour of human embryonic stem cell derived vascular smooth muscle cells.
Aishwarya G Jacob, Ilias Moutsopoulos, Alexander Petchey, Irina Mohorianu*, Sanjay Sinha*, Chris Smith*
Patterns of oncogene co-expression at single cell resolution in cancer influence survival
Michal Marek Hoppe, Patrick Jaynes, ... Ilias Moutsopoulos, Irina Mohorianu, Daniel J Hodson, ... Claudio Tripodo, Anand D Jeyasekharan
2021
Mapping the biogenesis of forward programmed megakaryocytes from induced pluripotent stem cells
Moyra Lawrence, Arash Shahsavari, Susanne Bornelöv, Thomas Moreau, Katarzyna Kania, Maike Paramor, Rebecca McDonald, James Baye, Marion Perrin, Maike Steindel, Paula Jimenez-Gomez, Christopher Penfold, Irina Mohorianu, Cedric Ghevaert
https://www.science.org/doi/10.1126/sciadv.abj8618
NOTCH1 drives immune-escape mechanisms in B cell malignancies
Maurizio Mangolini, Alba Maiques-Diaz, Stella Charalampopoulou, Elena Gerhard-Hartmann, Johannes Bloehdorn, Andrew Moore, Junyan Lu, Valar Nila Roamio Franklin, Chandra Sekkar Reddy Chilamakuri, Ilias Moutsoupoulos, Andreas Rosenwald, Stephan Stilgenbauer, Thorsten Zenz, Irina Mohorianu, Clive D’Santos, Silvia Deaglio, Jose I. Martin-Subero, Ingo Ringshausen
https://www.nature.com/articles/s41467-022-33739-2
ZAP-70 constitutively regulates gene expression and protein synthesis in chronic lymphocytic leukemia
Jingyu Chen, Vijitha Sathiaseelan, Andrew Moore, Shengjiang Tan, Chandra Sekkar Reddy Chilamakuri, Valar Nila Roamio Franklin, Arash Shahsavari, Constanze Jakwerth, Sandra B. Hake, Alan J. Warren, Irina Mohorianu, Clive D’Santos, Ingo Ringshausen
https://www.sciencedirect.com/science/article/pii/S000649712100416X
Defining the transcriptional signature of esophageal-to-skin lineage conversion
Maria T. Bejar, Paula Jimenez-Gomez, Ilias Moutsopoulos, Bartomeu Colom, Seungmin Han, Fernando J Calero-Nieto, Berthold Göttgens, Irina Mohorianu, Benjamin D. Simons, Maria P. Alcolea
https://www.biorxiv.org/content/10.1101/2021.02.19.431899v1
2020
Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis
Anna Maria Ranzoni, Andrea Tangherloni, Ivan Berest, Simone G Riva, Brynelle Myers, Paulina M. Strzelecka, Jiarui Xu, Elisa Panada, Irina Mohorianu, Judith B. Zaugg, Ana Cvejic
https://doi.org/10.1016/j.stem.2020.11.015
Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics
S Basu, O Shukron, A Ponjavic, P Parruto, W Boucher, W Zhang, N Reynolds, D Lando, D Shah, LH Sober, A Jartseva, R Ragheb, J Cramard, R Floyd, G Brown, K Gor, J Balmer, TA Drury, AR Carr, L-M Needham, A Aubert, G Communie, L Morey, E Blanco, MA Barber, I Mohorianu, T Bartke, L Di Croce, I Berger, C Schaffitzel, SF Lee, TJ Stevens, D Klenerman, BD Hendrich, D Holcman, ED Laue
https://doi.org/10.1101/2020.04.03.003178
