PUBLICATIONS

Interplay between regulatory elements and chromatin topology in cellular lineage determination

Vallari Shukla, Anna Cetnarowska, Mette Hyldahl, Susanne Mandrup

Trends in Genetcs – Published: 10, October 2022 https://doi.org/10.1016/j.tig.2022.05.011

Multi-scale phase separation by explosive percolation with single-chromatin loop resolution

Kaustav Sengupta, Micha? Denkiewicz, Mateusz Chili?ski, Teresa Szczepi?ska, Ayatullah Faruk Mollah, Sevastianos Korsak, Raissa D’Souza, Yijun Ruan, Dariusz Plewczynski

Computational and Structural Biotechnology Journal – Published: 2022 https://doi.org/10.1016/j.csbj.2022.06.063

MultiNet: A Diffusion-Based Approach to Assign Directionality in Protein Interactions Using a Consensus of Eight Protein Interaction Datasets

Kaustav Sengupta, Anna Gambin, Subhadip Basu & Dariusz Plewczynski

Proceedings of International Conference on Frontiers in Computing and Systems – Published: 28 June 2022 https://doi.org/10.1007/978-981-19-0105-8_2

NFnetFu: A novel workflow for microbiome data fusion

VartikaBisht, Animesh Acharjee and Georgios V.Gkoutos

Computers in Biology and Medicine : Published: 8 June 2021, https://doi.org/10.1016/j.compbiomed.2021.104556 

Nicotinic Acetylcholine Receptors Expressed by Striatal Interneurons Inhibit Striatal Activity and Control Striatal-Dependent Behaviors

Alice Abbondanza, Irina Ribeiro Bas, Martin Modrak, Martin Capek, Jessica Minich, Alexandra Tyshkevich, Shahed Naser, Revan Rangotis, Pavel Houdek, Alena Sumova, Sylvie Dumas, Veronique Bernard and Helena Janickova.

Journal of Neuroscience : 30 March 2022, https://doi.org/10.1523/JNEUROSCI.1627-21.2022

Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness

Tomas Pachano, Víctor Sánchez-Gaya, Thais Ealo, Maria Mariner-Faulí, Tore Bleckwehl, Helena G. Asenjo, Patricia Respuela, Sara Cruz-Molina, María Muñoz-San Martín, Endika Haro, Wilfred F. J. van IJcken, David Landeira & Alvaro Rada-Iglesias

Nature Genetics – Published: 28 June 2021 https://doi.org/10.1038/s41588-021-00888-x

PartSeg: a tool for quantitative feature extraction from 3D microscopy images for dummies

Grzegorz Bokota, Jacek Sroka, Subhadip Basu, Nirmal Das, Pawel Trzaskoma, Yana Yushkevich, Agnieszka Grabowska, Adriana Magalska & Dariusz Plewczynski

BMC Bioinformatics – Published: 17 February 2021 https://doi.org/10.1186/s12859-021-03984-1

Prediction of chromatin looping using deep hybrid learning (DHL)

Mateusz Chili?ski, Anup Kumar Halder, Dariusz Plewczynski

Quantitative Biology – Published: 01 June 2023 https://doi.org/10.15302/J-QB-022-0315

Protocol to study sufficiency of cis-regulatory elements in mouse embryonic stem cells using a CRISPR-mediated knockin approach

Tomas Pachano, Alvaro Rada-Iglesias

STAR Protocols – Published: 16 September 2022 https://doi.org/10.1016/j.xpro.2022.101492

Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy

Zofia Parteka-Tojek, Jacqueline Jufen Zhu, Byoungkoo Lee, Karolina Jodkowska, Ping Wang, Jesse Aaron, Teng-Leong Chew, Krzysztof Banecki, Dariusz Plewczynski & Yijun Ruan

Scientific Reports- Published: 20 December 2022 https://doi.org/10.1038/s41598-022-12568-9

The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo

Giuliano Crispatzu, Rizwan Rehimi, Tomas Pachano, Tore Bleckwehl, Sara Cruz-Molina, Cally Xiao, Esther Mahabir, Hisham Bazzi & Alvaro Rada-Iglesias

Nature Communications – Published: 16 July 2021 https://doi.org/10.1038/s41467-021-24641-4

The dynamic role of cohesin in maintaining human genome architecture

Abhishek Agarwal, Sevastianos Korsak, Ashutosh Choudhury, Dariusz Plewczynski

BioEssays: Pattern Recognition and Machine Intelligence – Published: 21 August 2023 https://doi.org/10.1002/bies.202200240

The Identification of Chromatin Contact Domains (CCD) in Human Genomes from ChIA-PET Data Using Graph Methods

Rafa? Chabasi?ski, Kaustav Sengupta & Dariusz Plewczynski

Algorithms for Intelligent Systems- Published: 22 November 2023 https://doi.org/10.1007/978-981-99-1509-5_23

Transcription factors: Bridge between cell signaling and gene regulation

Paula Weidemüller, Maksim Kholmatov, Evangelia Petsalaki, Judith B. Zaugg

Proteomics – Published: 27 July 2021 https://doi.org/10.1002/pmic.202000034

Integration of the Microbiome, Metabolome and Transcriptomics Data Identified Novel Metabolic Pathway Regulation in Colorectal Cancer

Vartika Bisht ,Katrina Nash ,Yuanwei Xu ,Prasoon Agarwal ,Sofie Bosch ,Georgios V. Gkoutos and Animesh Acharjee.

International Journal of molecular science, Received: 29 April 2021 / Revised: 25 May 2021 / Accepted: 26 May 2021 / Published: 28 May 2021, https://doi.org/10.3390/ijms22115763

Translational biomarkers in the era of precision medicine.

Laura Bravo-Merodio, Animesh Acharjee, Dominic Russab, VartikaBisht, John A.Williams, Loukia G.Tsaprounie, Georgios V. Gkoutos.

Advances in Clinical Chemistry, Available online 3 October 2020 – In Press, https://doi.org/10.1016/bs.acc.2020.08.002

COVID-19 prevalence and mortality in patients with cancer and the effect of primary tumour subtype and patient demographics: a prospective cohort study.

Lennard Y W Lee, DPhil, Prof Jean-Baptiste Cazier, PhD, Thomas Starkey, MSci, Sarah E W Briggs, MRCP
Roland Arnold, PhD, Vartika Bisht, MSc, Stephen Booth, FRCPath, Naomi A Campton, PhD, Vinton W T Cheng, DPhil, Graham Collins, DPhil, Helen M Curley, PhD,, Philip Earwaker, DPhil, Matthew W Fittall, PhD, Spyridon Gennatas, PhD, Anshita Goel, PhD, Simon Hartley, PhD, Daniel J Hughes, MRCP, David Kerr, FMedSci, Alvin J X Lee, PhD, Rebecca J Lee, PhD, Prof Siow, Ming Lee, FRCP, Hayley Mckenzie, MBBS, Chris P Middleton, PhD, Nirupa Murugaesu, PhD, Tom Newsom-Davis, FRCP
Anna C Olsson-Brown, MBChB, Claire Palles, PhD, Prof Thomas Powles, MD, Emily A Protheroe, Karin Purshouse, MBBS, Archana Sharma-Oates, PhD, Shivan Sivakumar, PhD, Ashley J Smith, MSc, Oliver Topping, MBChB, Chris D Turnbull, DPhil, Csilla Várnai, PhD, Adam D M Briggs, DPhil, Prof Gary Middleton, FRCP, Rachel Kerr, FRCP on behalf of theUK Coronavirus Cancer Monitoring Project Team

The Lancet Oncology VOLUME 21, ISSUE 10, P1309-1316, OCTOBER 01, 2020, https://doi.org/10.1016/S1470-2045(20)30442-3

COVID-19 mortality in patients with cancer on chemotherapy or other anticancer treatments: a prospective cohort study.

Lennard YW Lee, DPhil *, Jean-Baptiste Cazier, PhD *, Vasileios Angelis, PhD, Roland Arnold, PhD, Vartika Bisht, MSc, Naomi A Campton, PhD, Julia Chackathayil, PhD, Vinton WT Cheng, DPhil, Helen M Curley, PhD, Matthew W Fittall, PhD, Luke, Freeman-Mills, DPhil, Spyridon Gennatas, PhD, Anshita Goel, PhD, Simon Hartley, PhD, Daniel J Hughes, MRCP, David Kerr, FMedSci, Alvin JX Lee, PhD, Rebecca J Lee, PhD, Sophie E McGrath, PhD, Christopher P Middleton, PhD, Nirupa Murugaesu, PhD, Thomas Newsom-Davis, FRCP, Alicia FC Okines, FRCP, Anna C Olsson-Brown, MBChB, Claire Palles, PhD,, Yi Pan, PhD
Ruth Pettengell, FRACP, Thomas Powles, MD, Emily A Protheroe, Karin Purshouse, MBBS, Archana Sharma-Oates, PhD, Shivan Sivakumar, PhD, Ashley J Smith, MSc, Thomas Starkey, MSc, Chris D Turnbull, DPhil, Csilla Várnai, PhD, Nadia Yousaf, PhD, The UK Coronavirus Monitoring Project Team, Rachel Kerr, FRCP †, Gary Middleton, FRCP †.

The Lancet VOLUME 395, ISSUE 10241, P1919-1926, JUNE 20, 2020; https://doi.org/10.1016/S0140-6736(20)31173-9

Orphan CpG islands boost the regulatory activity of poised enhancers and dictate the responsiveness of their target genes.

Pachano T, Sánchez-Gaya V, Mariner-Faulí M, Ealo T, Asenjo H.G., Respuela P, Cruz-Molina S, van Ijcken W.F.J , Landeira D, Rada-Iglesias A#. bioRxiv 2020.08.05.237768; doi: https://doi.org/10.1101/2020.08.05.237768

Rare or Overlooked? Structural Disruption of Regulatory Domains in Human Neurocristopathies.

Sánchez-Gaya V, Mariner-Faulí M, Rada-Iglesias A#. Front Genet. 2020 Jul 20;11:688. doi: 10.3389/fgene.2020.00688. eCollection 2020. Review. PMID: 32765580

Systematic Chromatin Architecture Analysis in Xenopus tropicalis Reveals Conserved Three-Dimensional Folding Principles of Vertebrate Genomes.

Longjian Niu, Wei Shen, Zhaoying Shi, Na He, Jing Wan, Jialei Sun, Yuedong Zhang, Yingzhang Huang, Wenjing Wang, Chao Fang, Jiashuo Li, Piaopiao Zheng, Edwin Cheung, Yonglong Chen, Li Li, and Chunhui Hou. bioRxiv, 2020 – https://doi.org/10.1101/2020.04.02.021378

4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis

Krijger PHL, Geeven G, Bianchi V, Hilvering CRE, de Laat W. Methods. 2020 Jan 1;170:17-32. doi: 10.1016/j.ymeth.2019.07.014.

A repository of web-based bioinformatics resources developed in India.

Abhishek Agarwal, Piyush Agrawal, Aditi Sharma, Vinod Kumar, Chirag Mugdal, Gajendra P.S. Raghava: A repository of web-based bioinformatics resources developed in India. bioRxiv 2020; doi: https://doi.org/10.1101/2020.01.21.855627

3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome.

Wlasnowolski M, Sadowski M, Czarnota T, Jodkowska K, Szalaj P, Tang Z, Ruan Y, Plewczynski D. Nucleic Acids Res. 2020 May 22:gkaa388. doi: 10.1093/nar/gkaa388. PMID: 32442297

Chromatin topology reorganization and transcription repression by PML-RAR? in acute promyeloid leukemia.

Wang P, Tang Z, Lee B, Zhu JJ, Cai L, Szalaj P, Tian SZ, Zheng M, Plewczynski D, Ruan X, Liu ET, Wei CL, Ruan Y. Genome Biol. 2020 May 11;21(1):110. doi: 10.1186/s13059-020-02030-2. PMID: 32393309

Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization.

Trzaskoma P, Ruszczycki B, Lee B, Pels KK, Krawczyk K, Bokota G, Szczepankiewicz AA, Aaron J, Walczak A, ?liwi?ska MA, Magalska A, Kadlof M, Wolny A, Parteka Z, Arabasz S, Kiss-Arabasz M, Plewczy?ski D, Ruan Y, Wilczy?ski GM. Nat Commun. 2020 May 1;11(1):2120. doi: 10.1038/s41467-020-15987-2. PMID: 32358536

Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation.

Cieslak, A., G. Charbonnier, M. Tesio, E. L. Mathieu, M. Belhocine, A. Touzart, C. Smith, G. Hypolite, G. P. Andrieu, J. H. A. Martens, E. Janssen-Megens, M. Gut, I. Gut, N. Boissel, A. Petit, D. Puthier, E. Macintyre, H. G. Stunnenberg, S. Spicuglia* and V. Asnafi*. J Exp Med (2020). 217(9): (9): e20192360

Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions.

Ibarra IL, Hollmann NM, Klaus B, Augsten S, Velten B, Hennig J, Zaugg JB. Nat Commun. 2020 Jan 8;11(1):124. doi:10.1038/s41467-019-13888-7.

Resolving a Systematic Error in STARR-seq for Quantitative Enhancer Activity Mapping.

Longjian Niu,  Jing Wan, Jialei Sun, Yingzhang Huang, Na He, Li Li, Chunhui Hou. bioRxiv 2020 – doi: https://doi.org/10.1101/2020.10.20.346908

Spatial chromatin architecture alteration by structural variations in human genomes at the population scale.

Sadowski M, Kraft A, Szalaj P, Wlasnowolski M, Tang Z, Ruan Y, Plewczynski D. Genome Biol. 2019 Jul 30;20(1):148. doi:10.1186/s13059-019-1728-x.

Amplification-free library preparation with SAFE Hi-C uses ligation products for deep sequencing to improve traditional Hi-C analysis.

Longjian Niu, Wei Shen, Yingzhang Huang, Na He, Yuedong Zhang, Jialei Sun, Jing Wan, Daxin Jiang, Manyun Yang, Yu Chung Tse, Li Li, Chunhui Hou.

Communications biology, 2019, 2: 267-267. https://doi.org/10.1038/s42003-019-0519-y

Comparative analysis of expression of mutant and wild-type alleles is essential for reliable PCR-based detection of MET exon 14 skipping.

Mitiushkina N.V., Kholmatov M.M., Tiurin V.I., Romanko A.A., Yatsuk O.S., Sokolova T.N., Ivantsov A.O., Kuligina E.S., Stepanov I.A., Belyaev A.M., Togo A.V., Imyanitov E.N. Biochimie, 2019, Vol. 165, P. 267-274. doi:10.1016/j.biochi.2019.08.014

Computationally guided high-throughput design of self-assembling drug nanoparticles.

Daniel Reker, Yulia Rybakova, Ameya R. Kirtane, Ruonan Cao, Jee Won Yang, Natsuda Navamajiti, Apolonia Gardner, Rosanna M. Zhang, Tina Esfandiary, Johanna L’Heureux, Thomas von Erlach, Elena M. Smekalova, Dominique Leboeuf, Kaitlyn Hess, Aaron Lopes, Jaimie Rogner, Joy Collins, Siddartha M. Tamang, Keiko Ishida, Paul Chamberlain, DongSoo Yun, Abigail Lytoon-Jean, Christian K. Soule, Jaime H. Cheah, Alison M. Hayward, Robert Langer,  Giovanni Traverso. BioRxiv preprint 2019. doi: https://doi.org/10.1101/786251

Determinants of enhancer and promoter activities of regulatory elements.

Andersson R, Sandelin A. Nat Rev Genet. 2019 Oct 11. doi: 10.1038/s41576-019-0173-8.

Dissection of acute stimulus-inducible nucleosome remodeling in mammalian cells.

Comoglio F, Simonatto M, Polletti S, Liu X, Smale ST, Barozzi I, Natoli G. Genes Dev. 2019 Sep 1;33(17-18):1159-1174. doi: 10.1101/gad.326348.119.

Exome-based search for recurrent disease-causing alleles in Russian population.

Yanus G.A., Akhapkina T.A., Whitehead A.J., Bizin I.V., Iyevleva A.G., Kuligina E.S., Aleksakhina S.N., Anisimova M.O., Holmatov M.M., Romanko A.A., Zaitseva O.A., Yatsuk O.S., Zagorodnev K.A., Matsneva M.A., Koloskov A.V., Togo A.V., Suspitsin E.N., Imyanitov E.N. Eur J Med Genet, 2019, Vol. 62(7), P. 103656 (1-7). doi: 10.1016/j.ejmg.2019.04.013

High-Resolution Regulatory Maps Connect Vascular Risk Variants to Disease-Related Pathways.

Åkerborg Ö, Spalinskas R, Pradhananga S, Anil A, Höjer P, Poujade FA, Folkersen L, Eriksson PP, Sahlén P. Circ Genom Precis Med. 2019 Mar;12(3):e002353. doi: 10.1161/CIRCGEN.118.002353.

High-throughput identification of human SNPs affecting regulatory element activity.

van Arensbergen J, Pagie L, FitzPatrick VD, de Haas M, Baltissen MP, Comoglio F, van der Weide RH, Teunissen H, Võsa U, Franke L, de Wit E, Vermeulen M, Bussemaker HJ, van Steensel B. Nat Genet. 2019 Jul;51(7):1160-1169. doi:10.1038/s41588-019-0455-2.

Human pancreatic islet three-dimensional chromatin architecture provides insights into the genetics of type 2 diabetes.

Miguel-Escalada I, Bonàs-Guarch S, Cebola I, Ponsa-Cobas J, Mendieta-Esteban J, Atla G, Javierre BM, Rolando DMY, Farabella I, Morgan CC, García-Hurtado J,Beucher A, Morán I, Pasquali L, Ramos-Rodríguez M, Appel EVR, Linneberg A, Gjesing AP, Witte DR, Pedersen O, Grarup N, Ravassard P, Torrents D, Mercader JM, Piemonti L, Berney T, de Koning EJP, Kerr-Conte J, Pattou F, Fedko IO, Groop L, Prokopenko I, Hansen T, Marti Renom MA, Fraser P, Ferrer J. Nat Genet. 2019 Jul;51(7):1137-1148. doi:10.1038/s41588-019-0457-0.

Lack of response to vemurafenib in melanoma carrying BRAF K601E mutation.

Moiseyenko F.V., Egorenkov V.V., Kramchaninov M.M., Artemieva E.V., Aleksakhina S.N., Holmatov M.M., Moiseyenko V.M., Imyanitov E.N. Case Rep Oncol, 2019, Vol. 12(2), P. 339-343. doi : 10.1159/000500481