PUBLICATIONS

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 

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

Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells.

Al Bkhetan Z, Kadlof M, Kraft A, Plewczynski D. Methods. 2019 Aug 15;166:83-90. doi: 10.1016/j.ymeth.2019.03.002.

McBel-Plnc: A Deep Learning Model for Multiclass Multilabel Classification of Protein-lncRNA Interactions.

Natsuda Navamajiti, Thammakorn Saethang, Duangdao Wichadakul (2019). McBel-Plnc: A deep learning model for multiclass multilabel classification of protein-lncRNA interactions. ICBBE ’19: Proceedings of the 2019 6th International Conference on Biomedical and Bioinformatics Engineering, 21-28. https://doi.org/10.1145/3375923.3375953

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs.

Laugsch M, Bartusel M, Rehimi R, Alirzayeva H, Karaolidou A, Crispatzu G, Zentis P, Nikolic M, Bleckwehl T, Kolovos P, van Ijcken WFJ, Šari? T, Koehler K, Frommolt P, Lachlan K, Baptista J, Rada-Iglesias A. Cell Stem Cell. 2019 May 2;24(5):736-752.e12. doi:10.1016/j.stem.2019.03.004.

Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis.

Rauch A, Haakonsson AK, Madsen JGS, Larsen M, Forss I, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Röttger R, Baumbach J, Scheele C, Kassem M, Mandrup S. Nat Genet. 2019 Apr;51(4):716-727. doi: 10.1038/s41588-019-0359-1.

Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip.

Bio?anin M, Bues J, Dainese R, Amstad E, Deplancke B. Lab Chip. 2019 Apr 23;19(9):1610-1620. doi:10.1039/c9lc00014c.

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer.

Chen W, Schwalie PC, Pankevich EV, Gubelmann C, Raghav SK, Dainese R, Cassano M, Imbeault M, Jang SM, Russeil J, Delessa T, Duc J, Trono D, Wolfrum C, Deplancke B. Nat Commun. 2019 Apr 18;10(1):1809. doi: 10.1038/s41467-019-09803-9.

Widespread Enhancer Activity from Core Promoters.

Medina A, Santiago D, Puthier D, Spicuglia S. Wide-spread enhancer activity from core promoters. TiBS. (2018). 43(6):452-468

Putting hands to rest: efficient deep CNN-RNN architecture for chemical named entity recognition with no hand-crafted rules.

Korvigo I, Holmatov M, Zaikovskii A, Skoblov M. Journal of cheminformatics. 2018 Dec;10(1):28.

PRC2 facilitates the regulatory topology required for poised enhancer function during pluripotent stem cell differentiation.

Cruz-Molina S, Respuela P, Tebartz C, Kolovos P, Nikolic M, Fueyo R, van Ijcken W.F.J, Grosveld F, Frommolt P, Bazzi H, Rada-Iglesias A#.  Cell Stem Cell. 2017 May 4;20(5):689-705. PMID:28285903.

Genome-wide characterization of mammalian promoters with distal enhancer functions.

Dao LTM, Galindo-Albarrán AO, Castro-Mondragon JA, Andrieu-Soler C, Medina-Rivera A, Souaid C, Charbonnier G, Griffon A, Vanhille L, Stephen T, Alomairi J, Martin D, Torres M, Fernandez N, Soler E, van Helden J, Puthier D, Spicuglia S. Nat Genet. (2017). 49(7):1073-1081. PMID: 28581502.

GARLIC: A Bioinformatic Toolkit for Etiologically Connecting Diseases and Cell Type-Specific Regulatory Maps.

Nikoli? M, Papantonis A, Rada-Iglesias A#. Hum Mol Genet. 2017 Feb 15;26(4):742-752. PMID:28007912.

CapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals.

Vanhille L., A. Griffon, M.A. Maqbool, J. Zacarias, L.T.M. Dao, N. Fernandez, B. Ballester, J.C. Andrau, S. Spicuglia. Nat. Comm. 6:6905 (2015)

H3K4 tri-methylation provides an epigenetic signature of active enhancers.

Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau J.C, Ferrier P and Spicuglia S EMBO J., 30, 4198–10. (2011).