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

2020 Enhpathy publication, ESR publication

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

 

23 January 2024/by Vartika Bisht
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Vartika Bisht https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Vartika Bisht2024-01-23 17:02:432024-01-23 17:02:43Integration of the Microbiome, Metabolome and Transcriptomics Data Identified Novel Metabolic Pathway Regulation in Colorectal Cancer

Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells

2020 Enhpathy publication

Jesper G. S. Madsen, Maria S. Madsen, Alexander Rauch, Sofie Traynor, Elvira L. Van Hauwaert, Anders K. Haakonsson, Biola M. Javierre, Mette Hyldahl, Peter Fraser & Susanne Mandrup

Nature Genetics – Published: 05 October 2020 https://doi.org/10.1038/s41588-020-0709-z

23 January 2024/by Susanne Mandrup
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Susanne Mandrup https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Susanne Mandrup2024-01-23 15:42:422024-01-23 16:57:19Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells

Translational biomarkers in the era of precision medicine.

2020 ESR publication

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

 

29 May 2021/by Vartika Bisht
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Vartika Bisht https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Vartika Bisht2021-05-29 13:59:022024-01-23 16:57:20Translational biomarkers in the era of precision medicine.

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

2020 ESR publication

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

 

17 February 2021/by Vartika Bisht
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Vartika Bisht https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Vartika Bisht2021-02-17 08:47:532024-01-23 16:57:20COVID-19 prevalence and mortality in patients with cancer and the effect of primary tumour subtype and patient demographics: a prospective cohort study.

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

2020 ESR publication

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

 

17 February 2021/by Vartika Bisht
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Vartika Bisht https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Vartika Bisht2021-02-17 08:42:062024-01-23 16:57:20COVID-19 mortality in patients with cancer on chemotherapy or other anticancer treatments: a prospective cohort study.

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

2020 Seminal publication

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

16 December 2020/by Alvaro Rada-Iglesias
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Alvaro Rada-Iglesias https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Alvaro Rada-Iglesias2020-12-16 10:06:462024-01-23 16:57:20Orphan CpG islands boost the regulatory activity of poised enhancers and dictate the responsiveness of their target genes.

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

2020 Seminal publication

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

16 December 2020/by Alvaro Rada-Iglesias
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Alvaro Rada-Iglesias https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Alvaro Rada-Iglesias2020-12-16 10:04:502024-01-23 16:57:20Rare or Overlooked? Structural Disruption of Regulatory Domains in Human Neurocristopathies.

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

2020 Seminal publication

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

16 December 2020/by Salvatore Spicuglia
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Salvatore Spicuglia https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Salvatore Spicuglia2020-12-16 09:52:542024-01-23 16:57:20Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation.

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

2020 Seminal publication

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

16 December 2020/by Dariusz Plewczynski
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Dariusz Plewczynski https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Dariusz Plewczynski2020-12-16 09:33:012024-01-23 16:57:203D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome.

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

2020 Seminal publication

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

16 December 2020/by Dariusz Plewczynski
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Dariusz Plewczynski https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Dariusz Plewczynski2020-12-16 09:30:162024-01-23 16:57:20Chromatin topology reorganization and transcription repression by PML-RAR? in acute promyeloid leukemia.

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

2020 Seminal publication

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

16 December 2020/by Dariusz Plewczynski
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Dariusz Plewczynski https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Dariusz Plewczynski2020-12-16 09:27:102024-01-23 16:57:20Ultrastructural visualization of 3D chromatin folding using volume electron microscopy and DNA in situ hybridization.

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

2020 ESR publication

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

23 November 2020/by Abhishek Agarwal
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Abhishek Agarwal https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Abhishek Agarwal2020-11-23 10:19:312024-01-23 16:57:20A repository of web-based bioinformatics resources developed in India.

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

2020 ESR publication

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

23 November 2020/by Jing Wan
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Jing Wan https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Jing Wan2020-11-23 10:08:482024-01-23 16:57:20Systematic Chromatin Architecture Analysis in Xenopus tropicalis Reveals Conserved Three-Dimensional Folding Principles of Vertebrate Genomes.

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

2020 ESR publication

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

23 November 2020/by Jing Wan
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Jing Wan https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Jing Wan2020-11-23 10:06:472024-01-23 16:57:20Resolving a Systematic Error in STARR-seq for Quantitative Enhancer Activity Mapping.

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

2020 Seminal publication

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.

21 November 2020/by Wouter De Laat
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Wouter De Laat https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Wouter De Laat2020-11-21 04:16:572024-01-23 16:57:204C-seq from beginning to end: A detailed protocol for sample preparation and data analysis

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

2020 Seminal publication

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.

21 November 2020/by Judith Zaugg
https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png 0 0 Judith Zaugg https://www.enhpathy.eu/wp-content/uploads/2019/11/logo-enhpathy-1.png Judith Zaugg2020-11-21 04:13:562024-01-23 16:57:20Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions.

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