Epromoters are new players in the regulatory landscape with potential pleiotropic roles

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Juliette Malfait, Jing Wan, Salvatore Spicuglia

BioEssays – Published: 28 May 2023 https://doi.org/10.1002/bies.202300012

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CDK7/12/13 inhibition targets an oscillating leukemia stem cell network and synergizes with venetoclax in acute myeloid leukemia

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Lixiazi He, Christian Arnold, Judith Thoma, Christian Rohde, Maksim Kholmatov, Swati Garg, Cheng?Chih Hsiao, Linda Viol, Kaiqing Zhang, Rui Sun, Christina Schmidt, Maike Janssen, Tara MacRae, Karin Huber, Christian Thiede, Josée Hébert, Guy Sauvageau, Julia Spratte, Herbert Fluhr, Gabriela Aust, Carsten Müller?Tidow, Christof Niehrs, Gislene Pereira, Jörg Hamann, Motomu Tanaka, Judith B Zaugg and Caroline Pabst

EMBO Mol Med – Published: 7 March 2022 https://doi.org/10.15252/emmm.202114990

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GRaNIE and GRaNPA: inference and evaluation of enhancer?mediated gene regulatory networks

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Aryan Kamal, Christian Arnold, Annique Claringbould, Rim Moussa, Nila H Servaas, Maksim Kholmatov, Neha Daga, Daria Nogina, Sophia Mueller?Dott, Armando Reyes?Palomares, Giovanni Palla, Olga Sigalova, Daria Bunina, Caroline Pabst, and Judith B Zaugg

Molecular Systems Biology – Published: 19 April 2023 https://doi.org/10.15252/msb.202311627

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ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

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Wouter Saelens, Olga Pushkarev, Bart Deplancke

bioRxiv – Published: July 25, 2023 https://doi.org/10.1101/2023.07.21.549899

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Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

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Olga Pushkarev, Guido van Mierlo, Judith F. Kribelbauer, Wouter Saelens, Vincent Gardeux, Bart Deplancke

bioRxiv – Published: October 11, 2023 https://doi.org/10.1101/2023.10.11.561870

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Context transcription factors establish cooperative environments and mediate enhancer communication

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Judith F. Kribelbauer, Olga Pushkarev, Vincent Gardeux, Julie Russeil, Guido van Mierlo, Bart Deplancke

BioRxiv – Published: May 05, 2023 https://doi.org/10.1101/2023.05.05.539543

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Chromatin modules and their implication in genomic organization and gene regulation

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Guido van Mierlo, Olga Pushkarev, Judith F. Kribelbauer, Bart Deplancke

Trends in Genetics – Published: February 2023 https://doi.org/10.1016/j.tig.2022.11.003

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The role of rare enhancer variants in bicuspid aortic valve pathology

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A. Zhigulev, K. Lång, S. Pradhananga, H. Björck, P. Eriksson, P. Sahlén

Atherosclerosis – Published: August 2022 https://doi.org/10.1016/j.atherosclerosis.2022.06.194

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Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression

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Artemy Zhigulev, Zandra Norberg, Julie Cordier, Rapolas Spalinskas, Hassan Bassereh, Niclas Björn, Sailendra Pradhananga, Henrik Gréen, Pelin Sahlén

Life Science Alliance – Published: 16 January 2024 DOI: 10.26508/lsa.202302244

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Targeted Chromosome Conformation Capture (HiCap)

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Artemy Zhigulev & Pelin Sahlén

Spatial Genome Organization: Methods and Protocols – Published: 23 July 2022 https://doi.org/10.1007/978-1-0716-2497-5_5

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Hematopoietic stem cells undergo a lymphoid to myeloid switch in early stages of emergency granulopoiesis

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Karolina Vanickova, Mirko Milosevic, Irina Ribeiro Bas, Monika Burocziova, Asumi Yokota, Petr Danek, Srdjan Grusanovic, Mateusz Chili?ski, Dariusz Plewczynski, Jakub Rohlena, Hideyo Hirai, Katerina Rohlenova, and Meritxell Alberich?Jorda

The EMBO Journal – Published: 17 October 2023 https://doi.org/10.15252/embj.2023113527
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Chronic inflammation promotes cancer progression as a second hit

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Monika Burocziova, Srdjan Grusanovic, Karolina Vanickova, Sladjana Kosanovic, Meritxell Alberich-Jorda

Experimental Hematology – Published: September 12, 2023 https://doi.org/10.1016/j.exphem.2023.09.002

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Chronic inflammation decreases HSC fitness by activating the druggable Jak/Stat3 signaling pathway

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Srdjan Grusanovic, Petr Danek, Maria Kuzmina, Miroslava K Adamcova, Monika Burocziova, Romana Mikyskova, Karolina Vanickova, Sladjana Kosanovic, Jana Pokorna, Milan Reinis, Tomas Brdicka, and Meritxell Alberich?Jorda

EMBO Reports – Published: 7 November 2022 https://doi.org/10.15252/embr.202254729

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Targeted Chromosome Conformation Capture (HiCap)

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Artemy Zhigulev & Pelin Sahlén

Spatial Genome Organization: Methods and Protocols – Published: 23 July 2022 https://doi.org/10.1007/978-1-0716-2497-5_5

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The role of rare enhancer variants in bicuspid aortic valve pathology

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A. Zhigulev, K. Lång, S. Pradhananga, H. Björck, P. Eriksson, P. Sahlén

Atherosclerosis – Published: August 2022 https://doi.org/10.1016/j.atherosclerosis.2022.06.194

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Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression

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Artemy Zhigulev, Zandra Norberg, Julie Cordier, Rapolas Spalinskas, Hassan Bassereh, Niclas Björn, Sailendra Pradhananga, Henrik Gréen, Pelin Sahlén

Life Science Alliance – Published: 16 January 2024 DOI: 10.26508/lsa.202302244

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

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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

 

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Interplay between regulatory elements and chromatin topology in cellular lineage determination

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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

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Enhanced performance of gene expression predictive models with protein-mediated spatial chromatin interactions

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Mateusz Chili?ski, Jakub Lipi?ski, Abhishek Agarwal, Yijun Ruan & Dariusz Plewczynski

Scientific Report – Published: 20 July 2023 https://doi.org/10.1038/s41598-023-38865-5

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The dynamic role of cohesin in maintaining human genome architecture

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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

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Transcription factors: Bridge between cell signaling and gene regulation

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

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

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Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes

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Niels J. Rinzema, Konstantinos Sofiadis, Sjoerd J. D. Tjalsma, Marjon J. A. M. Verstegen, Yuva Oz, Christian Valdes-Quezada, Anna-Karina Felder, Teodora Filipovska, Stefan van der Elst, Zaria de Andrade dos Ramos, Ruiqi Han, Peter H. L. Krijger & Wouter de Laat

Nature Structural & Molecular Biology – Published: 16 June 2022 https://doi.org/10.1038/s41594-022-00787-7

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

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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

 

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NFnetFu: A novel workflow for microbiome data fusion

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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 

 

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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

 

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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

 

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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

 

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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.

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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

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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

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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

/by

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

/by

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

/by

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

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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

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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

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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

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Marie CurieThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 860002. The information contained in this website reflects only the authors’ view. REA and EC are not responsible for any use that may be made of this information.