Dr Salam Adli Assi

Institute of Cancer and Genomic Sciences
Honorary Research Fellow

Contact details

Email: s.a.assi@bham.ac.uk

Address: Institute of Cancer and Genomic Sciences
College of Medical and Dental Sciences
University of Birmingham
Edgbaston
Birmingham
B15 2TT

Salam Assi is an Honorary Research Fellow in bioinformatics in the Institute of Cancer and Genomic Sciences. She is most interested in carrying out research into the regulation of transcription during normal development and in cancerogenesis. Her work has studied normal development, but her recent work has been in understanding the molecular mechanism of Acute Myeloid Leukaemia (AML) development.

Qualifications

PhD in Computing and Mathematics, University of Bradford, 2008
MRes in Bioinformatics and Computational Biology, University of Leeds
MSc in Computing, University of Bradford
BSc in Sciences of Physics

Biography

Salam Assi graduated with a PhD in Computing and Mathematics from University of Bradford in 2008. In 2007, she studied MRes in Bioinformatics and Computational Biology at University of Leeds. From 2008 to 2010, Salam worked at University of Leeds as a research assistance in Computational Biology and then from 2010 to 2013 as a postdoc in Bioinformatics.

Salam joined the University of Birmingham in September 2013 as a research fellow in Bioinformatics with Professor Constanze Bonifer where she worked on a number of different projects studying the regulation of transcription during normal and aberrant haematopoiesis, using high-throughput Next Generation Sequencing (NGS) approaches. In July 2020, she moved to start up her independent line of research at University of Birmingham. Dr Assi’s research aims to use AML data to develop computational tools to enhance the understanding of this disease at the systems level by expanding the analysis of transcription factor and gene regulatory networks to identify the pathways required for leukaemia maintenance.

Teaching

MSc Bioinformatics: teaching in Genomics & Next Generation Sequencing & Interdisciplinary Bioinformatics Group Project modules

Research

Salam Assi is interested in carrying out research into the regulation of transcription during normal development and in cancerogenesis. Her work has been in understanding the molecular mechanism of Acute Myeloid Leukaemia (AML) development. Salam's speciality is to use high-throughput sequencing approaches and applying quantitative methods for the analysis and integration of high-throughput molecular biology data with the aim to understand disease mechanisms. Salam Assi is proficient in bioinformatics and statistical analysis techniques and she is interested in mathematical modelling in the context of system biology. In her recent work, she have been able to build AML subtype-specific gene regulatory networks by linking transcription factor (TF) binding events to the genes which these TFs regulate and elucidated how the epigenome is reprogrammed in specific sub-types of AML. These data were instrumental in defining the factors and mechanisms that are required for AML development and maintenance and informed screening approaches to validate these findings. Salam Assi is currently developing methods based on using such data for the development of AML-subtype classifiers as well as developing models for the response of transcriptional networks to perturbation. Here she will use AML data to develop computational tools to enhance the understanding of this disease at the systems level by expanding here previous work on transcription factor and gene regulatory networks to identify the pathways required for leukaemia maintenance. In addition, to develop methods capable of predicting network behaviour with the ultimate aim to assess the response of tumour cells to therapeutic intervention.

Salam’s previous research was aimed to develop a computational tool to model peptides for protein-protein interaction where she developed research experience in protein interactions, structural bioinformatics and Bayesian statistics.

Publications

Vasily Grinev, Farnaz Barneh, Ilya Ilyushonak, Sirintra Nakjang, Job Smink, Anita van Oort, Richard Clough, Michael Seyani, Hesta McNeill, Mojgan Reza, Natalia Martinez-Soria, Salam A. Assi, Tatsiana Ramanouskaya, Constanze Bonifer, and Olaf Heidenreich. RUNX1/RUNX1T1 mediates alternative splicing and reorganises the transcriptional landscape in leukemia. Nature Communications (2021)

Paulynn Suyin Chin*, Salam A Assi*, Anetta Ptasinska, Maria Rosaria Imperato, Peter N Cockerill, Constanze Bonifer. RUNX1/ETO and mutant KIT both contribute to programming the transcriptional and chromatin landscape in t (8; 21) acute myeloid leukemia. Experimental Hematology (2020)

Anetta Ptasinska*, Anna Pickin*, Salam A. Assi*, Paulynn S. Chin, Peter N. Cockerill, Cameron S. Osborne and Constanze Bonifer, RUNX1-ETO Depletion in t (8; 21) AML Leads to C/EBPα-and AP-1-Mediated Alterations in Enhancer-Promoter Interaction, Cell Reports (2019)

Salam A. Assi, Constanze Bonifer, Peter N Cockerill, Rewiring of the Transcription Factor Network in Acute Myeloid Leukemia. Cancer Informatics, (2019)

Natalia Martinez-Soria, Lynsey McKenzie, Julia Draper, Anetta Ptasinska, Hasan Issa, Sandeep Potluri, Helen J Blair, Anna Pickin, Asmida Isa, Paulynn Suyin Chin, Ricky Tirtakusuma, Daniel Coleman, Sirintra Nakjang, Salam A. Assi, Victoria Forster, Mojgan Reza. The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation. Cancer cell, (2019)

Salam A. Assi, Maria Rosaria Imperato, Daniel JL Coleman, Anna Pickin, Sandeep Potluri, Anetta Ptasinska, Paulynn Suyin Chin, Helen Blair, Pierre Cauchy, Sally R James, Joaquin Zacarias-Cabeza, L Niall Gilding, Andrew Beggs, Sam Clokie, Justin C Loke, Phil Jenkin, Ash Uddin, Ruud Delwel, Stephen J Richards, Manoj Raghavan, Michael J Griffiths, Olaf Heidenreich, Peter N Cockerill, Constanze Bonifer. Subtype-specific regulatory network rewiring in acute myeloid leukemia. Nature genetics, (2019)

Benjamin Edginton-White, Pierre Cauchy, Salam A. Assi, Sylvia Hartmann, Arthur G Riggs, Stephan Mathas, Peter N Cockerill, Constanze Bonifer. Global long terminal repeat activation participates in establishing the unique gene expression programme of classical Hodgkin lymphoma. Leukemia, (2019)

Jane Gilmour, Salam A. Assi, Laura Noailles, Monika Lichtinger, Nadine Obier, Constanze Bonifer. The Co-operation of RUNX1 with LDB1, CDK9 and BRD4 Drives Transcription Factor Complex Relocation During Haematopoietic Specification. Scientific reports, (2018)

Justin Loke, Paulynn Suyin Chin, Peter Keane, Anna Pickin, Salam A. Assi, Anetta Ptasinska, Maria Rosaria Imperato, Peter N Cockerill, Constanze Bonifer. C/EBPα overrides epigenetic reprogramming by oncogenic transcription factors in acute myeloid leukemia. Blood Advance, (2018)

Shan Lin, Anetta Ptasinska, Xiaoting Chen, Mahesh Shrestha, Salam A. Assi, Paulynn S Chin, Maria R Imperato, BJ Aronow, Jingsong Zhang, Matthew T Weirauch, Constanze Bonifer, James C Mulloy. A FOXO1-induced oncogenic network defines the AML1-ETO preleukemic program. Blood, (2017)

Vesna S Stanulović, Pierre Cauchy, Salam A Assi, Maarten Hoogenkamp. LMO2 is required for TAL1 DNA binding activity and initiation of definitive haematopoiesis at the haemangioblast stage. Nucleic Acids Res. (2017)

Justin Loke, Salam A Assi*, Maria Rosaria Imperato, Anetta Ptasinska, Pierre Cauchy, Yura Grabovska, Natalia Martinez Soria, Manoj Raghavan, H Ruud Delwel, Peter N Cockerill, Olaf Heidenreich, Constanze Bonifer. RUNX1-ETO and RUNX1-EVI1 differentially reprogram the chromatin landscape in t (8; 21) and t (3; 21) AML. Cell Rep. (2017)

Shan Lin, Anetta Ptasinska, Salam A. Assi, Jon Kerry, Ruhikanta A Meetei, Roger T Luo, Michael J Thirman, Thomas Milne, Constanze Bonifer, James C Mulloy. The Transcriptome Heterogeneity of MLL-Fusion ALL Is Driven By Fusion Partners Via Distinct Chromatin Binding. Blood (2016)

Nadine Obier, Pierre Cauchy, Salam A. Assi, Jane Gilmour, Michael Lie-A-Ling, Monika Lichtinger, Maarten Hoogenkamp, Laura Noailles, Peter N Cockerill, Georges Lacaud, Valerie Kouskoff,Constanze Bonifer. Cooperative binding of AP1 and TEAD4 modulates the balance between vascular smooth muscleand hemogenic cell fate. Development. (2016)

Shan Lin, Roger T Luo, Anetta Ptasinska, Jon Kerry, Salam A. Assi, Mark Wunderlich, Toshihiko Imamura, Joseph J Kaberlein, Ahmad Rayes, Mark J Althoff, John Anastasi, Maureen M O’Brien, Amom Ruhikanta Meetei, Thomas A Milne, Constanze Bonifer, James C Mulloy, Michael J Thirman. Instructive role of MLL-fusion proteins revealed by a model of t (4; 11) pro-B acute lymphoblastic leukemia Cancer Cell. (2016)

Debbie K Goode, Nadine Obier, MS Vijayabaskar, Michael Lie-A-Ling, Andrew J Lilly, Rebecca Hannah, Monika Lichtinger, Kiran Batta, Magdalena Florkowska, Rahima Patel, Mairi Challinor, Kirstie Wallace, Jane Gilmour, Salam A. Assi, Pierre Cauchy, Maarten Hoogenkamp, David R Westhead, Georges Lacaud, Valerie Kouskoff, Berthold Göttgens, Constanze Bonifer. Dynamic gene regulatory networks drive hematopoietic specification and differentiation. Dev Cell. (2016)

Susumu Goyama, Janet Schibler, Anjelika Gasilina, Mahesh Shrestha, Shan Lin, Kevin A Link, Jianjun Chen, Susan P Whitman, Clara D Bloomfield, Deedra Nicolet, Salam A. Assi, Anetta Ptasinska, Olaf Heidenreich, Constanze Bonifer, Toshio Kitamura, Nicolas N Nassar, James C Mulloy. UBASH3B/Sts-1-CBL axis regulates myeloid proliferation in human preleukemia induced by AML1-ETO. Leukemia, (2016)

VJ Forster, MH Nahari, N Martinez-Soria, AK Bradburn, A Ptasinska, Salam A. Assi, SE Fordham, H McNeil, C Bonifer, O Heidenreich, JM Allan. The leukemia-associated RUNX1/ETO oncoprotein confers a mutator phenotype. Leukemia. (2016)

V Forster, M Nahari, N Martinez-Soria, A Bradburn, A Ptasinska, S A Assi, H McNeill, C Bonifer, O Heidenreich, J Allan. The Leukemia-Associated RUNX1/ETO Oncoprotein Confers a Mutator Phenotype. Leukemia. (2016)

Jason Piper, Salam A. Assi, Pierre Cauchy, Christophe Ladroue, Peter N Cockerill, Constanze Bonifer, Sascha Ott. Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors. BMC Genomics. (2015)

Pierre Cauchy, Sally R James, Joaquin Zacarias-Cabeza, Anetta Ptasinska, Maria Rosaria Imperato, Salam A. Assi, Jason Piper, Martina Canestraro, Maarten Hoogenkamp, Manoj Raghavan, Justin Loke, Susanna Akiki, Samuel J Clokie, Stephen J Richards, David R Westhead, Michael J Griffiths, Sascha Ott, Constanze Bonifer, Peter N Cockerill. Chronic FLT3-ITD signaling in acute myeloid leukemia is connected to a specific chromatin signature. Cell Reports, (2015)

Kakkad Regha, Salam A. Assi, Olga Tsoulaki, Jane Gilmour, Georges Lacaud, Constanze Bonifer. Developmental-stage-dependent transcriptional response to leukaemic oncogene expression. Nat Commun. (2015)

K Ponnusamy, N Kohrs, A Ptasinska, SA Assi, T Herold, W Hiddemann, J Lausen, C Bonifer, R Henschler, C Wichmann. RUNX1/ETO blocks selectin-mediated adhesion via epigenetic silencing of PSGL-1. Oncogenesis. (2015)

Anetta Ptasinska*, Salam A. Assi*, Natalia Martinez-Soria, Maria Rosaria Imperato, Jason Piper, Pierre Cauchy, Anna Pickin, Sally R James, Maarten Hoogenkamp, Dan Williamson, Mengchu Wu, Daniel G Tenen, Sascha Ott, David R Westhead, Peter N Cockerill, Olaf Heidenreich, Constanze Bonifer. Identification of a dynamic core transcriptional network in t (8; 21) AML that regulates differentiation block and self-renewal. (2014)

Jane Gilmour*, Salam A. Assi*, Ulrike Jaegle, Divine Kulu, Harmen van de Werken, Deborah Clarke, David R Westhead, Sjaak Philipsen, Constanze Bonifer. A crucial role for the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification. Development. (2014)

Monika Lichtinger, Richard Ingram, Rebecca Hannah, Dorothee Müller, Deborah Clarke, Salam A. Assi, Michael Lie‐A‐Ling, Laura Noailles, MS Vijayabaskar, Mengchu Wu, Daniel G Tenen, David R Westhead, Valerie Kouskoff, Georges Lacaud, Berthold Göttgens, Constanze Bonifer. RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis. EMBO J. (2012)

Anetta Ptasinska*, Salam A. Assi*, D Mannari, SR James, D Williamson, J Dunne, Maarten Hoogenkamp, M Wu, M Care, H McNeill, Pierre Cauchy, M Cullen, RM Tooze, DG Tenen, BD Young, PN Cockerill, DR Westhead, O Heidenreich, Constanze Bonifer. Depletion of RUNX1/ETO in t (8; 21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding. Leukemia. (2012)

Mathias Leddin, Chiara Perrod, Maarten Hoogenkamp, Saeed Ghani, Salam A. Assi, Sven Heinz, Nicola K Wilson, George Follows, Jörg Schönheit, Lena Vockentanz, Ali M Mosammam, Wei Chen, Daniel G Tenen, David R Westhead, Berthold Göttgens, Constanze Bonifer, Frank Rosenbauer. Two distinct auto-regulatory loops operate at the PU. 1 locus in B cells and myeloid cells. Blood. (2011)

Demetres D Kouvatsos and Salam A. Assi. Generalised entropy maximisation and queues with bursty and/or heavy tails. Network performance engineering. (2011)

Joan Segura Mora*, Salam A. Assi*, Narcis Fernandez-Fuentes. Presaging critical residues in protein interfaces-web server (PCRPi-W): a web server to chart hot spots in protein interfaces. PLoS One. (2010)

Salam A. Assi, Tomoyuki Tanaka, Terence H Rabbitts, Narcis Fernandez-Fuentes. PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces. Nucleic Acids Res. (2010)

Demetres D Kouvatsos and Salam A. Assi. On the analysis of queues with heavy tails: a non-extensive maximum entropy formalism and a generalisation of the zipf-mandelbrot distribution. Performance Evaluation of Computer and Communication Systems. (2010)

(*joint 1^st authorship)

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