Publications

book coverBooks and book chapters

  1. Basel Abu-Jamous, Rui Fa, and Asoke K. Nandi. “Integrative cluster analysis in bioinformatics”. John Wiley & Sons, 2015, ISBN: 978-1118906538. Link
  2. Basel Abu-Jamous, Chao Liu, David J. Roberts, Elvira Brattico, Asoke K. Nandi. “Data-driven analysis of collections of big datasets by the Bi-CoPaM method yields field-specific novel insights” in Frontiers in Electronic Technologies, 2017, Springer. ISBN: 9789811042348. Link.

Pre-print manuscripts

  1. Basel Abu-Jamous and Steven Kelly. “Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data”. BioRxiv, 2017, doi: 10.1101/221309. View online | Download PDF.

Journal publications

  1. Basel Abu-Jamous, Steven Kelly. “Clust: automatic extraction of optimal co-expressed gene clusters from gene expression data”. Genome Biology2018, 19: 172. doi: 10.1186/s13059-018-1536-8. View online | Download PDF.
  2. Basel Abu-Jamous, Francesca M. Buffa, Adrian L. Harris, Asoke K. Nandi. “In vitro downregulated hypoxia transcriptome is associated with poor prognosis in breast cancer”. Molecular Cancer, 2017, 16: 105. doi: 10.1186/s12943-017-0673-0. View online | Download PDF.
  3. Chao Liu, Elvira Brattico, Basel Abu-Jamous, Carlos Pereira, Thomas Jacobsen, Asoke K. Nandi. “Effect of explicit evaluation on neural connectivity related to listening to unfamiliar music”. Frontiers in Human Neuroscience, 2017, 11: 611. doi: 10.3389/fnhum.2017.00611. View online | Download PDF.
  4. Peng Wang, Shanta Karki, Akshaya Biswal, Hsiang-Chun Lin, Mary Jacqueline Dionora, Govinda Rizal, Xiaojia yin, Mara Schuler, Tom Hughes, Jim Fouracre, Basel Abu-Jamous, Olga Sedelnikova, Shuen-Fang Lo, Anindya Bandyopadhyay, Su-May Yu, Steve Kelly, Paul Quick, Jane Langdale. “Candidate regulators of early leaf development in maize perturb hormone signalling and secondary cell wall formation when constitutively expressed in rice”. Scientific Reports, 2017, 7: 4535. doi: 10.1038/s41598-017-04361-w. View online | Download PDF.
  5. Chao Liu, Basel Abu-Jamous, Elvira Brattico, Asoke K. Nandi. “Towards tunable consensus clustering for studying functional brain connectivity during affective processing”. International Journal of Neural Systems (IJNS), 2017, 27(2): 1650042. doi: 10.1142/S0129065716500428. View online | Download PDF.
  6. Alison T. Merryweather-Clarke*, Alex J. Tipping*, Abigail A. Lamikanra*, Rui Fa*, Basel Abu-Jamous*, Hoi Pat Tsang, Lee Carpenter, Kathryn J. H. Robson, Asoke K. Nandi, David J. Roberts. “Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors”. BMC Genomics, 2016, 17: 817. (*Contributed equally). View online | Download PDF.
  7. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “UNCLES: Method for the identification of genes differentially consistently co-expressed in a specific subset of datasets”. BMC Bioinformatics, 2015, 16: 184, doi: 10.1186/s12859-015-0614-0. View online | Download PDF
  8. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “Application of the Bi-CoPaM method to five Escherichia coli datasets generated under various biological conditions”. Journal of Signal Processing Systems, 2015, 79(2): 159-166, doi: 10.1007/s11265-014-0919-7. View online | Download PDF
  9. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “Comprehensive analysis of forty yeast microarray datasets reveals a novel subset of genes (APha-RiB) consistently negatively associated with ribosome biogenesis”. BMC Bioinformatics, 2014, 15: 322, doi: 10.1186/1471-2105-15-322. View online | Download PDF
  10. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “Yeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experiments”. Journal of the Royal Society Interface, 2013, 10(81): 20120990, doi: 10.1098/rsif.2012.0990. View online | Download PDF
  11. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “Paradigm of Tunable Clustering using Binarization of Consensus Partition Matrices (Bi-CoPaM) for Gene Discovery”. PLOS ONE, 2013, 8(2): e56432, doi: 10.1371/journal.pone.0056432. View online | Download PDF
  12. Fengyu Cong, Vinoo Alluri, Asoke K. Nandi, Petri Toiviainen, Rui Fa, Basel Abu-Jamous, Li-yun Gong, Bart G. W. Craenen, et al., “Linking brain responses to naturalistic music through analysis of ongoing EEG and stimulus features”, IEEE Transactions on Multimedia, 2013, 15(5): 1060-1069, doi: 10.1109/TMM.2013.2253452. View online | Download PDF

Invited articles

ـ1. باسل أبو جاموس. ”خوارزميات جديدة تعالج البيانات المتعاظمة“ مجلة التقدم العلمي، العدد 97 إبريل 2017، عدد خاص حول  المعلوماتية الحيوية، صفحة 16-20، مؤسسة الكويت للتقدم العلمي. رابط للتحميل

Translated: Basel Abu-Jamous, “New algorithms for big data analysis” in Scientific Advancements Magazine, Issue 97 April 2017, a special issue on bioinformatics, pp. 16-20, Kuwait Foundation for the Advancement of Sciences.  Download PDF

Full-length peer-reviewed international conference publications

  1. Basel Abu-Jamous and Steven Kelly, “Simultaneous Clustering of Multiple
    Heterogeneous Gene Expression Datasets”. Proceedings of the IEEE Jordan Conference on Applied Electrical Engineering and Computing Technologies (AEECT), 2017, Amman, Jordan. In press.
  2. Chao Liu, Elvira Brattico, Basel Abu-Jamous, Asoke Nandi. “Exploration of distance metrics in consensus clustering analysis of FMRI data”. Proceedings of the 22nd International Conference on Digital Signal Processing (DSP), 2017, London, UK.
  3. Chao Liu, Rui Fa, Basel Abu-Jamous, Elvira Brattico, and Asoke K. Nandi. “Scalable clustering based on enhanced-smart for large-scale fMRI datasets”. Proceedings of the International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2015, Brisbane, Australia, pp.962-966.
  4. Rui Fa, Basel Abu-Jamous, David J. Roberts, and Asoke K. Nandi. “CoCE-SMART: consensus clustering based on enhanced splitting-merging awareness tactics”. Proceedings of the International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2015, Brisbane, Australia, pp.2011-2015.
  5. Chao Liu, Basel Abu-Jamous, Elvira Brattico, Asoke Nandi. “Clustering consistency in neuroimaging data analysis”. Proceedings of the International Conference on Fuzzy Systems and Knowledge Discovery (FSKD), 2015, Zhangjiajie, China, pp.1118-1122.
  6. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “M-N scatter plots technique for evaluating varying-size clusters and setting the parameters of Bi-CoPaM and UNCLES methods”. Proceedings of the International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2014, Florence, Italy, pp.6726-6730.
  7. Rui Fa, Basel Abu-Jamous, David J. Roberts, and Asoke K. Nandi. “Splitting-while-merging framework for clustering high-dimension data with component-wise expectation conditional maximisation”. Proceedings of the International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2014, Florence, Italy, pp. 2932-2936.
  8. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “Bi-CoPaM ensemble clustering application to five Escherichia coli bacterial datasets”. Proceedings of the European Signal Processing Conference (EUSIPCO), 2014, Lisbon, Portugal.
  9. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “Identification of genes consistently co-expressed in multiple microarray datasets by a genome-wide Bi-CoPaM approach”. Proceedings of International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2013, Vancouver, Canada, pp.1172-1176.
  10. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “Method for the identification of the subsets of genes specifically consistently co-expressed in a set of datasets”. Proceedings of the IEEE International Workshop on Machine Learning for Signal Processing (MLSP), 2013, Southampton, UK, doi: 10.1109/MLSP.2013.6661907.
  11. Rui Fa, Basel Abu-Jamous, David J. Roberts, and Asoke K. Nandi. “Enhanced SMART framework for gene clustering using successive processing”. Proceedings of the IEEE International Workshop on Machine Learning for Signal Processing (MLSP), 2013, Southampton, UK, doi: 10.1109/MLSP.2013.6661964.
  12. Rui Fa, Basel Abu-Jamous, and Asoke K. Nandi. “Bi-CoPaM ensemble clustering application to five Escherichia coli bacterial datasets”. Proceedings of the European Signal Processing Conference (EUSIPCO), 2013, Marrakech, Morocco.
  13. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “Hybrid binarisation technique for the Bi-CoPaM method”. Proceedings of the Constantinides International Workshop on Signal Processing (CIWSP), 2013, London, UK, doi: 10.1049/ic.2013.0006.
  14. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “Comprehensive analysis of multiple microarray datasets by binarization of consensus partition matrix”. Proceedings of the IEEE International Workshop on Machine Learning for Signal Processing (MLSP), 2012, Santander, Spain, paper no. 62, doi: 10.1109/MLSP.2012.6349787.
  15. Basel Abu-Jamous, Rui Fa, David J. Roberts, and Asoke K. Nandi. “Binarization of consensus partition matrix for ensemble clustering”. Proceedings of the European Signal Processing Conference (EUSIPCO), 2012, Bucharest, Romania, pp. 2193-2197.
  16. Rui Fa, Basel Abu-Jamous, and Asoke K. Nandi. “Development and evaluation of kernel-based clustering validity indices”. Proceedings of the European Signal Processing Conference (EUSIPCO), 2012, Bucharest, Romania, pp. 634-638.

Conference posters / talks (without full-length papers)

  1. Basel Abu-Jamous and Steven Kelly, “Clust: automatic identification and optimisation of consensus clusters of co-expressed genes from multiple heterogeneous transcriptomic datasets”. Great Lakes Bioinformatics (GLBIO) conference, 2017, Chicago, IL, USA. [Talk].
  2. Basel Abu-Jamous and Steven Kelly, “Bi-CoPaM: an automated method to identify clusters of consistently co-expressed genes from multiple heterogeneous transcriptomic datasets”. Next Generation Sequencing (NGS) conference, 2017, Barcelona, Spain. [Talk].
  3. Basel Abu-Jamous and Steven Kelly, “Differential maturation of bundlesheath and mesophyll cells during photosynthetic activation in C4 species”. Enhancing photosynthesis in crop plants: targets for improvement, 2016, The Royal Society, London, UK. [Poster].
  4. Chao Liu, Basel Abu-Jamous, Elvira Brattico, and Asoke K. Nandi. “Consensus clustering reveals neural networks during affective music processing”. The Neurosciences and Music V, 2014, Dijon, France. [Poster].
  5. Basel Abu-Jamous, Maysam Abbod, Asoke K. Nandi. “Comprehensive analysis of high throughput biological datasets”. Brunel Annual Student Research Conference (ResCon), 2014, London, UK. [Talk].
  6. Basel Abu-Jamous, Maysam Abbod, Asoke K. Nandi. “Comprehensive analysis of high throughput biological datasets”. Brunel Annual Student Research Conference (ResCon), 2013, London, UK. [Poster].
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