Sriganesh Srihari's Publications

Books
 

• Srihari S (Guest Editor) (2017). Systems Approaches for Identifying Disease Genes and Drug Targets. Methods (Elsevier Netherlands), 01 Dec 2017 [PDF].


• Srihari S, Yong CH, Wong L (2017). Computational Prediction of Protein Complexes from Protein Interaction Networks. ACM Books and Morgan & Claypool (California, USA) (~300 pages) [PDF] via ACM Digital library. Available also from Amazon and Barnes & Noble. Check out the Book Promo!

Peer-reviewed journal publications (Profile on UQ Researchers; Google Scholar; ResearchGate; ORCID; ResearcherID ; PubMed ) (*Co-first author; #(Co-)Corresponding author)

• Panikkar A,...Srihari S...Khanna R, Smith C (2022). SARS-CoV-2-specific T cells generated for adoptive immunotherapy are capable of recognizing multiple SARS-CoV-2 variants. PLoS Pathogens 18(2): e1010339.


• Moreno M*, Srihari S*...Khanna R, Aftab B (2021). Comprehensive profiling of ATA188, an off-the-shelf, allogeneic epstein-barr virus-specific T-cell immunotherapy for progressive multiple sclerosis Cytotherapy (*Joint first authors)


• Pinoli P, Srihari S, Wong L, Stefano C (2021). Identifying collateral and synthetic lethal vulnerabilities within the DNA-damage response. BMC Bioinformatics [PDF]


• Lineberg K, Neller M,...Srihari S, Khanna R, Smith C (2021). Rapid whole-blood assay to detect SARS-CoV-2-specific memory T-cell immunity following a single dose of AstraZeneca ChAdOx1-S COVID-19 vaccine Clinical & Translational Immunology [PDF]


• Sinha D, Srihari S,...,Smith C, Khanna R (2021). 'Off-the-shelf' allogeneic antigen-specific adoptive T-cell therapy for the treatment of multiple EBV-associated malignancies. J immunotherapy of cancer 9(2): e001608. [PDF]


• Lineburg K, Srihari S, ..., Khanna R, Smith C (2020). Rapid detection of SARS-CoV2-specific memory T-cell immunity in recovered COVID-19 cases. Clinical and Translational Immunology [IF: 7.2], DOI 10.1002/cti2.1219 [PDF] [Media release]


• Smith C,...Srihari S, Walker D, Khanna R (2020). Autologous CMV-specific T cells as adjuvant immunotherapy for primary glioblastoma multiforme: single-arm open-label phase I clinical trial. Journal of Clinical Investigation, 10.1172/JCI138649 [IF:12.282] [PDF]


• Bhatt KH, Neller MA, Srihari S,... Khanna R (2020). Profiling HPV-16-specific T cell responses reveals broad antigen reactivities in oropharyngeal cancer patients. J Exp Med, 217 (10): e20200389. [PDF] [IF: 11.743]


• Kennedy S*, Jarboi M*, Srihari S*, ..., Lynn DJ, Koch W (2020). Extensive Rewiring of the EGFR Network in Colorectal Cancer Cells Expressing Transforming Levels of KRASG13D. Nature Communications 11:499, [PDF] [IF: 11.88] (*Joint first authors) [Medical Express News] [Commentary]


• Ambalathingal G, Francis R, Corvino D, Srihari S, Aftab B, Smith C, Khanna R (2020). Proteome-wide analysis of T cell response to BK polyomavirus in healthy virus carriers and renal transplant recipients reveals unique transcriptional and functional profile. Clinical & Translational Immunology, e1102 [IF: 7.271]


• Charitou T, Srihari S, Lynn M, ...,Kolch W, Lynn D (2019). Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS-G13D mutation. British Journal of Cancer, [PDF] [IF: 5.922]


• Nones K, Johnson J, .... Srihari S, ... Simpson P (2019). Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancer. Annals of Oncology, mdz132, [PDF] [IF: 13.926].


• Duijf P, Nanayakarra D, Nones K, Srihari S, Kalimutho M, Khanna KK (2019). Mechanisms of genomic instability in breast cancer. Trends in Molecular Medicine (Cell Press). Accepted. [PDF]


• Kalimutho M, Nones K, Srihari S, Duijf P, Waddell N, Khanna KK (2019). Patterns of genomic instability in breast cancer. Trends in Pharmacological Sciences (Cell Press) [IF: 10.14]. Acccepted. [PDF]


• Kalimutho M, Sinha D, Mittal D, Srihari S, Nanayakkara D, Shafique S, Raninga P, Nag P, Parson K, Khanna KK (2019). Blockade of PDGFRb circumvents resistance to MEK-JAK inhibition via intratumoral CD8+ T-cells in triple-negative breast cancer. Journal of Experimental & Clinical Cancer Research [IF: 6.22]. Accepted [PDF].


• Srihari S, Tattam P, Simpson R, Smith E (2018). Metabolic deregulation in prostate cancer, Molecular Omics (Royal Society of Chemistry) 14:320-329. [PDF] (selected for front cover of the issue). Presented at AACR Special Conference on Convergence of AI, Prediction and Cancer, Newport, RI, USA, Oct 2018. ♚


• Ivazeh A, Zahiri J, Rahgozar M, Srihari S (2018). Performance evaluation measures for protein complex prediction. Genomics (Elsevier), S0888-7543(18)30470-1. [PDF]


• Kalimutho M, Sinha D, Jeffrey J, Nones K, Srihari S,..., Khanna KK (2018). CEP55 is a determinant of cell fate during perturbed mitosis in breast cancer. EMBO Molecular Medicine, DOI: 10.15252/emmm.201708566 [PDF] [IF 9.25](TB)


• Kalimutho M, Bain A, Mukherjee B, Nag P, Nanayakkara D, Harten S, Hancock J, Subramanian G, Sinha D, Shirasawa S, Srihari S, Burma S, Khanna KK (2017). Enhanced dependency of KRAS-mutant colorectal cancer cells on RAD51-dependent homologous recombination repair identified from genetic interactions in Saccharomyces cerevisiae. Molecular Oncology (Elsevier), doi: 10.1002/1878-0261.12040.[PDF] [IF 5.37] (TB).


• Srihari S*, Kalimutho M*, Lal S, Singla J, Patel D, Simpson PT, Khanna KK, Ragan MA (2016). Understanding the functional impact of copy number alterations in breast cancer using a network modeling approach. Molecular Biosystems (Royal Society of Chemistry), 12:963-972 [PDF] [IF: 3.21]. (TB, B/CB)


• Liu C, Srihari S, Lal S, Gautier B, Simpson PT, Khanna KK, Ragan MA, Le Cao K-A (2016). Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer. Molecular Oncology, 10(1):179-193 [IF: 5.31]. [PDF] (TB, CB/B)


• Taherian-Fard A, Srihari S, Mar JC, Ragan MA (2016). Not just a colourful metaphor: Modelling the landscape of cellular development using Hopfield networks. Systems Biology and Applications (Nature Partner Journal), 2:16001.


• Srihari S, Singla J, Wong L, Ragan MA (2015). Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Biology Direct, 10:57 [PDF] [IF: 4.66]. [Article in Biotechin.asia] Presented at San Antonio Breast Cancer Symposium, San Antonio, Texas, USA, Dec 2015; American Association for Cancer Research (AACR) -- Susan G. Komen for the Cure 'Scholar-in-training' award [Abstract] ♚. (TB, B/CB)


• Kalimutho M, Parsons K, Mittal D, Lopez A, Srihari S, Khanna KK (2015). Targeted therapies for triple-negative breast cancer: Combating a stubborn disease. Trends in Pharmacological Sciences (Cell Press), 36(12):822-846 [PDF] [IF: 11.539]. (TB)


• Nguyen NN, Srihari S, Leong HW, Chong KF (2015). Enzdp: Improved enzyme annotation for metabolic network reconstruction based on domain composition profiles. Journal of Bioinformatics and Computational Biology, 13(5):1543003 [PDF] [IF: 0.93]. (CB/B)


• Srihari S#, Yong CH, Patil A, Wong L (2015). Methods for protein complex prediction and their contributions towards understanding the organization, function and dynamics of complexes. FEBS Letters, 589 (19A):2590-2602 [IF: 3.519] (Invited refereed paper to Special Issue on Intrinsically Disordered Proteins; Eds. Wilhelm Just & Vladimir Uversky) [PDF] [Supplementary] ♚ (B/CB)


• Jeffery J, Sinha D, Srihari S, Kalimutho M, Khanna KK (2015). Beyond cytokinesis: the emerging roles of CEP55 in tumorigenesis. Oncogene (Nature Publishing Group), 35:683-690 [IF:8.56] [PDF] (TB)


• Taherian-Fard A*, Srihari S*, Ragan MA (2015). Breast cancer classification: linking molecular mechanisms to disease prognosis. Briefings in Bioinformatics, 16(3):461-474 [PDF] [IF: 5.919] (TB,CB/B)


• Srihari S#, Madhamshettiwar PB, Song S, Liu C, Simpson PT, Khanna KK, Ragan MA# (2014). Complex-based analysis of dysregulated cellular mechanisms in cancer. BMC Systems Biology, 8(Suppl 3):S2 [IF:2.85] [PDF] [Software] (TB,CB/B)


• Liu C*, Srihari S*, Lê Cao K-A, Chevenix-Trench G, Simpson PT, Ragan MA, Khanna KK (2014). A fine-scale dissection of the DNA double-strand break repair machinery and its implications for breast cancer therapy. Nucleic Acids Research, 42(10):6106-6127 [IF: 8.808] [PDF] (TB)


• Srihari S, Raman V, Leong HW, Ragan MA (2014). Evolution and controllability of cancer networks: a Boolean perspective. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(1):83-94 [IF: 1.616] [PDF] [Software] ♚ (B/CB, SB, TCS)


• Srihari S, Ragan MA (2013). Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics 29(12): 1553--1561 [IF: 5.468] [PDF] [Software] ♚ (B/CB,SB)


• Nguyen P-V, Srihari S, Leong HW (2013). Identifying conserved protein complexes between species by constructing interolog networks. BMC Bioinformatics, 14(Suppl 12):S8 [IF:3.02] [PDF] (B/CB,SB)


• Srihari S, Leong HW (2013). A survey of computational methods for protein complex prediction from protein interaction networks. Journal of Computational Biology and Bioinformatics, 11(2): 1230002 (Invited review, Ed. Limsoon Wong). [PDF] (Among the top cited articles for the journal [Link]) (B/CB,SB)


• Srihari S, Leong HW (2012). Temporal dynamics of protein complexes in PPI networks: A case study using yeast cell cycle dynamics. BMC Bioinformatics, 13(Suppl 17):S16. [PDF] (B/CB,SB)


• Srihari S, Leong HW (2012). Employing functional interactions for characterization and detection of sparse complexes from yeast PPI networks. International Journal of Bioinformatics Research and Applications (IJBRA) 8(3/4):286--304; invited from the 10th Asia Pacific Bioinformatics Conference (APBC), Melbourne, Australia. [PDF] (B/CB,SB)


• Srihari S, Ning K, Leong HW (2010). MCL-CAw: A refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. BMC Bioinformatics, 11:504 (IF:3.43) [PDF] [Software] ♚ (B/CB,SB)


• Ning K, Ng HK, Srihari, S, Leong HW, Nesvizhskii A (2010). Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. BMC Bioinformatics, 11:505. [PDF] (B/CB,SB)


• Quah TS*, M Sriganesh* (2008). Real-time credit card fraud detection using computational intelligence. Elsevier Expert Systems with Applications, 35(4):1721--1732. [PDF] (DM)

Peer-reviewed conference proceedings

• Srihari S, Singla J, Wong L, Simpson PT, Khanna KK, Ragan MA (2016). Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response. Cancer Research 76 (Supplement 4), PD6-05 [PDF] [IF:9.329]. (TB, B/CB)


• Srihari S, Chandrashekar S, Parthasarathy S (2010). A framework for SQL-based mining of large graphs on relational databases. 14th Pacific Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Hyderabad, India, Springer LNCS 6119(2):160--167. [PDF] [Software] (D,DM)


• Srihari S, Ning K, Leong HW (2009). Refining Markov Clustering for protein complex detection by incorporating core-attachment structure. 20th International Conference on Genome Informatics (GIW), Yokohama, Japan, Genome Informatics Series - World Scientific 23: 159--169. (B/CB,SB)


• Srihari S, Ng HK, Ning K, Leong HW (2008). Detecting hubs and quasi cliques in scale-free networks. 19th International Conference on Pattern Recognition (ICPR), Tampa, Florida, 1: 1--4. [PDF] (TCS,DM)


• Raman V, Saket S, Srihari S (2008). Parameterized algorithms for generalized domination. 2nd International Conference on Combinatorial Optimization and Applications (COCOA), St. John, Canada, Springer LNCS 5156: 116--126. (TCS)


• Quah TS*, M Sriganesh* (2007). Real-time credit card fraud detection using computational intelligence. 20th International Joint Conference on Neural Networks (IJCNN), Orlando, Florida, pp.863--868. (DM)

Non-peer-reviewed articles (for Biotechin.asia)

• Srihari S. Maybe you don't need chemo! Biotechin.asia, 07 Sep, 2016 [Link].


• Srihari S, and Srihari S. Microbes and cancer: Coming a full circle. PeerJ Preprints 2016, e2448v1 [Link].


• Srihari S. Antibiotics, probiotics, superbugs, and all that jazz: For the layman. Biotechin.asia, 06 Oct, 2016 [Link].


• Srihari S. Computational prediction of protein complexes. Biotechin.asia, 25 April, 2016 [Link].


• Srihari S. Genomically unstable cancer genomes: deciphering order from apparant chaos. Biotechin.asia, 29 November, 2015 [Link].


• Srihari S. Exploiting synthetic lethal vulnerabilities for cancer therapy. Biotechin.asia, 20 November, 2015 [Link].

Talks, short papers and posters

• Srihari S. Is Genomics Ready for Clinical Practice? How can startups help? Genomics: Is it ready for routine clinical practice? HealthTech Qld meetup, Startup Precinct, Brisbane, 28 Nov 2018 (conceptualized and helped organize the event).


• Srihari S, Simpson R, Tattam P, Smith E. Metabolic Deregulation in Prostate Cancer. 30th Anniversary AACR Special Conference Convergence: Artificial Intelligence, Big Data, and Prediction in Cancer, Newport, RI, USA, 14-17 Oct 2018, poster #42.


• Srihari S, Simpson R, Tattam P, Smith E. Glycolysis and lipid metabolism as predictors of prostate cancer aggressiveness. 19th Asia-Pacific Prostate Cancer Conference 2018, Brisbane, Australia, Aug 23-24; Abstract 76, British Journal of Urology (BJUI), Wiley publishers, [PDF] (abstract #76) (TB, B/CB)


• Nones K, Johnson J, De Luca X, Srihari S,...,Waddell N, Simpson P. The Mutational Landscape of Familial Breast Cancers. 30th Lorne Cancer Conference 2018, Lorne, Australia [PDF] (TB, B/CB)


• Srihari S, Wong L, Simpson PT, Khanna KK, Ragan MA (2017). Identifying genetic vulnerabilities in cancers driven by defects in the DNA-damage response. 13th Indo-Australian Biotechnology Conference "Omics in Health", Brisbane, Queensland, Australia; 30-31 Oct 2017. Appreciation award for presentation [PDF] (TB, B/CB)


• Srihari S, Singla J, Wong L, Simpson PT, Khanna KK, Ragan MA (2015). Identifying genetic vulnerabilities in cancers driven by defects in DNA-damage response. San Antonio Breast Cancer Conference (SABCS), San Antonio Texas, USA, Dec 8 - 12; Abstract PD6-05 Poster Discussion at Translational Genomics session [Abstract] (TB, B/CB)
  AACR Scholar-in-Training Award - Supported by Susan G. Komen ®; Travel award from the Ian Potter Foundation (Australia)


• Kalimutho M, Waddell N, Jeffry J, Srihari S and Khanna KK (2015). CEP55 is a determinant of genomic instability in aneuploid breast cancer cells and facilitates anti-mitotic drug resistance by interacting directly with HSF1. Cancer Research (Suppl 15):3008. 6th Annual Meeting of the American Association for Cancer Research (AACR), Philadelphia USA, Apr 18-22. [PDF] (TB)


• Taherian-Fard A, Srihari S, Ragan MA (2015). Modeling the landscape of cellular development using Hopfield network. 19th International Conference on Research in Computational Molecular Biology (RECOMB), Warsaw Poland, April 12-15.


• Srihari S (2014). Lectures on Cancer - Parts I & II, Talk at International Institute of Information Technology (IIIT) Bangalore, 8 Oct (hosted by Prof Neelam Sinha). (TB)


• Srihari S (2014). Harnessing DNA-damage response pathways for breast cancer therapy: a synthetic lethality paradigm. Divisional seminar, Genomics of Development and Disease, Institute for Molecular Bioscience, The University of Queensland, Australia, 11 Sept. (TB,B/CB,SB)


• Srihari S, Liu C, Taherian-Fard A, Simpson PT, Ragan MA, Khanna KK (2013, 2014) Harnessing DNA-damage repair pathways in breast cancer therapy: a synthetic lethality paradigm. Australian Breast Cancer Conference (Poster), Melbourne, Australia 7-8 Nov 2013; 24th Genome Informatics Conference (Poster), Singapore 16-18 Dec 2013; Systems Biology of the Human Disease (Poster), Boston, MA, USA 17-19 June 2014; [PDF] (B/CB, SB).


• Srihari S (2014). Deciphering cancer mechanisms by integrative network analysis. The Jackson Laboratory for Genomic Medicine, Farmington CT, USA, 23 June (hosted by Dr Duygu Ucar) (TB, B/CB)


• Srihari S (2014). Deciphering cancer mechanisms by integrative network analysis. Talk at Duke-NUS Graduate Medical School, Singapore, 03 June (TB, B/CB)


• Srihari S, Ragan MA (2013) Evolution and controllability of cancer networks: a Boolean perspective. Cold Spring Harbor Meeting -- Frontiers in Bioinformatics and Computational Biology (Poster), Suzhou China, 23-27 Sep [PDF] (B/CB, SB).


• Srihari S (2013). Harnessing DNA-damage repair pathways in breast cancer therapy. Short talk at 12th International Conference on Bioinformatics InCoB 2013, Taicang China, 20 Sep (B/CB, SB)


• Srihari S (2013). Deciphering novel cellular mechanisms in cancer by integrative network analysis. Talk at MPG-CAS Partner Institute for Computational Biology (PICB), Shanghai, 19 Aug (hosted by Dr Jing-Dong Han) (B/CB, SB)


• Srihari S (2013). Deciphering novel cellular mechanisms in cancer by integrative network analysis. Early Career Researcher (ECR) talk (IMB Friday Seminar), 02 Aug [Link] (B/CB,SB)


• Srihari S (2013). Network-based methods for deciphering mechanisms in cancer. Talk at the CS Dept, NUS Singapore, 29 May (hosted by A/Prof Hon Wai Leong) [Link] [Talk] (B/CB,SB).


• Srihari S (2013). Introduction to Computational Biology. "Online" guest talk for the students of CSE Dept, IIT Roorkee, 11 May (hosted by Asst/Prof Dhaval Patel) (B/CB,SB)


• Nguyen P-V, Srihari S, Leong HW (2013) Identifying conserved protein complexes between species by constructing interolog interaction networks. 17th International Conference on Research in Computational Molecular Biology (RECOMB) (Poster), Beijing China, April 7-10 (B/CB,SB)


• Srihari S (2012) Controllability of cancer networks: a BoØ1ean perspective. BioInfoSummer: Australian Mathematical Sciences Institute (AMSI) Summer Symposium on Bioinformatics (Poster), Adelaide. [Link] (B/CB,SB)


• Srihari S, Ragan MA (2012): Computing pathways to systems biology: key contributions of computational methods in pathway identification (Technical report), IMB UQ. [Link](B/CB,SB)


• Srihari S, Leong HW (2012): Computational methods for detecting protein complexes from whole-genome PPI networks. three-hour tutorial at ISCB-APBioNet 11th International Conference on Bioinformatics (InCoB) 2012, Bangkok. (B/CB,SB)


• Srihari S, Leong HW (2012) A survey of algorithms for detecting protein complexes from protein-protein interaction networks. 5th Annual Meeting of the Asian Association for Algorithms and Computation (AAAC) (Short paper), Shanghai. (B/CB,SB)


• Srihari S, Leong HW (2011) Temporal "reusuability" of 'static' protein complex components during the yeast cell cycle. 10th International Conference on Bioinformatics (InCoB) (Poster), Kuala Lumpur Malaysia, December. [Link] (B/CB,SB)


• Srihari S (2011). Methods integrating biological insights with topology for analysis of protein interaction networks. Talk at Department of Biotechnology, IIT Guwahati India, May (Chaired by Asst/Prof B. Anand). [Link] (B/CB,SB)


• Srihari S (2011). Methods integrating biological insights with topology for analysis of protein interaction networks. Public seminar (my thesis proposal), Department of Computer Science, NUS Singapore, 23 Nov (B/CB,SB)


• Srihari S, Leong HW (2010) Extending the MCL-CA algorithm for protein complex detection from weighted PPI networks. 8th Asia Pacific Bioinformatics Conference (Poster), Bangalore India, Jan 2010 [Link] (B/CB,SB)


• Srihari S, Leong HW (2009) Detecting complexes from protein interaction networks. 11th International Conference on Molecular Systems Biology (ICMSB) (Short paper), PICB Shanghai, July 2009 (B/CB,SB)


• Srihari S (2008). Parameterized complexity: theory and applications in bioinformatics. Talk at Department of EECS, University of Central Florida, December 10 (Chaired by Asst/Prof Shaojie Zhang). [Link] (B/CB,TCS)

Slides
(Please cite or acknowledge my papers or this website if you are using these slides)

• Basics of cancer and cancer genomics. [PDF] (2014)
• Deciphering cancer mechanisms by integrative network analysis. [PDF] (2014)
• Evolution and controllability of cancer networks: a Boolean perspective. [PDF] (2013)
• Detecting conserved protein complexes between species by constructing interolog networks. [PDF](2013)
• Protein complex prediction from protein interaction networks. [PDF] (2012)

Theses

• [PhD thesis] Sriganesh Srihari: Integrating Biological Insights with Topological Characteristics for Improved Complex Prediction from Protein Interaction Networks. Department of Computer Science, National University of Singapore, May 2012. [PDF] (Available from the NUS digital library)


• [Masters thesis] Sriganesh Srihari: Credit Card Fraud Detection System using Computational Intelligence. School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore, May 2007. [PDF] (Available from the NTU digital library)


• [Bachelors thesis] Minimum Variance Huffman Coding for On-the-fly Text Compression over Networks. Department of Computer Science and Engineering, National Institute of Technology Calicut, India, May 2003.