Research Themes
RESEARCH
RESEARCH
LAB FACILITIES
LINKS
An integrative analysis of biological and clinical data can help researchers develop a deeper appreciation of the principles underpinning life. Towards this goal, we construct integrative models of complex pathologies such as cancer ontowards building decision support systems for conditions such as pre-eclampsia. The current research focuses of BIRL include multiscale integrative investigation of cancer, development of next-generation cancer modeling software, top-down proteomics search engine, drug development of Hepatitis-C virus, and e-health monitoring systems.
Below, the publications from our work within each of the above-mentioned areas have been listed.
Below, the publications from our work within each of the above-mentioned areas have been listed.
| A. Cancer Systems Biology | ||
| 5. | M. N. Gondal, S. U. Chaudhary*, “Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics“, Frontiers in Oncology, 11 (712505), Oct. 2021. [I.F. 6.2] * Paper appeared in the “Special Issue” on “Combinatorial Approaches for Cancer Treatment: from Basic to Translational Research“. | |
| 4. | M. N. Gondal, R. N. Butt, O. S. Shah, U. Sultan, G. Mustafa, Z. Nasir, R. Hussain, H. Khawar, R. Qazi, M. Tariq, A. Faisal, and S. U. Chaudhary*, “A personalized therapeutics approach using an in silico Drosophila Patient Model reveals optimal chemo- and targeted therapy combinations for colorectal cancer“. Frontiers in Oncology, 11 (692592), Jul. 2021. [I.F. 6.2] * Paper appeared in the “Special Issue” on “Combinatorial Approaches for Cancer Treatment: from Basic to Translational Research“. | |
| 3. | O. S. Shah, M. F. A. Chaudhary, H. A. Awan, F. Fatima, Z. Arshad, A. Bibi, M. Ahmed, H. Hameed, M. Furqan, S. Khalid, A. Faisal, S. U. Chaudhary*, “ATLANTIS-Attractor Landscape Analysis Toolbox for Cell Fate Discovery & Reprogramming“, Scientific Reports – Nature, Vol. 8, No. 3554, Feb. 2018. [I.F. 4.2] | |
| 2. | S. U. Chaudhary, S.-Y. Shin, D. W. Lee, J.-H. Song and K.-H. Cho*, “ELECANS-An Integrated Model Development Environment for Multiscale Cancer Systems Biology“, Bioinformatics, Vol. 29, Issue 7, pp. 957-959, ISSN 1460-2059 (Online),1367-4803 (Print), Apr. 2013. [I.F. 5.3] | |
| 1. | S. U. Chaudhary, S.-Y. Shin, J.-K. Won, and K.-H. Cho*, “Multi-Scale Modeling of Tumorigenesis Induced by Mitochondrial Incapacitation in Cell Death“, IEEE Transactions on Biomedical Engineering, Vol. 58, Issue 10, pp. 3028-3032, ISSN 0018-9294, Oct. 2011. [I.F. 4.28] | |
| B. Plant Systems Biology | ||
| 4. | A. Z. Abbasi, M. Bilal, G. Khurshid, C. Yiotis, I. Zeb, J. Hussain, A. Baig, M. M. Shah, S. U. Chaudhary, B. Osborne*, R. Ahmad*, “Expression of Cyanobacterial Genes Enhanced CO2 Assimilation and Biomass Production in Transgenic Arabidopsis thaliana“, PeerJ, Jul. 2021. [I.F. 2.98] | |
| 3. | G. Khurshid, A. Z. Abbassi, M. F. Khalid, M. N. Gondal, T. A. Naqvi, M. M. Shah, S. U. Chaudhary*, R. Ahmad*, “An integrated model of cyanobacterial decarboxylation and C3 photosynthetic pathways to bypass photorespiration for enhancing photosynthesis“, Scientific Reports – Nature, Vol. 10, No. 20879, Nov. 2020. [I.F. 4.38] | |
| 2. | N. Nisar*, K. Cheema, G. Powell, M. Bennett, S. U. Chaudhary, R. Qadri, Y. Yang, M. Azam, J. Rossiter, “Reduced metabolites of nitroaromatics are distributed in the environment via the food chain“, Journal of Hazardous Materials, Vol. 355, pp. 170-179, Aug. 2018, [I.F. 7.6] | |
| 1. | S. Hamera*, Y. Yan, X. Song, S. U. Chaudhary, I. Murtaza, L. Su, M. Tariq, X. Chen*, and R. Fang*, “Expression of Cucumber mosaic virus suppressor 2b alters FWA methylation and its siRNA accumulation in Arabidopsis thaliana“, Biology Open, Vol. 5, pp. 1727-1734, Sep. 2016. [I.F. 2.4] | |
| C. Proteomics | ||
| 9. | A. A. Shami, M. T. Akhtar*, W. Mumtaz, H. Mukhtar, A. Tahir, S. Shahzad-ul Hussan*, S. U. Chaudhary, B, Muneer, H. Iftikhar, and M. Neophytou, “NMR-based metabolomics: a new paradigm to unravel defense-related metabolites in insect-resistant cotton variety through different multivariate data analysis approaches“, Molecules, Jan. 2023. [I.F. 4.93] | |
| 8. | Z. Nasir, A. Sabir, H. M. Salman, M. U. Ashraf, M. F. Khalid, M. B. Khalid, Z. Khalid, A. Tahir, F. Arshad, H. G. Ejaz, S. Ashraf, S. H. Liaqat, H. Khawar, R. Hussain, M. U. Sultan, I. Afzal, S. Hamera, N. Nisar, S. Sikander, and S. U. Chaudhary*, “Fingerprinting of heavy metal and microbial contamination uncovers the unprecedented scale of water pollution and its implication on human health around transboundary Hudiara drain in South Asia“, Environmental Technology & Innovation, Feb. 2023. [I.F. 7.76] | |
| 7. | M. Hamid, M. F. Khalid, S. U. Chaudhary*, and S. Khan*, “The Solvation of the E. coli CheY Phosphorylation Site Mapped by XFMS“, International Journal of Molecular Sciences, 23(21), 12771, Oct. 2022. [I.F. 6.2] * Paper appeared in the “Special Issue” on “Understanding Allosteric Control of Enzymatic and Cellular Activities with Integrated Computational and Experimental Approaches“ | |
| 6. | L. Ajmal, A. Hamid, F. Raza, S. U. Chaudhary, K. Iman, S. Ajmal, H. Younas, R. Khalid, M. Iqbal, R. Tasadduq*, “Determination of the repellent activity of trans-anethol and tea tree oil against Aedes aegypti and their interaction with AaegOBP1“, Entomologia Experimentalis et Applicata, 7 (170), Apr. 2022. [I.F. 2.42] | |
| 5. | M. T. Akhtar*, M. Samar, A. A. Shami, M. W. Mumtaz, H. Mukhtar, A. Tahir, S. Shahzad-ul-Hussan, S. U. Chaudhary, and U. Kaka*, “1H-NMR-based metabolomics: An integrated approach for the detection of adulteration in chicken, mutton, beef and donkey meats”, Molecules, Vol. 26, Issue 15, 4643, Jun. 2021. [I.F. 4.4] * Paper appeared in the “Special Issue” on “NMR-based Metabolomics“. | |
| 4. | M. F. Khalid♰, K. Iman♰, A. Ghafoor♰, M. Saboor, A. Ali, U. Muaz, A. R. Basharat, T. Tahir, M. Abubakar, M. A. Akhter, W. Nabi, W. Vanderbauwhede, F. Ahmad, B. Wajid, S. U. Chaudhary*, “PERCEPTRON – An open-source GPU-accelerated proteoform identification pipeline for top-down proteomics“, Nucleic Acids Research, 49(W1), pp 510-515, May 2021. [I.F. 19.1] | |
| 3. | M. U. Ashraf♰, H. M. Salman♰, M. F. Khalid, M. H. F. Khan, S. Anwar, S. Afzal, I. Khan, S. U. Chaudhary*, “CRISPR-Cas13a Mediated Targeting of Hepatitis C Virus Internal-Ribosomal Entry Site (IRES) as an Effective Antiviral Strategy“, Biomedicine & Pharmacotherapy, Vol. 136, No. 111239, Apr. 2021. [I.F. 6.5] | |
| 2. | M. U. Ashraf♱, K. Iman♱, M. F. Khalid, H. M. Salman, T. Shafi, M. Rafi, N. Javaid, R. Hussain, F. Ahmad, S. Shahzad-ul-Hussan, S. Mirza, M. Shafiq, S. Afzal, M. Idrees, S. Hamera, S. Anwar, R. Qazi, S. A. Qureshi, S. U. Chaudhary*, “Evolution of Efficacious Pan-Genotypic HCV Therapies“, Medicinal Research Reviews, Vol. 39, Issue 3, pp. 1091-1136, May 2019. [I.F. 12.94] | |
| 1. | A. R. Basharat, K. Iman, Z. Bibi, R. Hussain, H. G. Kabir, A. Shahid, M. Humayun, H. A. Hayat, M. Mustafa, M. Shoaib, Z. Ullah, S. Zarina, S. Ahmed, E. Uddin, S. Hamera, F. Ahmad, S. U. Chaudhary*, “SPECTRUM – A MATLAB Toolbox for Identifying Proteins from Top-down Proteomics Data“, Scientific Reports – Nature, Vol. 9, No. 11267, Jun. 2019. [I.F. 4.38] | |
| D. Public Health & Epidemiology | ||
| 4. | A. Ambreen, A. Khalid, S. Z. H. Naqvi, A. Tahir, M. Mustafa, S. U. Chaudhary, S. Mirza, T. Mustafa*, “Host Biomarkers for Monitoring Therapeutic Response in Extra-Pulmonary Tuberculosis“, Cytokine, Vol. 142, No. 155499, Jun. 2021. [I.F. 3.8] | |
| 3. | N. Javaid, Q. Sultana, K. Rasool, S. Gandra, F. Ahmad, S. U. Chaudhary, S. Mirza*, “Trends in antimicrobial resistance amongst invasive pathogens in Pakistan (2011-2015): A retrospective cross-sectional study“, PLOS One, Apr. 2021. [I.F. 3.2] | |
| 2. | A. Tahir♰, P. J. Martinez♰, F. Ahmad, S. P. Fisher-Hoch, J. L. Gay, S. Mirza*, S. U. Chaudhary*, “An Evaluation of Lipid Profile and Pro-inflammatory Cytokines as Determinants of Cardiovascular Disease in Diabetics“, Scientific Reports – Nature, Vol. 11, No. 2435, Jan. 2021. [I.F. 4.38] | |
| 1. | A. Ahsan; A. Z. Khan; H. Javed; S. Mirza; S. U. Chaudhary, S. Shahzad-ul-Hussan*, “Estimation of hepatitis C prevalence in the Punjab province of Pakistan: A retrospective study on general population“, PLOS One, Apr. 2019. [I.F. 3.2] | |
| E. Neuroscience | ||
| 4. | H. Abid, F. Ahmad*, S.-Y. Lee, H. Park, D. Im, I. Ahmed, and S. U. Chaudhary*, “An fMRI Investigation of Visual Hallucination in Human Visual Cortex“, Behavioral and Brain Functions, Vol. 12, Issue 21, Nov. 2016. [I.F. 3.75] | |
| 3. | F. Ahmad*, A. Hussain, S. U. Chaudhary, I. Ahmad, S. M. Ramay, “A Novel Method for Detection of Voxels for Decision Making: an fMRI Study“, International Journal of Imaging Systems and Technology, Vol. 26, Issue. 2, Jun. 2016. [I.F. 2.0] | |
| 2. | M. Ahmed, S. U. Chaudhary, A. J. Afzal*, and M. Tariq*, “Starvation-Induced Dietary Behaviour in Drosophila Melanogaster Larvae and Adults“, Scientific Reports – Nature, Vol. 5, No. 14285, Sep. 2015. [I.F. 5.2] | |
| 1. | F. Ahmad, S. U. Chaudhary, S. Kim, and H. Park*, “A Slice-wise Latent Structure Regression Method for Analysis of Functional Magnetic Resonance Imaging Data“, Concepts in Magnetic Resonance Part A, Vol. 42, Issue 4, pp. 130-139, ISSN 1552-5023, Aug. 2013. [I.F. 1.1] | |