1. PUBLISHED ARTICLES
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26.
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M. N. Gondal, A. Rehman, A Arif, M. U. Sultan, H. A. Awan, Z. Arshad, M. F. A. Chaudhary, W. Ahmed, R Hussain, H. Khawar, S. Khan, B. Amina, R. N. Butt, F. Abbas, M. N. Jami, R. Akbar, Z. Nasir, O. S. Shah, H. Hameed, M. F. A. Butt, M. M. Ahmad, M. A. Talal, S. Ahmed, F. Ahmed, O. Ishaq, S. W. Nabi, W. Vanderbauwhede, B. Wajid, H. Shehwana, E. Uddin, M. Safdar, I. Javed, M. Tariq, A. Faisal, and S. U. Chaudhary,* "TISON: a Next-generation Multi-scale Modeling Theatre for in silico Systems Oncology", (In Preparation)
Pre-print [Link]
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25.
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A. Sabir¥, Z. Nasir¥, Z. Khalid¥, H. M. Salman, M. F. Khalid, M. B. Khalid, F. Arshad, K. Iman, M. U. Ashraf, A. Tahir, H. G. Ejaz, S. A., S. H. Liaqat, H. Khawar, R. Hussain, A. Rehman, N. Javaid, M. Saleem, S. N. Arshad, S. Mirza, N. Nisar, S. Sikander, Z. Ahmad, M. Abubakar, S. Hamera, A. Bashir, B. Wajid, M. Tariq, and S. U. Chaudhary*, "Profiling microbial and heavy metal contamination of Hudiara drain and its adjoining areas in Lahore, Pakistan". (In Preparation)
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24.
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F. Ahmad, Z. Saghir, S. U. Chaudhary*, S. Bashir*, "Causality Mapping in Schizophrenia Patients using Resting-State fMRI Reveals Aberrant Functional and Causal Connectivity in the Brain". (In Preparation)
Preprint: [BiorXiv]
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23.
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K. Iman, K. Kwon, S. H. Kim, K. H. Park, M. Hur, Y. S. Cho, H. S. Kim, S. U. Chaudhary*, J. S. Yoo*, "De novo-based Complementary Ion Search (COINS) Algorithm for Enhanced Proteoform Identification and Characterization in Top-Down Proteomics", Bioinformatics. (In Review)
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22.
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M. N. Gondal, S. U. Chaudhary*, "Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics", Frontiers in Oncology. (In Review)
Preprint: [BiorXiv]
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21.
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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], [Link]
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20.
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M. N. Gondal, R. N. Butt, O. S. Shah, U. Sultan, G. Mustafa, Z. Nasir, R. Hussain, H. Khawar, 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], [Link]
Preprint: [BiorXiv]
* Paper appeared in the "Special Issue" on "Combinatorial Approaches for Cancer Treatment: from Basic to Translational Research".
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19.
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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], [Link]
* Paper appeared in the "Special Issue" on "NMR-based Metabolomics".
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18.
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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. 16.9], [Link]
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17.
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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], [Link]
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16.
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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], [Link]
Preprint: [ResearchSquare]
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15.
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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], [Link]
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14.
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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], [Link]
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13.
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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], [Link]
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12.
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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], [Link]
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11.
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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], [Link]
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10.
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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], [Link]
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9.
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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], [Link]
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8.
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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], [Link]
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7.
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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], [Link]
* Editor's choice as a "Featured Article" for the issue
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6.
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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], [Link]
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5.
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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], [Link]
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4.
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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], [Link]
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3.
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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], [Link]
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2.
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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], [Link]
* Paper also selected and featured in the World Biomedical Frontiers (ISSN: 2328-0166) due to its potentially significant impact in biomedical and cancer research. [Link]
For videos, please click: [ELECANS Videos]
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1.
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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], [Link]
* Paper appeared in the "Special Issue" on “Multi-Scale Modeling and Analysis in Computational Biology and Medicine".
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2. PUBLISHED ABSTRACTS
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1.
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K. H. Kwon, S. U. Chaudhary, M. H. Hur, S. H. Kim, H. S. Kim, and J. S. Yoo*, "Database Search Analysis using Flipped Mass Spectrum in Top-down Proteomics", Molecular and Cellular Proteomics, Vol. HUPO2007, pp. 38, Oct. 2007. [I.F. 8.83]
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