Research Publications
PUBLICATIONS
PUBLICATIONS
40.
[Upcoming] 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, S. Ahmed, M. Tariq, A. Faisal, and S. U. Chaudhary,* “TISON: a Next-generation Multi-scale Modeling Theatre for in silico Systems Oncology”.
Pre-print [BiorXiv]
39.
[Upcoming] 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”.
38.
[Upcoming] S. M. Alam, M. S. Khan, Z. Nisar, A. Iqbal, S. M. Irtaza, S. Anwar, S. U. Chaudhary*, “A minimally invasive low-cost continuous glucose monitoring system for the developing world“.
37.
[Upcoming] W. Abdullah♰, F. Ahmad♰, S. Bashir*, and S. U. Chaudhary*, “Causality Mapping in Schizophrenia Patients using Resting-State fMRI Reveals Aberrant Functional and Causal Connectivity in the Brain“.
Preprint: [BiorXiv]
37.
[Upcoming] Z. Nasir, M. U. Sultan, S. R. A. Gilani, A. Hassan, M. Kamal, A. Saqib, B. Amina, M. Azhar, M. A. Hassan, and S. U. Chaudhary*, “AutoNetCancer: A Web Server to Automate Network Construction for Translational Cancer Systems Biology“, Journal of Molecular Biology.
36.
[Under Review] A. Tahir, K. Asghar, W. Shafiq, A. Loya, S. Bashir, S. U. Chaudhary*, “Routine Diagnostics-derived Hematological and Inflammatory Markers as Risk Predictors of Diabetes and its Cardiometabolic Complications: An Observational Study on Diagnostic Biomarkers “, Diabetologica.
35.
[Under Review] A. Faisal, K. Bashir, M. Shoaib, S. U. Chaudhary*, “The Cancer Noise Atlas (TCNA) – Mapping Tissue-specific Transcriptional Noise for Tumor Heterogeneity and Therapeutic Prognostication”, Journal of Molecular Biology.
34.
[Under Review] M. Hamid, M. F. Khalid, S. Khan*, S. U. Chaudhary*, “PERCEPTRON-XFMS: A Web Server for X-ray Foot Printing with Mass Spectrometry (XFMS) Data Analysis”, Journal of Molecular Biology.
Preprint: [SSRN]
33.
[Under Review] R. N. Butt, B. Amina, M. U. Sultan, Z. B. Tanveer, R. Hussain, R. Akbar, S. Khan, M. N. Gondal, M. F. Khalid, A. Khan*, A. Faisal, M. Shoaib, and S. U. Chaudhary*, “CanSeer: A Method for Development and Clinical Translation of Personalized Cancer Therapeutics“, Scientific Reports – Nature.
Preprint: [BiorXiv]
32.
[Under Review] A. Tahir, M. Hassan, A. Farooq, S. Ashfaq, M. Ayub, I. Hameed, A. Z. Sheikh, A. Ahad, J. Azad, U. Ahmed, A. Aleem, A. Masood, K. Asghar*, A. W. Khan*, and S. U. Chaudhary* “In-hospital Mortality Prognostication for Cancer Patients with Febrile Neutropenia“, Communications Medicine – Nature.
Preprint: [Research Square] [BiorXiv]
31.
[Under Review] S. Hamera*, S. U. Chaudhary, H. Lemcke, M. Sklorz, F. Schilling, C. Schumacher, J. Hackauf, R. Zimmerman, R. Horn, and R. Uptmoor, “StACS3 Protein negatively regulates drought tolerance in potatoes, influenced by StPP2C2“, Journal of Experimental Botany.
30.
K. Iman, M. U. Mirza*, F. Sadia, M. Froeyen, J. F. Trant, S. U. Chaudhary*, “Pharmacophore-Assisted Covalent Docking Identifies a Potential Covalent Inhibitor for Drug-Resistant Genotype 3 Variants of Hepatitis C Viral NS3/4A Serine Protease“, Viruses, 16(8), 1250, Aug. 2024. [Link]
29.
R. Abid, H. Nisar, S. U. Chaudhary, M. Hamid, K. I. Sahibzada, S. Firdous, M. Mudassar, and S. Sadaf, “Association of epilepsy and neurological impairments with homozygous recessive missense mutations found in the genes responsible for ganglioside biosynthesis (ST3GAL5) and calcium voltage-gated channels (CACNA1H) – gaining insights through molecular dynamic simulations“, Journal of Biomolecular Structure and Dynamics, Feb. 2024. [Link]
28.
A. S. Malik*, M. Hussain, and S. U. Chaudhary, “Editorial: From Assessment to Intervention: Role of Consumer Technology and Neurotech in Preventive Mental Health“, Frontiers in Psychology, Vol. 15, No. 1372708, Feb. 2024. [Link]
27.
A. Tahir, K. Asghar, W. Shafiq, H. Batool, D. Khan, O. Chugtai, and S. U. Chaudhary*, “Fingerprinting Hyperglycemia using Predictive Modelling Approach based on Low-Cost Routine CBC and CRP Diagnostics“, Scientific Reports – Nature, Vol. 14, No. 1090, Jan. 2024. [Link]
26.
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. [Link]
* Paper appeared in the “Special Issue” on “Natural Polyphenols: Isolation, Characterization and Health Benefits”
25.
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], [Link]
24.
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, Vol. 23, Issue 21, No. 12771, Oct. 2022. [I.F. 6.2], [Link]
Preprint: [BiorXiv]
* Paper appeared in the “Special Issue” on “Understanding Allosteric Control of Enzymatic and Cellular Activities with Integrated Computational and Experimental Approaches“
23.
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, Vol. 7, No. 170, Apr. 2022. [I.F. 2.42], [Link]
22.
M. N. Gondal, S. U. Chaudhary*, “Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics“, Frontiers in Oncology, Vol. 11, Issue 712505, Oct. 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“.
21.
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]
20.
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, Vol. 11, No. 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“.
19.
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“.
18.
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], [Link]
17.
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]
16.
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]
15.
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]
14.
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]
13.
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]
12.
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]
11.
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]
10.
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]
9.
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]
8.
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]
7.
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
6.
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]6. , [Link]
5.
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]
4.
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]
3.
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]
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], [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]
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], [Link]
* Paper appeared in the “Special Issue” on “Multi-Scale Modeling and Analysis in Computational Biology and Medicine”.
2. PUBLISHED ABSTRACTS
1.
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]
