Microbial- Genomics and Bioinformatics

  1. Mehboob, S, Ullah N, Haq F, Amjad Ali, Rahman MU Genomic characterization and comparative genomic analysis of HS-associated Pasteurella multocida serotype B:2 strains from Pakistan BMC Genomics 2023
  2. Sidsel Nag. Aarestru FM, Amjad Ali et al., Whole genomes from bacteria collected at diagnostic units around the world 2020 Scientific Data 2023
  3. Sareen Fatima, Ali Akbar, Muhammad Irfan, Zaara Ishaq, Amjad Ali. Whole-Genome sequencing of MDR Salmonella typhi clinical strains isolated from Balochistan, Pakistan Front. in Public Health May 2023
  4. Virulence factors and antimicrobial resistance of Uropathogenic Escherichia coli EQ101 (UPEC) isolated from UTI patient in Quetta-Balochistan, Pakistan Biomed Res Int 2023
  5. Sherdin H, Ahmed S, Zaheer T, Amjad Ali, Husnain J, Javed A. Employing computational tools to design a multi-epitope vaccine targeting human immunodeficiency virus-1 (HIV-1). BMC Genomics May 2023
  6. Jalil M, Fatima Quddos F, Anwer F, Nasir S, Rahman A, Metab Alharbi, Alshammari A, Alshammari H, Amjad Ali* Comparative Pan-Genomic Analysis Revealed an Improved Multi-Locus Sequence Typing Scheme for Staphylococcus aureus. Genes Nov 2022
  7. Sumera, Anwer F, Fatima A, Malik N, Amjad Ali. Zahid. Molecular docking and molecular dynamics studies reveal secretory proteins as novel targets of Temozolomide in Glioblastoma Multiforme. Molecule Oct 2022
  8. Zafar S, Bai, Baogang, Gua Jinlei, Mohammad SA, Nazqvi STQ, Muhammad NS, Imran I, Sheikh RS and Amjad Ali. Experimental study of potential CD+8 trivalent synthetic peptides for live cancer vaccine development using Sprague Dawley rat model. Biomed Res Int. May 2022.

  9. Ullah N, Nasir S, Ishaq, Z Anwar F, Raza T, Rahman M, shammari A, Alharbi M, Bae T, Rahman A, Amjad Ali* Comparative genomic analysis of a Panton-Valentine Leuko-2 cidin-positive ST22 community-acquired methicillin-resistant 3 Staphylococcus aureus from Pakistan Antibiotics April 2022

  10. Zafar H, Ain NU, Alshammari A, Saeed A, Raja H, Amjad Ali, Siddique A, Tahir SD, Akbar S, Arif M, Alharbi M, Abdur Rahman Lacticaseibacillus rhamnosus FM9 and Limosilactobacillus fermentum Y57 are as effective as statins at improving blood lipid profile in high cholesterol, high-fat diet model in male Wistar rats. Nutrients April 2022

  11. Ullah N, Anwar F, Ishaq Z, Siddique A, Shah MA, Rahman M, Rahman A, Mao X, Jiang TT, Lee BL, Bao T, Amjad Ali* In silico designed Staphylococcus aureus B-cell multi-epitope vaccine did not elicit antibodies against target antigens suggesting a multi-domain approach. J. of Immunological Methods March 2022

  12. Nisa I, Haroon M, Driessen A, Nijland J, Rahman, H, Yasin N, Hussain M, Amjad Ali, Khan TA, Khan SA, Qasim M. Antimicrobial resistance of Shigella flexneri in Pakistani pediatric population reveals an increasing trend of third-generation cephalosporin resistance. Current Microbiology Feb 2022

  13. Rashid MI, Rashid H, Andeeb S, Amjad Ali, Evaluation of Blood-Brain-Barrier Permeability, Neurotoxicity, and Potential Cognitive Impairment by Pseudomonas aeruginosa’s Virulence Factor Pyocyanin. Oxidative Medicine and Cellular Longevity March 2022

  14. CNCB-NGDC Members and Partners (Amjad Ali) Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Research Jan 2021
  15. Ullah N, Dar HA, Naz K, Andleeb S, Rahman A, Muhammad Tariq Saeed, Taeok Bae *, Amjad Ali* Genomic investigation of Methicillin-resistant Staphylococcus aureus ST113 strains isolated from tertiary care hospitals in Pakistan Antibiotics 2021
  16. Siddique A, Azim S, Amjad Ali, Adnan F, Arif M, Imran M, Ganda E and Rahman A. Lactobacillus reuteri and Enterococcus faecium from poultry gut reduce mucin adhesion and biofilm formation of cephalosporin and fluoroquinolone-resistant Salmonella enterica. Animals 2021
  17. Yeo WS, Jeong B, Ullah N, Amjad Ali, Kim KK, Bae T. FtsH sensitizes methicillin-resistant Staphylococcus aureus to β-lactam antibiotics by degrading YpfP, a lipoteichoic acid synthesis enzyme Antibiotics 2021
  18. Irum S, Naz K, Ullah N, Mustafa, Amjad Ali, Arslan M, Khalid K, Andleeb S Antimicrobial Resistance and Genomic Characterization of Six New Sequence Types in Multidrug-Resistant Pseudomonas aeruginosa Isolates from Pakistan Antibiotics 2021
  19. Shahid F, Zaheer T, Ashraf ST, Shehroz M, Answer F, Naz A & Amjad Ali * Chimeric Vaccine Designs against Acinetobacter baumannii using Pan genome and Reverse Vaccinology Approaches. Scientific Reports 2021
  20. Siddique A, Azim S, Amjad Ali, Andleeb S, Ahsan A, Imran M, Rahman A. Antimicrobial resistance profiling of biofilm forming non typhoidal Salmonella enterica isolates from poultry and its associated food products from Pakistan. Antibiotics 2021
  21. Rashid MI, Irum S, Amjad Ali, Majid M, Andleeb S. Quest for novel preventive and therapeutic options against multidrug-resistant Pseudomonas aeruginosa. Peptide Res and Therapeutics 2021
  22. Ismail M, Sajid Z, Amjad Ali, Wu X, Muhammad SA, Shaikh RS Designing of Potential Polyvalent Vaccine Model for Respiratory Syncytial Virus by System Level Immunoinformatics Approaches. BioMed Res. Int. 2021
  23. Naz K, Ullah N, Naz A, Irum S, Dar HA, Zaheer T, Shahid F, Amjad Ali* The epidemiological and pangenome landscape of Staphylococcus aureus and identification of conserved novel candidate vaccine antigens Current Proteomics Feb 2021.
  24. Dar HA, Zaheer T, Ullah N, Bakhtiar SM, Zhang T, Yasir M, Esam I. Azhar, Amjad Ali * Pangenome analysis of Mycobacterium tuberculosis revealed potential core- drug targets and their promising lead compounds: A computer-aided drug discovery against tuberculosis – Antibiotics. 2020
  25. Mehmood A, Naseer S, Amjad Ali, Fatimah H, Rehman S, Identification of novel vaccine candidates against carbapenem resistant Klebsiella pneumoniae: A systematic reverse proteomic approach Comp Bio & Chem Sept 2020
  26. Naz A, Shahid F, Butt TT, Awan FM, Amjad Ali, Malik AA. Designing a multi-epitope vaccine to combat emerging coronavirus disease 2019 (COVID-19) employing immuno-informatics approach Frontiers in Immunology June 2020
  27. Zaheer T, Waseem M, Waqar W, Dar HA, Shehroz M, Naz Kanwal, Ishaq Z, Ahmad T, Ullah N, Bakhtiar SM, Muhammad SA, Amjad Ali*. Anti-COVID-19 multi-epitope vaccine designs employing global viral genome sequences PeerJ June 2020
  28.  Awan FM, Yang BB, Naz A, Hanif A, Ikram A, Obaid A, Malik A Janjua HA, Amjad Ali, Sharif S. The emerging role and significance of circular RNAs in viral infections and antiviral immune responses: possible implication as theranostic agents RNA Biology June 2020
  29. Naz A, Zaheer T, Dar HA, Awan FM, Obaid A, Ashraf ST, Paracha RZ, Malik A and Amjad Ali*. A Multi-Method and Structure-Based In Silico Vaccine Designing Against Helicobacter pylori Employing Immuno-Informatics Approach C. Proteomics May 2020
  30. Noora S, Shah Z, Javed A, Amjad Ali, Hussain B, Zafar S, Ali H, Muhammad SA. A fungal based synthesis method for copper nanoparticles with the determination of anticancer, antidiabetic and antibacterial activities J. Microbiological Methods May 29, 2020
  31. Rashid MI, Andeeb, Amjad Ali Evaluation of Pyocyanin induced systemic pathogenicity of Pseudomonas aeruginosa Pak. J. Pharm. Sci. May 2020,
  32. Ismai M, Sajid Z, Amjad Ali, Wu X, Muhammad SA, Shiekh RS. Prediction of Prophylactic Peptide Vaccine Candidates for Human Papillomavirus (HPV): An Immunoinformatics and Reverse Vaccinology Approach C. Proteomics May 2020
  33. Muhammad SA, Zafar S, Rizvi S, Imran, Munir F, Jamshed M, Amjad Ali, Wu X, Shahid N, Zaeem M, and Zhang Q. Experimental Analysis of T-Cell Epitopes for Designing Liver Cancer Vaccine Predicted by System Level Immunoinformatics Approach American J. of Physio April 2020
  34. Chhotaray C, Wang S, Tan Y, Amjad Ali*, Shehroz M, Fang C, Liu Y, Lu Z, Cai X, Hameed H.M. A, Islam MM, Surineni G, Tan S, Liu J, Zhang T Comparative analysis of whole-genome and methylome profiles of a smooth and a rough Mycobacterium abscessus clinical strain G3-Genes Genomes Genetic Jan 2020
  35. Ullah N, Raza T, Dar HA, Sheroz M, Zaheer T, Naz K, Amjad Ali*, Whole-genome sequencing of a new sequence type (ST5352) strain of community-acquired methicillin-resistant Staphylococcus aureus from a hospital in Pakistan. J. glob antimicrob resist 2019
  36. Dar HA, Zaheer T, Sheroz M, Ullah N, Naz K, Muhammad SA, Zhang T and Amjad Ali* Immunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against Klebsiella Pneumoniae. Vaccines 2019
  37. Naz K, Naz A, Ashraf ST, Rizwan M, Ahsan M, Ahmad J, Baumbach J, and Amjad Ali*. PanRV: Pangenome-Reverse vaccinology package for identifications of potential vaccine candidates by exploiting the microbial pangenome BMC Bioinformatics 2019
  38. Zeb S, Bokhari H, Amjad Ali, Gulfam SM. Preliminary Work Towards Finding Proteins as Potential Vaccine Candidates for Vibrio cholera Pakistani Isolates through Reverse Vaccinology Medicina 2019
  39. Rashid MI, Amjad Ali and Andleeb S. Fishing for vaccines against Vibrio cholerae using in silico pan-proteomic reverse vaccinology approach PeerJ 2019
  40. Rashid MI, Amjad Ali, and Andleeb S Functional Annotation and Analysis of Dual Oxidase 1 (DUOX1): A potential Anti-Pyocyanin Immune Component Interdisc. Sci.: Comput. Life Sci. Nov 2018
  41.  Ikram A, Awan FM, Obaid A, Naz A, Amjad Ali, Janjua HA Exploring NS3/4A, NS5A and NS5B proteins to design conserved subunit multi-epitope vaccine against HCV utilizing immunoinformatics approaches Scientific Reports Oct 2018
  42. Obaid A, Naz A, Awan FM, Ikram A, Raza A, Ahmad J, Amjad Ali. Model of the adaptive immune response system against HCV infection reveals potential immunomodulatory agents for combination therapy Scientific Reports June 2018
  43. Humayun A, Siddiqui FM, Akram N, Saleem S, Amjad Ali, Iqbal T, Kumar A, Kamran R, Bokahri H. Incidence of Metallo Beta-Lactamase producing Klebsiella pneumoniae Isolates from Hospital Setting in Pakistan. Inter. Microbiology May 2018
  44. Rashid MI, Tariq P, Rashid H, Amjad Ali, Andleeb S. In silico drug repurposing via chemical protein interaction analysis, a proof of concept study: targeting pyocyanin based virulence of antibiotic resistant Pseudomonas aeruginosa Inter. J. of Biosci. (IJB) March 2018
  45. Gul D, Potter RF, Riaz H, Ashraf ST, Wallace MA, Munir T, Amjad Ali, Burnham CA, Dantas G, Andleeb S. Draft Genome Sequence of a Salmonella enterica Serovar Typhi Strain Resistant to Fourth-Generation Cephalosporin and Fluoroquinolone Antibiotics. Genome Announc. Oct 2017
  46. Awan FM, Naz A, Obaid A, Ikram A, Amjad Ali, Ahmad J, Naveed AK, and Janjua HA. MicroRNA pharmacogenomics based integrated model of miR-17-92 cluster in sorafenib resistant HCC cells reveals a strategy to forestall drug resistance. Scientific Reports Sep 2017
  47. Naz A, Obaid A, Awan FM, Ikram A, Ahmad J and Amjad Ali. Petri Net-based model of Helicobacter pylori mediated disruption of tight junction proteins in stomach lining during gastric carcinoma. Frontiers in Microbiology Sep 2017
  48. Bokhari H, Amjad Ali, Zobia Noreen, Nicholas Thomson, Brendan W. Wren. Galleria mellonella is low cost and suitable surrogate host for studying virulence of human pathogenic Vibrio cholera. Gene July 2017
  49. Rashid MI, Naz A, Amjad Ali*, Saadia Andleeb Prediction of vaccine candidates against Pseudomonas aeruginosa: An integrated genomics and proteomics approach. Genomics May 2017
  50. Naqvi STH, Shah, Nighat F, Qadir MI, Amjad Ali, Muhammad SA Characterization and Biological Studies of Copper Nanoparticles Synthesized by Aspergillus niger. Journal of Bionanoscience, April 2017
  51. Bano F, Baber M, Amjad Ali, Shah, Muhammad SA. Biosynthesis, characterization, and biological activities of iron nanoparticles using Sesamum indicum seeds extract. Phcog Mag Suppl S1:33-6 April 7, 2017
  52. Dar HA, Zaheer T, Paracha RZ, Amjad Ali* Structural analysis and insight into zika virus NS5 mediated interferon inhibition. Infection, Genetics and Evolution. March 2017
  53. Rizwan M, Naz A, Ahmad J, Naz K, Obaid A, Parveen T, Ahsan M, Amjad Ali. VacSol: a high throughput in silico pipeline to predict potential therapeutic targets in prokaryotic pathogens using subtractive reverse vaccinology BMC Bioinformatics Feb 2017
  54. Malik U, Javed A, Amjad Ali, Asghar K. Structural and Functional Annotation of Human FAM26F: A Multifaceted Protein having a Critical Role in the Immune System. GENE Jan 2017.
  55. Ikram A, Awan FM, Paracha RZ, Hanif R, Amjad Ali, Janjua HA. Identification of drug resistance and immune-driven variations in hepatitis C virus (HCV) NS3/4A, NS5A, and NS5B regions reveals a new approach toward personalized medicine. Antiviral Research, Jan 2017
  56. Hassan A, Naz A, Obaid A, Paracha RZ, Naz K, Awan FM, Muhammad SA, Hussnain A. Janjua, Ahmad J, Amjad Ali. Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets. BMC Genomics Sep 2016.
  57. Dar HA, Zaheer T, Rehman MT, Amjad Ali, Javed A, Khan GA, Babar M, Waheed Y. Prediction of promiscuous T-cell epitopes in the Zika virus polyprotein: An in silico approach Asian Pac J Trop Med. July 2016
  58. Mansoor S, Javed A, Amjad Ali, Mansoor A. Heterogeneous genomic locations within NS3, NS4A, and NS4B identified for genotyping and subtyping of Hepatitis C virus: A simple genome analysis approach. Infection Genetics Evolution. Jun 2016
  59. Muhammad SA, Amjad Ali*, Naz A, Hassan A, Riaz N, Saeed-ul-Hassan S, Andleeb S, Barh D A new broad-spectrum peptide antibiotic produced by Bacillus brevis strain MH9 isolated from Margalla Hills of Islamabad, Pakistan. Int J Pept Res Ther Jan 2016
  60. Faryal M. Awan, Naz A, Obaid A, Amjad Ali, Ahmad J, Anjum S, Hussnain A. Janjua. Identification of Circulating Biomarker Candidates for Hepatocellular Carcinoma (HCC): An Integrated Prioritization Approach. PLoS ONE. 2015
  61. Radusky LG, Hassan SS, Lanzarotti E, Tiwari S, Jamal SB, Ali J, Amjad Ali, Ferreira RS, Barh D, Silva A, Turjanski AG, Azevedo V. An Integrated Structural Proteomics Approach along the Druggable Genome of Corynebacterium Pseudotuberculosis Species for Putative Druggable Targets. BMC Genomics, 16 (Suppl 5) 2015
  62. Obaid A, Ahmad J, Naz A, Faryal M Awan, Paracha RZ, Tareen SHK, Anjum S, Raza A, Baumbach J and Amjad Ali. Modeling of innate immune responses induced by the host cells against Hepatitis C Virus (HCV) infection applying Petri net approach. Integrative Biology. 2015
  63. Naz A, Obaid A, Muhammad SA, Paracha RZ, Ahmad J, Amjad Ali. Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: A reverse Vaccinology based approach. Infec, Genet and Evol. 2015.
  64. Amjad Ali, Naz A, Soares SC, Bakhtiar SM, Tiwari S, Hassan S, Hanan F, Ramos R, Pereira U, Barh D, Figueiredo HP, Ussery DW, Miyoshi A, Silva A Azevedo V. Pan-genome Analysis of Human Gastric Pathogen H. pylori: Comparative Genomics and Pathogenomics Approaches to Identify Regions Associated with Pathogenicity and Prediction of Potential Core Therapeutic Targets. Biomed Res Int. 2015
  65. Tahir Ahmad, Sadia Anjum, Sadaf Zaidi, Amjad Ali, Muhammad Waqas, Muhammad S Afzal, Najma Arshad. Frequency of hepatitis E and Hepatitis A virus in water sample collected from Faisalabad, Pakistan. Ann Agric Environ Med. 2015
  66. Sanoobar G, Ahmad J, Paracha RZ, Naz A, Aslam B, Obaid A, Amjad Ali* Helicobacter pylori virulence regulatory network: Insights into the Host-Environment and Pathogen Interactions. NUST Journal of Natural Sciences (NJNS), 3(1), 2015
  67. Hassan SS, Tiwari S, Guimarães L, Jamal SB, Folador E, Sharma N, Soares SC, Almeida S, Amjad Ali, Islam A, Póvoa F, Vinicius , Bhattacharya A, Juneja L, Miyoshi A, Silva A, Barh D, Turjanski AG, Azevedo V, Ferreira R. Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. BMC Genomics 2014
  68. Faryal M. Awan, Sadia Anjum, Obaid A, Amjad Ali, Rehan Zafar , Hussnain A. Janjua. In-silico analysis of claudin-5 reveals novel putative sites for post-translational modifications: insights into potential molecular determinants of blood-brain barrier breach during HIV-1 infiltration. Infec, Genet. and Evol. 2014
  69. Marriam SM, Amjad Ali, Baig SM, Barh D, Miyoshi A, V. Azevedo. Identifying human disease genes: advances in molecular biology and computer approaches. Genet. & Mol. Res. 2014. 13 3) 5073-5087.
  70. Muhammad SA, Ahmed S, Amjad Ali*, Huang H, Wu X, Yang XF, Naz A, Chen J. Prioritizing Drug Targets in Clostridium botulinum with a Computational Systems-Level Analysis. Genomics 2014. 104(1):24-35
  71. Rehan Zafar, Amjad Ali*, Ahmad J, Riaz Hussain, Niazi U, Muhammad SA. Structural evaluation of BTK and PKCδ mediated phosphorylation of MAL at positions Tyr86 and Tyr10 Comp. Biol. and Chem. 2014, 51:22-35.
  72. Muhammad SA, Amjad Ali*, Ismail T, Paracha RZ, Ilyas U, Ahmad J. Insilico study of anti-carcinogenic lysyl oxidase-like 2 inhibitors. Comp. Biol. and Chem. 2014, Pages 71–82.
  73. Bakhtiar SM, Leblanc JG, Salvucci E, Ali Amjad, Martin R, Langella P, Chatel JM, Miyoshi A, Bermúdez-Humarán LG, Azevedo V. Implications of the human microbiome in Inflammatory Bowel Diseases. FEMS Microbiol Lett. 2013 342(1):10-7.
  74. Amjad Ali, Soares SC, Santos AR, Barbos E, Barh D, Bakhtiar SM, Hassan SS, Miyoshi A,Azevedo V, Microbial Comparative Genomics: An Overview of Tools and Insights into the Genus Corynebacterium. J. Bacteriol Parasitol. 2013.
  75. Soares SC, Silva A, Trost E, Blom J, Ramos R, Carneiro A, Amjad Ali, Santos AR, Pinto AC, Diniz C, Barbosa EG, Dorella FA, Aburjaile F, Rocha FS, Nascimento KK, Guimarães LC, Almeida S, Hassan SS, Bakhtiar SM, Pereira UP, Abreu VA, Schneider MP, Miyoshi A, Tauch A, Azevedo V. The Pan-Genome of the Animal Pathogen Corynebacterium pseudotuberculosis Reveals Differences in Genome Plasticity between the Biovar ovis and equi Strains. PLoS One 2013.
  76. Barh D, Amjad Ali, Baumbach J, Azevedo V et al. Conserved host-pathogen PPIs: Globally conserved inter-species bacterial PPIs based conserved host-pathogen interactome derived novel target in C. pseudotuberculosis, C. diphtheriae, M. tuberculosis, C. ulcerans, Y. pestis, and E. coli targeted by Piper betel compounds. Integrative Biology 2013.
  77. Ulisses P. Pereira, Amjad Ali, Bakhtiar SM, Fernanda, Guilherme Oliveira, Miyoshi A, Silva A, Azevedo V, Figueiredo et al. Complete genome sequence of Streptococcus agalactiae strain SA20-06, a fish pathogen associated to meningoencephalitis outbreaks. Stand Genomic Sci. 2013.
  78. Amjad Ali, Soares SC, Santos AR, Guimarães LC, Barbos Ea, Almeida S, Abreu VA, Carneiro AR, Ramos TTJ, Bakhtiar SM, Hassan SS, Ussery DW, On S, Silva A, Maria P Schneider,Andrey P Lage, Miyoshi A, Azevedo V. Campylobacter fetus subspecies: Comparative Genomics and Prediction of Potential Virulence Targets. Gene 2012
  79. Hassan SS, Guimarães L, Pereira U, Islam A, Amjad Ali, Bakhtiar SM, Dayana Ribeiro, Anderson Santos, Soares SC, Dorella F, Aburjaile F, Barh D, Anderson Barh, Miyoshi A, Borna Miller, Silva A, Azevedo V. Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by Rapid Next Generation Sequencing Technology. Stand Genomic Sci. 2012.
  80. Soares SC, Trost E, Ramos RT, Carneiro AR, Santos AR, Pinto AC, Barbosa E, Aburjaile F, Amjad Ali, Diniz CA, Hassan SS, Fiaux K, Guimarães LC, Bakhtiar SM, Pereira U, Almeida SS, Abreu VA, Rocha FS, Dorella FA, Miyoshi A, Silva A,Azevedo V, Tauch A Genome sequence of Corynebacterium pseudotuberculosis biovar equi strain 258 and prediction of antigenic targets to improve biotechnological vaccine production. Journal of Biotechnology 2012.
  81. Adriana R Carneiro, Ramos RT, HivanaDall’Agnol, Anne CP, Soares SC, Santos AR, Luis C Guimarães, Amjad Ali, Bakhtiar SM, Vilela D, Nóbrega F, Santos AL, Marta SP. Carepo, Azevedo V, Maria, Silva A. Genome Sequence of Exiguo bacteriumantarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica. Journal of Bacteriology 2012.
  82. Hassan SS, Schneider, Amjad Ali, Bakhtiar SM, Pereira Ude P, Santos AR, Soares Sde C, Dorella F, Pinto AC, , Pacheco LG, Dowson CG, Kumar A, Barh D, Miyoshi A, Azevedo V, Silva A. Whole-Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp162, Isolated from Camel. Journal of Bacteriology 2012.
  83. Pethick. PE, Amjad Ali, Bakhtiar SM, Dorella F, Carneiro AR, Ramos RT, Rocha ES, Schneider MPC, Miyoshi A, Azevedo V, and Fontaine MC. Complete Genome Sequences of Corynebacterium pseudotuberculosis Strains 3/99-5 and 42/02-A, Isolated from Sheep in Scotland and Australia, respectively. Journal of Bacteriology 2012
  84. Pethick. PE, Barbosa EGV, Pereira UP, Hassan SS, Amjad Ali, Bakhtiar SM,Dorella FA, Carneiro AR,Ramos RTJ,Rocha ES, Schneider MPC, Miyoshi A, Azevedo V, and Fontaine MC. Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain 1/06-A, Isolated from a Horse in North America. Journal of Bacteriology 2012
  85. Lopes T, Silva A, Thiago R, Hassan SS, Amjad Ali, Bakhtiar SM, Aburjaile FF, Pinto AC, Soares SC, Pereira UP, Schneider MP, Miyoshi A, Edman J, Spier S, Azevedo V. Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp267, Isolated from a Llama. Journal of Bacteriology 2012
  86. Afonseca V, Soares SC, Amjad Ali, Santos AR, Pinto AC,, Miyoshi A, Azevedo V, Reannotation of the Corynebacterium diphtheriae NCTC13129 genome as a new approach to studying gene targets connected to virulence and pathogenicity in diphtheria, Dove press 2012.
  87. R. T. J, Carneiro., D’Afonseca, V., Silva, A, Amjad Ali, Pinto, A. C., Santos AR, Eva Trost, Jan Baumbach, Andreas Tauch, Newton P. Carneiro, Paula R. K., Santuza M. R. Teixeira, Miyoshi, A., Guilherme C. Oliveira, Azevedo, V. Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in Two Corynebacterium pseudotuberculosis Strains. PLoS ONE 2011.
  88. Cerdeira LT, Schneider MP, Pinto AC, Almeida SS, Santos AR, Barbosa EG, Amjad Ali, Aburjaile FF, de Abreu VA, Lopes TS , Raja R, Zambare V, Ghosh P, Trost E, Tauch A, Miyoshi A, Azevedo V, Silva A. Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain CIP 52.97, Isolated from a Horse in Kenya. Journal of Bacteriology 2011,193 (24):7025-6.
  89. Barh D, Tiwari S, Jain N, Amjad Ali, Santos AR, Misra AN, Azevedo V, and Anil Kumar, In Silico Subtractive Genomics for Target Identification in Human Bacterial Pathogens. Drug Development Research 72 (2011).
  90. Anderson Santos, Amjad Ali, Barbos Ea, Silva A, Miyoshi A, Barh D, Azevedo V. The reverse Vaccinology, a contextual overview. IIOABJ, Vol. 2, Issue 4, 2011: 8␣15
  91. Cerdeira LT, Pinto AC, Schneider MP, de Almeida SS, Dos Santos AR, Barbosa EG, Amjad Ali, Barbosa MS, Carneiro AR, Ramos RT, de Oliveira RS, Barh D, de Castro Soares S, Dorella FA, Rocha FS, de Abreu VA, Tauch A, Trost E, Miyoshi A, Azevedo V, Silva A. Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina. Journal of Bacteriology 2011,193 6420-6421.
  92. Barh D, Jain N, Tiwari S, Vivian D’Afonseca, Liwei Li, Amjad Ali, Anderson Rodrigues Santos, Narayan, Silva A, Anil Kumar, Azevedo V. A novel comparative genomics analysis for common drug and vaccine targets in Corynebacterium pseudotuberculosis and other CMN group of human pathogens. Chem Biol Drug Des 2011.
  93. Silva, A. Schneider, M. P. C. Cerdeira, L. Barbosa, M. S. Ramos, RTJ, Carneiro, A.R. Santos, R. Lima, M. D’Afonseca, V. Almeida, S. S., Santos, AR. Soares, SC. Pinto, AC., Amjad, Ali., Dorella, FA. , Rocha,F. Abreu, VAC. , Shpigel, N. Miyoshi, A., Azevedo V. Complete Genome Sequence of Corynebacterium pseudotuberculosis I-19, strain isolated from Israel Bovine mastitis. Journal of Bacteriology, p. 1-1, 2011.

Systems and Network Biology, and Genomics

  1. Khalid, M, Parach RZ, Nisaar M, M Sumaira, Tariq S, Arshad I, Siddiqa A, Hussain Z, Ahamd J, Amjad Ali, Long non‐coding RNAs and their targets as potential biomarkers in breast cancer IET Systems Biology 2021
  2. Siddiqa A, Ahmad J, Amjad Ali, Khan S. Deciphering the expression dynamics of ANGPTL8 associated regulatory network in insulin resistance using formal modeling approaches IET Systems Biology April 2020
  3. Fahim A, Rehman Z, Bhatti MF, Virk N, Amjad Ali, Rashid A, Paracha RZ. The Route to ‘Chemobrain’ – Computational probing of neuronal LTP pathway. Scientific Reports 2019
  4. Ashraf ST, Obaid A, Saeed MT, Naz A, Shahid F, Ahmad J and Amjad Ali. Formal model of the interplay between TGF-β1 and MMP-9 and their dynamics in hepatocellular carcinoma Meth Biosc. Eng 2019
  5. Muhammad SA, Fatima N, Paracha RZ, Amjad Ali; Chen JY, A systematic simulation-based meta-analytical framework for prediction of physiological biomarkers in Alopecia J of Biol Res-Thessaloniki 2019
  6. Ashraf H, Ahmad J, Hassan A, Amjad Ali. Computational Modeling and Analysis of the Impacts of Sleep Deprivation on Glucose Stimulated Insulin Secretion BioSystems 2019
  7. Siddiqa A, Cirillo E, Tareen SHK, Amjad Ali, Kutmon MS, Eijssen LMT Ahmad J, Evelo CT, Coort SL Biological pathways leading from ANGPTL8 to Diabetes Mellitus – A co-expression network based analysis Frontiers in Physiology. 2018
  8. Saeed T Ahmad J, Baumbach J Pauling J, Shafi A, Paracha RZ Hayat A, Amjad Ali. Parameter Estimation of Qualitative Biological Regulatory Networks on High Performance Computing Hardware. BMC Systems Biology 2018
  9. Rahman S, Obaid A, Naz A, Ahmad J, Amjad Ali* Model-based in silico analysis of the PI3K/Akt pathway: The elucidation of crosstalk between diabetes and breast cancer PeerJ Oct 2018
  10. Hasan A, Ahmad J, Ashraf H, Amjad Ali. Modeling and analysis of the impacts of jet lag on circadian rhythm and its role in tumor growth. PeerJ June 2018
  11. Ashraf J, Ahmad J, Amjad Ali, Ul-Haq Z, Analyzing the behavior of neuronal pathways in Alzheimers using petri net modeling approach Frontiers in Neuroinformatic May 2018
  12. Siddiqa A, Ahmad J, Cirillo E, Tareen SH, Amjad Ali, Kutmon M, Lars M Eijssen, Chris T Evelo, Susan L Coort. Visualizing the regulatory role of Angiopoietin-like protein 8 (ANGPTL8) in glucose and lipid metabolic pathways. Genomics June 2017
  13. Zurah Bibi, Ahmad J, Siddiqa A, Paracha RZ, Saeed T, Amjad Ali, Janjua HA, Shakir Ullah, Emna Ben Abdallah, Olivier Roux. Formal modeling of mTor associated biological regulatory network reveals novel therapeutic strategy for the treatment of cancer. Frontiers In Physiology. June 2017
  14. Muhammad SA, Fatima N, Hasan Afzaal, Shah Z and Amjad Ali. Human Drug Targets Identification in Breast Cancer by Computationally Based DNA Microarray Analysis. BJPR 15(3): 1-9, March 2017
  15. Saeed MT, Ahmad J, Kanwal S, Holowatyj AN, Sheikh IA, Shafi A, Paracha RZ, Siddiqa A, Abbasi Z, Khan M and Amjad Ali. Formal modeling and analysis of the hexosamine biosynthetic pathway: role of o-linked n-acetylglucosamine transferase in oncogenesis and cancer progression. PeerJ Sep
  16. Siddiqa A, Ahmad J, Amjad Ali, Paracha RZ, Shafi Z, Aslam B. Structural Characterization of ANGPTL8 (Betatrophin) With its Interacting Partner Lipoprotein Lipase. Biol Chem. April 2016
  17. Bibi Z, Amjad Ali, Siddiqa A, Samar HK Tareen, Shaheen Shahzad, Hussnain A. Janjua, Khusro S, Ahmad J. On the Modeling and Analysis of the Biological Regulatory Network of NF-kB Activation in HIV-1 Infection. Complex Adapt. Syst Model Jan 2016
  18. Aslam B, J. Ahmad, Ali, R.Z. Paracha, Tareen SHK, Khusro S, T. Ahmad, S.A. Muhammad, Niazi U and V. Azevedo. Structural modeling and analysis of dengue-mediated inhibition of interferon signaling pathway. Genet. and Molecular Research: 14 (2): 2015
  19. Amjad Ali, Bakhtiar SM, and Azevedo V. Autism Spectrum Disorders (ASD): From Diagnosis to Management (invited article). J Mol Genet Med. 2015
  20. Rehan Zafer, Ahmad J, Amjad Ali*, Sammar Tareen, Aslam B. Formal modelling of toll like receptor 4 and jak/stat signalling pathways: insights into the roles of socs-1, interferon-β and pro-inflammatory cytokines in sepsis. Plos One 2014
  21. Aslam B, Ahmad J, Amjad Ali, Rehan Zafer, Tareen SHK, Niazi U, Saeed T. On the Modelling and Analysis of the Regulatory Network of Dengue Virus Pathogenesis and Clearance. Biol. and Chemist. 201

Human Genetics and Genomics

  1. Mehmood S, Dad D, Ahmad A, Ullah MI, John P, Amjad Ali, Hubner CA, Mohyuddin A, Hassan MJ. Structural and functional annotation of PR/SET Domain (PRDM) protein family: In-silico study elaborating role of PRDM12 mutation in congenital insensitivity to pain Comp Bio & Chem Sept 2020
  2. Paracha RZ, Malik S, Khalid M; Nisar M, Siddiqa A, Hussain Z, Nawaz R, Amjad Ali, Ahmad J. MicroRNAs and their target mRNAs as Potential Biomarkers among Smokers and Non-Smokers with Lung Adenocarcinnoma IET Systems Biology Sep 2018
  3. Dad R, Ullah MI, Amjad Ali, Hassan MJ. Identification of biological functions of risk loci associated with complex epilepsy: An in-silico approach for data analysis. J. Biosci., April 2017
  4. Anwar A, Murad S, Gu Sl, Paracha RZ, Amjad Ali, Bloodsworth P. Identification of novel mutations in the CDKN1B gene in invasive carcinoma of breast cancer. Journal of Eng. App. Sci. & Tech. (IJEAST) Sep 2016
  5. Ullah MI, Ahmad A, Raza SI, Amar, Amjad Ali, Attya Bhatti, Peter John, Mohyuddin A Wasim, Hassan MJ. In silico analysis of SIGMAR1 variant (rs4879809) segregating in a consanguineous Pakistani family showing amyotrophic lateral sclerosis without frontotemporal lobar dementia. Neurogenetics, 2015
  6. Baig SM, Koschak A, Lieb A, Gebhart M, Dafinger C, Nürnberg G, Amjad Ali, Ahmad I, Sinnegger-Brauns MJ, Brandt N, Enge J, Matteo E Mangoni, M. Farooq M, Khan UH, Nürnberg P, Striessnig J & Bolz HJ. Loss of Cav1.3 (CACNA1D) function in a human channelopathy with bradycardia and congenital deafness. Nature Neuroscience 2011.
  7. Farooq, M., Troelsen, J.T., Boyd, M., Hansen, L., Eiberg, H., Hussain, M.S., Rehman, U.S., Azhar, A., Amjad Ali., Bakhtiar, SM., Tommerup, N., Baig, S.M. and Klaus, W.K. Preaxialpolydactyly/triphalangeal thumb is associated with changed transcription factor binding affinity in a family with a novel point mutation in the long range cis-regulatory element ZRS. Eur J Hum Genet. 2010.
  8. Rasool, M., Schuster, J., Aslam, M., Tariq, M., Ahmad, I., Amjad Ali., Entesarian, M., Dahl, N., Baig, S.M. A novel missense mutation in the EDA gene associated with X-linked recessive isolated hypodantia. J Hum Genet, 2008, 53(10): 894-8. 2008.

Peer-Reviewed Conference Papers (Full length):

  1. Obaid A, Naz A, Ashraf ST, Awan FM, Ikram A, Saeed T, Raza A, Ahmad J, Amjad Ali. Formal modeling of the key determinants of Hepatitis C Virus (HCV) induced adaptive immune response network: An integrative approach to map the cellular and cytokine-mediated host immune regulations. Springer LNCS proceedings, ICCSA 2018, Melbourne, Australia

  2. Saeed MT, Jamil Ahmed and Amjad Ali. On the use of Betweenness Centrality for selection of plausible trajectories in Qualitative Biological Regulatory Networks. International Conference on Bioinformatics and Biomedical Engineering IWBBIO 2018 Granada, SPAIN. pp 543-552 April 2018.

  3. Obaid A, Naz A, Awan FM, Ikram A, Ahmad J, Amjad Ali. Modelling of adaptive and innate immune responses and identification of crosstalk amongst various signaling pathways involved in hcv infection using systems biology approach. Proceedings of ISERD International Conference, Rawalpindi, Pakistan, 29th-30th January 2018.

  4. Zia A, Amjad Ali, Bhatti A, John P. Deciphering the genetic architecture of Type 2 Diabetes through SNP-SNP interaction – IWBBIO Spain, 2015

  5. Asghar K, Ahmed J, Ashraf J, Amjad Ali, Janjua HA, Murad S. Qualitative Modeling and Analysis of the Indoleamine 2, 3-dioxygenase Regulatory Network in Homeostasis and Disease. 2014 11th International Conference on Fuzzy Systems and Knowledge Discovery. 978-1-4799-5148-2/14/$31.00 © IEEE. China 2014.

Conferences Proceedings and Talks:

  1. Amjad Ali Microbial pangenome and reverse vaccinology: From bench to beside Publisher: ICWEES-2021. Frontiers Media SA ISBN: 978-2-88971-007-2
  2. 2. Amjad Ali, Talk on “Pangenome of bacterial species: tools & applications. Guangzhou Institute of Biomedicine and Health (GIBH), CAS, Guangzhou, China, June 17, 2019.
  3. Amjad Ali. Talk on Advances in Microbial Genomics at Biological Sciences Department Allama Iqbal Open University, Islamabad 2018
  4. Amjad Ali et al, Poster in ProkaGenomics2017: Pangenome analysis of indigenous multidrug-resistant Staphylococcus aureus to identify potential novel therapeutic GÖTTINGEN, Germany, 19–22 September 2017.
  5. Amjad Ali et al, Poster in 14th Symposium on Bacterial Genetics and Ecology: BAGECO. Combating Antimicrobial Resistance – genome dynamics of resistant pathogens and prediction of alternative targets for vaccine development. Aberdeen/Scotland 4-8 June 2017
  6. Amjad Ali et al, Sysbio2016: Advanced Lecture Course on Systems Biology. Modeling of innate and adaptive immune pathways and analyzing various virus escape strategies: the role of NS5b, NS3/4a, and core proteins. Innsbruck, Austria Feb 28 – Mar 5, 2016.
  7. Amjad Ali, et al, Participation and Awarded with a grant for the “EACR-OECI Conference on “Precision Medicine for Cancer”, 1-4 March 2015. Formal Analysis of Normal and Induced Apoptosis Pathway for Identification of Therapeutic targets against Cancer. Luxembourg 1-4 March 2015.
  8. Amjad Ali, IBRO-APRC Associate School of Neuroscience: From Basic Neuroscience to Advanced Applications. Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology Islamabad, Pakistan Sep 30 – Oct 4, 2013.
  9. Naz A, Awan FM, Obaid A, Amjad Ali. In-silico identification of novel bacterial antigenic proteins as potential vaccine targets against gastric cancer using reverse Vaccinology approaches. Int. Inst anticancer research Sep 2014: 34.10 6079-6080
  10. Faiz Q., Zarif S. Nadeem A, Amjad Ali, Bakhtiar S.M. Graphical Representation of Biological Regulatory Network Involved In Wnt Signaling. 1st Student Research Conference on Biological sciences, NIBGE, Faisalabad. March 2014.
  11. Amjad Ali, D’afonseca V, Santos ARD, Pinto AC, Magalhães AAC, Faria CJ, Barbosa E, Dorella FA, Pacheco LGC, Almeida SS, Soares SC, Abreu VAC, Silva A, Moore R, Miyoshi A, Azevedo V. Identification, Characterization and Insilco comparisons of Corynebacterium pseudotuberculosis Pathogenicity Islands (PAIs) using PIPS. 6th International conference of Brazilian association for Bioinformatics and computational biology, X-meeting 15th-18th 2010. Ouro Preto MG Brazil.
  12. D’afonseca V, Amjad Ali, Santos ARD, Pinto AC, Magalhães AAC, Faria CJ, Barbosa E, Dorella FA, Pacheco LGC, Almeida SS, Soares SC, Abreu VAC, Silva A, Moore R, Miyoshi A, Azevedo V. Computational approach to study the genome reduction and life style of Corynebacterium pseudotuberculosis strains. 6th International conference of Brazilian association for bioinformatics and computational biology, X-meeting 15th-18th 2010. Ouro Preto MG Brazil.

Book Chapters:

  1. 1. Tufail S, Shah, MA, Zafar M, Iqbal M, Amjad Ali Shehzad A, Rahman Moazur “Tools for prediction and validation of epitopic regions on protein targets for vaccine development and diagnostics” Frontiers in Proteins and Peptide Sciences 2021.
  2. Jaiswal AK, S Tiwari S, Wanderson Silva A, Soares SC, Amjad Ali et al.,Pan-omics focused to Crick’s central dogma” Pan-genomics: Applications, Challenges, and Future Prospects, 2020.
  3. Shahid F, Shehroz M, Zaheer T and Amjad Ali. “Subtractive Genomics Approaches: Towards Anti-Bacterial Drug Discovery” Frontiers in Anti-Infective Drug Discovery, 2020
  4. Naz K, Ullah T, Zaheer T, Shehroz M, Naz A, Amjad Ali “Pan-genomics of model bacteria and their outcomes” Pan-genomics: Applications, Challenges, and Future Prospects,1st Edition, Elsevier, 6th march, 2020.
  5. Naz A, Obaid A, Fatima Shahid, Dar HA, Naz K, Nimat Ullah, Amjad Ali “Reverse Vaccinology and drug target identification through Pan-genomics” Pan-genomics: Applications, Challenges, and Future Prospects,1st Edition, Elsevier, 6th march, 2020.
  6. Systems-level approaches in Single Cell Omics – Elsevier Book on Single-cell Omics Vol 1: (978-0-12-814919-5) 2019.
  7. Shahid F, Ashraf ST, Amjad Ali, Reverse Vaccinology Approach to Potential Vaccine Candidates Against Acinetobacter baumannii. Methods Mol Biol. Feb 2019; 1946:329-336. doi: 10.1007/978-1-4939-9118-1_29.
  8. Saeed MT, Ahmed J and Amjad Ali. On the use of Betweenness Centrality for selection of plausible trajectories in Qualitative Biological Regulatory Networks. Bioinformatics and Biomedical Engineering. DOI: 10.1007/978-3-319-78723-7_47. 2018.
  9. Khan F, Amjad Ali, Gul A, Bioengineering Towards Fighting Against Superbugs. ELSEVIER Book: Omics Technologies and Bio-Engineering Vol 2 April 2018.
  10. Amjad Ali, Awan FM, Ikram A, Ashraf ST. Recent Advances and Challenges in microRNA Based Cancer Therapeutics. Topics in Anti-Cancer Research – Volume 6. Bentham eBooks Dec 2017.
  11. Amjad Ali, Dar HA, Zaheer T, Advances in Biotechnology in the Post Genomics era. E-Book on Advances in Biotechnology May 2018.
  12. Amjad Ali, Tanzeela Raza, Hira Sikandar. Advances in Microbial Genomics in the Post-genomics Era. eBook on Advances in Biotechnology Dec 2017.
  13. Amjad Ali, Hassan A, Sammia Rehman, Shifa Tariq Ashraf, Naz K, Naz A. Regulation of Genomic Testing in the Era of Precision Medicine. Elsevier Book: Progress and Challenges in Precision Medicine, 1st Edition ISBN: 9780128094112- Jan 2017
  14. Paracha RZ, Obaid A and Amjad Ali, Phenotyping in precision medicine. Elsevier Book: Progress and Challenges in Precision Medicine, 1st Edition ISBN: 9780128094112- Jan 2017
  15. Syeda Bakhtiar SM, Amjad Ali, and Barh D (2015) Epigenetics in Head and Neck Cancer. Springer: Cancer Epigenetics Book ISBN 978-1-4939-1803-4.
  16. Azevedo V, Abreu V, Almeida S, Santos A, Soares SC, Amjad Ali, Pinto AC, Magalhães A, Barbos Ea, Ramos RJ, Louise Cerdeira, Carneiro A, Schneider P, Silva A and Miyoshi A (2011). Whole Genome Annotation: In Silico Analysis, InTech: Bioinformatics – Trends and Methodologies, ISBN: 978-953-307-282-1

Intellectual Property: IPs (IPO Registered):

  1. 2021: Reg. 44121 (VacSol)
  2. 2021: Reg. 44122 (PanRV)
Integrative Biology Laboratory, Atta-ur-Rahman School of Applied Biosciences (ASAB) 
1st floor, D Block, National University of Sciences and Technology (NUST), H-12 Islamabad.
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