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Dr. Amjad Ali
Assistant Professor
Industrial Biotechnology

ASAB
National University of Sciences and Technology (NUST)
Sector H-12, Islamabad
Tel : Office Ph: +92 51 9085 6138 Cell Ph: +92 333 9191903

Specialization
Microbial Genetics and Genomics, Bioinformatics and Systems Biology

Education
PhD. Genetics and Genomics, Universidade Federal de Minas Gerais (UFMG), Belo Horizote, Brazil; BS (Hons.) & MPhil Biotechnology, Quaid-i-Azam University (QAU), Islamabad, Pakistan

Dr. Amjad Ali joined ASAB, NUST in August 2013. Since then, he has been actively involved in both academic and research activities. Dr. Amjad have been pursuing research in the area of Microbial Genomics and Systems Biology, his group producing interesting genomic data and findings, thus far, he has published more than Ninety (90) research articles in prestigious International Journals (Google Scholar: citations 1492 and h-index 21) along with 11 book chapters. These International journals include Nature Neuroscience, Scientific Reports, Frontiers in Microbiology, and Physiology, Integrative Biology, Plos One, BMC Genomics and, Bioinformatics and J. Bacteriology, etc. Dr. Amjad has secured 5 research grants (2 as PI and 3 as Co-PI), on a highly competitive ground. During the past years, Dr. Amjad Ali has been awarded the “Best Research Paper Award” for the year 2013/14 by Higher Education Commission (HEC) Pakistan (2016). Awarded “Best Researcher Award” for the year 2016/17 by ASAB, NUST. Also, awarded with “Research Productivity Award (RPA)” (Cat C) in Biological Sciences (2017) by Pakistan Council for Science and Technology (PCST), 2018.​​​​​​​​
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Research Interests:

Dr. Amjad have been pursuing research in the area of Microbial Genomics and Systems Biology. 

A. Microbial Genomics and Bioinformatics
They are microbial- genomics and bioinformatics group interested in genomic epidemiology and comparative genomics to study the evolution and transmission of bacterial pathogens. They are particularly interested in the regional crisis of growing antimicrobial resistance and dissemination of multidrug resistant pathogens, also like to develop of tools, databases for pathogen genome analysis, prospective surveillance and tracking of emerging pathogens in the environment and clinical settings using whole genome sequencing and bioinformatics analysis. They using comparative pangenome analysis and phylogenetics approaches to study the genome evolution, transmission and resistance patterns in bacterial pathogens such as staphylococcus, pseudomonas, Klebsiella and Acinetobacter etc. 
They have developed high-throughput screening Tools/Software capable to analyses microbial pangenome (big data) and therapeutic (vaccine/drugs) candidates identification, these include: 

1. VacSol - https://sourceforge.net/projects/vacsol/
 
 2. PanRV - https://sourceforge.net/projects/panrv2/

B. Systems and Network Biology
They are also interested in system-level analysis and tools for studying the complex biological systems and processes such as diseases and pathways, Together with collaborators they construct and analyses the Biological Regulatory Networks (BRNs) and Models through formal modeling approaches. They are interested in understanding the behavior of an entire biological system (holistic) and relationships between its components (individual entities) and identification markers (states/paths/trajectories) involved in genomic variation and their association with diseases or processes. 



Research Supervision of Student Projects:

PhD Students:
2015 Rehan Zafar Paracha 
2018  Obaid Obaid
2018 Anam Naz
        Kanwal Naz
        Nimat Ullah
        Farah Anwar

Co-supervised
2016 Babar Aslam 
2019 Muhammad Ibrahim

MS Students: 
2016 Aneeq Arshad
2018 Shifa Tariq
2018 Tanzeela Raza
2018 Hira Sikandar
2018 Fatima Shahid
2019 Tahreem Zaheer
2019 Hamza Ahmad Dar
2019 Muhammad Shehroz
        Maaz Waseem
        Zaara Ishaq

BS (Biosciences) Students
2019 Aysha Lala Rukh, Dania Khalil, Anam Ghafoor, Iraj Ishfaq
2018 Fatima Quddos and Maira Jalil
2017 Tahreem Zaheer and Hamza Ahmad Dar
2017 Maha Kaisar
2015 Rafia Sidiqui
2014 Gul Sanobar
2014 Saba Naseem


Research Grants: (PI & Co-PI):

08/16 - Pangenome analysis of multidrug-resistant Staphylococcus aureus strains to get insights into the mechanism of pathogenicity and to identify new therapeutic interventions to replace the current antimicrobial drugs. PI -NRPU–HEC 2015 PKR 1.05 M.

08/15 - Analysis of gene variants and investigation of novel prognostic host factor targets to predict treatment response to peg- IFN/RBV therapy in HCV infected Pakistani patients and, qualitative and quantitative modeling of pathways associated with HCV infection and the host immune response. PI -NRPU-HEC 2015 PKR 2.486 M

08/15 - Formal Analysis of the Impact of Feeding on Hepatocyte Circadian Oscillators. Co-PI –NRPU-HEC 2015 PKR 0.929 

04/17 - Analyzing the Tumor Educated Platelets (TEP) as Potential Bio-Marker in Molecular Diagnosis of Liver Cancer: A Minimally Invasive Approach alternative to Tissue Biopsy. Co-PI NRPU – HEC 2016 PKR 4.76 M.

11/18  Assessment of indigenous Lactobacillus spp. for cholesterol reduction; a step towards probiotic designer foods. Co-PI NRPU – HEC2.58 M

06/18 - Genome-wide meta-analysis of cDNA datasets and molecular validation of genetic variants in type II diabetes mellitus. Co-PI NRPU – HEC 2017                         PKR.3.03 M (With PI, Dr. Syed Aun Muhammad, BZU Multan).


Honors and Awards:

Research Productivity Award (Cat. C) in Biological Sciences ( 2017-18). Awarded by Pakistan Council for Science and Technology (PCST), 2018

143rd Productive Scientist of Pakistan (Overall) in Biological Sciences (2017). Ranked by Pakistan Council for Science & Technology (PCST), 2018

31st   Young Productive Scientist of Pakistan (under 40),  in Biological Sciences (2016). Awarded by Pakistan Council for Science & Technology (PCST)

Best Researcher Award (2016/17) Awarded by Atta-ur-Rahman School of Applied Biosciences, NUST, 2017

Best Research Paper Award (2013/14) Awarded by the Higher Education Commission (HEC) of Pakistan, 2016

48th Young Productive Scientist of Pakistan (Overall) in Biological Sciences (2015). Awarded by Pakistan Council for Science & Technology (PCST),          


Professional Experience and Trainings:

2019 - Scientific Researcher at BiG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing Science Park, Chaoyang, Beijing, China.

2011: Visiting Research Fellow  (EMBO) at Comparative Microbial Genomics Group, Centre for Biological Sequence Analysis (CBS), Technical University of Denmark, Denmark.

2010: Ph.D. Research Fellow at Laboratory of Cellular and Molecular Genetics, Dept. of General Biology (ICB), Federal University of Minas Gerais, Belo Horizonte, Brazil

2009​Senior Research Associate at Human Mol. Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.

2008: Research Associate at Human Mol. Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.

2006: Technical Support Executive at BIO-RAD Laboratories Inc.; USA, M/S Chemical House Lahore, Pakistan.​


Academic ​Reviewing: 

Current Proteomics. Scientific Reports, Genomics (Elsevier) BMC Bioinformatics, BMC Microbiology, BMC Genomics, BMC Bioinformatics, Infection Genetics 

and Evolution, Genomics Proteomics & Bioinformatics, Journal of Medical Microbiology, Current Proteomics, Gene, Int. Arch. of Medical Microbiology, etc.

Scientific Memberships:

ESCMID, ISID, NYAS
​​
 
Journal Publications/Conferences/Book Chapters/Trainings/Visits (A-F):

A. Microbial Genomics and Bioinformatics


1. 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 2019

1. 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

2. 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

3. 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 Bioinfromatics  2019

4. 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

5. Rashid MI, Amjad Ali and Andleeb S. Fishing for vaccines against Vibrio cholerae using in silico pan-proteomic reverse vaccinology approach PeerJ  2019

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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 19, 2017

12. 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

13. 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 

14. 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

15. Rashid MI, Naz A, Amjad Ali*, Saadia Andleeb Prediction of vaccine candidates against Pseudomonas aeruginosa: An integrated genomics and proteomics approach. Genomics  May 2017

16. 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

17. 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

18. 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

19. 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 

20. 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.

21. 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

22. 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.

23. 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

24. 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 

25. 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 

26. 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

27. 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

28. 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

29. 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.  

30. 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

31. B. Aslam, J. Ahmad, Amjad. 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

32. 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

33. 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 

34. 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 

35. 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

36. 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.

37. 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 

38. 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. 

39. 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. 

40. 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. 

41. 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. 

42. 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. 

43. 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.

44. 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. 

45. 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 

46. 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. 

47. 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. J Biotechnol. 2012. 

48. 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. 

49. 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. 

50. 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

51. 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 

52. 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 

53. D'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. 

54. 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. 

55. 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. 

56. 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). 

57. 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

58. 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. 

59. 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 pathogen. Chem Biol Drug Des 2011. 

60. 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.

B. Computational Systems Biology and Genomics

61. 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

62. 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

63. 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

64. Siddiqa A, Ahmad J, Amjad Ali. Deciphering the expression dynamics of ANGPTL8 associated regulatory network in insulin resistance using formal modeling approaches IET Systems Biology 2019 

65. 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

66. 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

67. 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

68. Rahman S, Obaid A, Naz A, Ahmad J, Amjad Ali, Model-based in silico analysis of the PI3K/Akt pathway: The elucidation of cross-talk between diabetes and breast cancer PeerJ Oct 2018

69. 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

70. 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

71. Ashraf J, Ahmad J, Amjad Ali, Ul-Haq Z, Analyzing the behavior of neuronal pathways in Alzheimers using petri net modeling approach Frontiers in Neuroinformatics May 2018 

72. 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

73. 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

74. 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. Int. J. Biosci., April 2017

75. 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

76. 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 2016.  

77. Siddiqa A, Ahmad J, Amjad Ali, Paracha RZ, Shafi Z, Aslam B. Structural Characterization of ANGPTL8 (Betatrophin) With its Interacting Partner Lipoprotein Lipase. Comput. Biol Chem. April 2016

78. 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

79. 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. Int. Journal of Eng. App. Sci. & Tech. (IJEAST) Sep 2016  

80. 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

81. Amjad Ali, Bakhtiar SM, and Azevedo V. Autism Spectrum Disorders (ASD): From Diagnosis to Management (invited article). J Mol Genet Med.  2015

82. 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 

83. 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. Comput. Biol. and Chemist. 2014

84. 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.

85. 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. 

86. 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. 


C. Peer Reviewed Conference Papers:

87. 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 2018.
88. 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.

89. 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.

90. Kashif Asghar, Jamil Ahmed, Javaria Ashraf, Amjad Ali, Janjua HA, Sheeba Murad. 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.

D. Conferences Proceedings:

1. Amjad Ali, Poster in ProkaGenomics2017: Pangenome analysis of indigenous multidrug-resistant Staphylococcus aureus to identify potential novel therapeutic targets. GÖTTINGEN, Germany, 19–22 September 2017.

2. Amjad Ali, 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

3. Amjad Ali, Saeed T, Rahman S, Naz A, Obaid A and Ahmad J. 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.

4. Amjad Ali, Saeed T, Shazina Kanwal and Ahmad J. 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.

5. 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.

6. 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

7. 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.

8. 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 Nov. 2010. Ouro Preto MG Brazil.

9. 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 Nov. 2010. Ouro Preto MG Brazil. 

E. Book Chapters:

1.   Naz K, Nimat Ullah, Tahreem Zaheer, Muhammad Shehroz, Naz A, Amjad Ali “Pan-genomics of model bacteria and their outcomes” Pan-genomics: Applications, Challenges, and Future Prospects,1st Edition, Elsevier, 10th Jan, 2020

2. 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, 10th Jan, 2020

3. Systems-level approaches in Single Cell Omics – Elsevier Book on Single-cell Omics Vol 1: (978-0-12-814919-5) 2019.

4. 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.

5. 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.

6. Khan F, Amjad Ali, Gul A, Bioengineering Towards Fighting Against Superbugs.  ELSEVIER Book: Omics Technologies and Bio-Engineering  Vol 2 April 2018.

7. 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.

8. Amjad Ali, Dar HA, Zaheer T, Advances in Biotechnology in the Post Genomics era. E-Book on Advances in Biotechnology May 2018.

9. Amjad Ali, Tanzeela Raza, Hira Sikandar. Advances in Microbial Genomics in the Post-genomics Era. eBook on Advances in Biotechnology Dec 2017. 

10. 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

11. 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 

12. 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. 

13. 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.

F. Talks/Training/Courses and Workshops 

1. Training and collaborative research visit, Big Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences (CAS) Beijing  Sep-Nov 2019.
2. Belt and Road & Developing Countries Workshop on mycobacterial disease, GIBH, Guangzhou, China June 3-19, 2019.
3. Biosafety Leadership Summit, BPSA Pak, Fogartry NIH US, Marriott, Isb-Pak. Mar 18-20, 2019.
4. Pak-China Genomics Workshop at NCB, Quaid-I-Azam University, Islamabad 2018.
5. Invited Talk on Advances in Microbial Genomics at IIOU, Islamabad 2018 
6. Sysbio2018: Adv. Lecture Course on Systems Biology, Innsbruck, Austria Feb 28-Mar 5, 2018.
7. Sysbio2016: Adv. Lecture Course on Systems Biology, Innsbruck, Austria Feb 28 -Mar 5, 2016. ICGBE Training Course on “Basic Biotechnology Techniques” Organized          by National Academy of Young Scientists- ASAB, NUST. (Resource Person) Feb 23-25, 2016.
8. EACR-OECI Conference on “Precision Medicine for Cancer”, Luxembourg 1-4 March, 2015.
9. Two days hands-on workshop on “How to Use and Program Supercomputers” Research Centre for Modeling and Simulation, NUST, Islamabad 2-3 Oct 2013.
10. From Bench to Bedside: Bacterial Pathogenesis and its Impact on the Clinical Outcome of Infections. School of Veterinary Sciences, Federal University of Minas Gerais,                  Brazil 2011.
11. Comparative Microbial Genomic - Course/Training, CBS, DTU, Denmark (2011).  Perl for Bioinformatics, Course, Brazilian Association for Bioinformatics Ouro Preto 2011.
12. Platform for Next Generation Sequencing "NGS-SOLiD" Sequencing, Assembly and Annotation of Bacterial Genomes (90hrs). UFPA, Belem, Brazil. Aug 30 - Sep 10, 2010.            Research Ethics Certificate Course-96hrs Aga Khan University /John Hopkins USA Aug 2009.
13. Nuclear & Advance Techniques in Agricultural & Biological Sciences, NIAB, Fsd-Pak 2006.  
14. Molecular Detection and Genotyping of HCV/ HBV by PCR Methods and Quality Assurance Issues. NIBGE, Faisalabad (2004).

G. Scholarships/Participation Grants Awards

1. Grant from TWAS-CNPq for Ph.D. Study in Brazil (2010-2013).
2. Grant from European Molecular Biology Organization (EMBO) Fellowship (2011). 
3. Grant from Moroccan Agency for Int. Coopr (AMCI) for Research Fellowship (2009) 
4. Grant from Higher Education Commission (HEC) Post Graduate Fellowship (2008).
5. Grant for the EACR-OECI Conference Precision Medicine for Cancer, Luxembourg 2015
6. Grant for the Sysbio2016: Advanced Lecture Course on Systems Biology, Innsbruck 2016
7. Grant for the Sysbio2018: Advanced Lecture Course on Systems Biology, Innsbruck 2018
8. Grant for Belt & Road and Developing countries Workshop, GIBH, Guangzhou, China 2019

Teaching following Undergraduate & Postgraduate courses at NUST since 2013:

1.    Genomics, Proteomics and Bioinformatics (PG)
2.    Advances in Computational Biology (PG)
3.    Microbial Genomics (PG)
4.    Introduction to Bioinformatics (UG)
2019 - Visiting Researcher at BiG Data Center, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing Science Park, Beijing, China.

2011: Visiting Research Fellow  (EMBO) at Comparative Microbial Genomics Group, Centre for Biological Sequence Analysis, Technical University of Denmark, Denmark

2010: Ph.D. Research Fellow at Laboratory of Cellular and Molecular Genetics, Dept. of General Biology (ICB), Federal University of Minas Gerais, Belo Horizonte, Brazil

2009​Senior Research Associate at Human Mol. Genetics Laboratory, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.

2008: Research Associate at Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.

2006: Technical Support Executive at BIO-RAD Laboratories Inc.; USA, M/S Chemical House Lahore, Pakistan.