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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
Genomics, Bioinformatics and Systems Biology

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

My current research focuses on microbial genomics and systems biology approached to understand the complex biological process and systems. From genomics perspective, to explore the genome dynamics of pathogens for exploring the mechanism of virulence and antibiotic resistance and, from a systems biology viewpoint to get a comprehensive understanding of the biological processes such as host-pathogen-interactions, infections and disease progression through identification, modeling and simulation of transcriptional regulatory networks and signalling pathways. Alternatively, I am interested in analysing the whole genomic data to understand the physiology, behavior, disease and variation between species. Also, applying various microbial genomics approaches such as pan-genomics and patho-genomics to identify the conserved and unique genomic features in closely related pathogenic bacteria. I am also applying reverse vaccinology approaches for prediction of potential immunogenic and therapeutic targets (vaccines and drugs) against bacterial pathogens
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Research Grants
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1. 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.

2. 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.

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

Research Supervision of Students (Projects)
​Name ​Research Area - Thesis
   ​       PhD   ​Rehan Zafar
Paracha
​Modelling of TLR4 and JAK/STAT Signalling Pathways and Protein-Protein Interaction Studies to Examine the Patho-physiology of Sepsis (Completed –Sep. 2015).
​PhD ​Babar Aslam
(Co-supervised)
​Modelling and analysis of TLR4 pathway and Dengue virus mediated interferon inhibition (Foreign evaluation).
​PhD ​Ayesha Obaid ​Gene variants in Pakistani Population and its role in Hepatitis C Virus (HCV) Clearance in Response to (PegIFN/R) Therapy and Formal Modelling of IFNL3 and IFNL4 associated pathway to study the expression profiles in pathogenic and patho-physiological conditions in HCV infection (Final Year).
​PhD ​Anam Naz ​Prediction and analysis of H. Pylori genomes to predict potential peptide vaccine candidates: an approach towards computer aided biotechnology (3rd Year).
​PhD Afreenish Hassan ​Pangenome analysis of indigenous Acinetobacter baumannii strains (Initial stages)
​PhD ​Kanwal Naz ​Integrative pipeline for Pangenome-Reverse Vaccinology (PRV): Prediction and analyses of bacterial protein vaccine targets (Initial stages)
​MS ​Aneeq Arshad ​Isolation and characterization of industrial important Enzyme from extremophile  Bacteria (Completed Sep. 2015)
​MS ​Mariam Rasheed
(Co-supervised)
​To evaluate the effect of Tamoxifin load green tea silvar nanoparticles in MCF-7 cell line (completed Aug. 2015)
​BS ​Raffia Sidique ​Comparative genomics analysis of Chlamydophila pneumoniae genomes and prediction of potential core immunogenic targets (Completed in 2015).
​BS ​Gul Sanoobar ​Identification and Modeling of Virulence Regulatory Mechanism in Helicobacter Pylori (Completed in 2014)
​BS ​Saba Naseem ​Comparative genome analysis of campylobacter jejuni subspecies and prediction of core pathogenic proteins in the genome (Completed in 2014)

Research Student Supervision + Supervised

PhD students under supervision = 4 +1

Master student = 2+ 2

Undergraduate students = 3 + 2​ 
List of Peer Reviewed Publications
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2017

1. Faryal Mehwish Awan, Anam Naz, Ayesha Obaid, Aqsa Ikram, Amjad Ali, Jamil Ahmad, Abdul Khaliq Naveed & Hussnain Ahmed Janjua. MicroRNA pharmacogenomics based integrated model of miR-17-92 cluster in sorafenib resistant HCC cells reveals a strategy to forestall drug resistance. Scientific Reports Sept 2017.​

2.     Anam Naz, Ayesha Obaid, Faryal Mehwish Awan, Aqsa Ikram, Jamil Ahmad and Amjad Ali. Petri Net-based model of Helicobacter pylori mediated disruption of tight junction proteins in stomach lining during gastric carcinoma. Front Microbiology. Sept, 2017


3.     Kanwal Naz, Anam Naz, Shifa Tariq Ashraf, Muhammad Rizwan, Muhammad Ahsan, Jamil Ahmad and Amjad Ali* PanRV: Pangenome-Reverse vaccinology package for identifications of potential vaccine candidates by exploiting the microbial pangenome. In review:
 

4.     Habib Bokhari, 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.


5.     Amnah Siddiqa, Jamil Ahmad, Elisa Cirillo, Samar  H Tareen, Amjad Ali Martina Kutmon, 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.
 

6.     Zurah Bibi, Jamil Ahmad, Amnah Siddiqa, Rehan Zafar Paracha, Tariq Saeed, Amjad Ali, Hussnain Ahmed Janjua, Shakir Ullah, Emna Ben Abdallah, Olivier Roux. Formal modeling of mTor associated biological regulatory ntwork reveals novel therapeutic strategy for the treatment of cancer.  Front. Physiology. doi: 10.3389/fphys.2017.00416 June 2017.


7.     Muhammad Ibrahim Rashid, Anam Naz, Amjad Ali*, Saadia Andleeb Prediction of vaccine candidates against Pseudomonas aeruginosa: An integrated genomics and proteomics approach. Genomics  May 2017


8.     Rubina Dad, Muhammad Ikram Ullah, Amjad Ali, Muhammad Jawad Hassan. Identification of biological functions of risk loci associated with complex epilepsy: An in-silico approach for data analysis. Int. J. Biosci. 10:3, p. 388-98, April 2017.


9.     Farah Bano, Muhammad Baber, Amjad Ali, Ziaullah Shah, Syed Aun Muhammad. Biosynthesis, characterization, and biological activities of iron nanoparticles using Sesamum indicum seeds extract. Phcog Mag ;13, Suppl S1:33-6, April 2017


10.     Hamza Arshad Dar, Tahreem Zaheer, Rehan Zafar Paracha, Amjad Ali* Structural analysis and insight into zika virus NS5 mediated interferon inhibition. Infection, Genetics and Evolution March 2017


11.   Syed Aun Muhammad, Nighat Fatima, Hasan Afzaal, Ziaullah Shah and Amjad Ali. Human Drug Targets Identification in Breast Cancer by Computationally Based DNA Microarray Analysis BJPR 15(3): 1-9, March 2017

 
12.   Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan, 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 18:106 DOI : 10.1186/s12859-017-1540-0


13.   Uzma Malik, Aneela Javed, Amjad Ali, Kashif Asghar. Structural and Functional Annotation of Human FAM26F: A Multifaceted Protein having a Critical Role in the Immune System. GENE Jan, 2017.

14.   Aqsa Ikram, Faryal Mehwish Rehan Zafar, Rumeza Hanif, Amjad Ali, Hussnain A Janjua. 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; 137:112-124

2016
1. Aqsa Ikram, Faryal Mehwish Rehan Zafar, Rumeza Hanif, Amjad Ali, Hussnain A Janjua. 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 Oct, 2016 

2. Uzma Malik1 Aneela Javed1 Amjad Ali, Kashif Asghar. Structural and Functional Annotation of Human FAM26F: A Multifaceted Protein having a Critical Role in the Immune System. Oct 2016 GENE 

3. Muhammad Tariq Saeed, Jamil Ahmad, Shahzina Kanwal,  Andreana N. Holowatyj, Iftikhar A. Sheikh, Aamir Shafi, Rehan Zafar Paracha, Amnah Siddiqa, Zurah Abbasi, Mukaram Khan 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  2016  

4. Afreenish Hassan; Anam Naz; Ayesha Obaid; Rehan Zafar Paracha; Kanwal Naz; Faryal Mehwish Awan; Syed Aun Muhammad; Hussnain A. Janjua; Jamil Ahmad; Amjad Ali.  Pangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets. BMC Genomics Sep. 2016 doi: 10.1186/s12864-016-2951-4.

5. Sajid Mansoor, Aneela Javed, Amjad Ali, Atika Mansoor. Heterogeneous genomic locations within NS3, NS4A and NS4B identified for genotyping and subtyping of Hepatitis C virus: A simple genome analysis approach. Infect Genet Evol. 2016 Jun 15. 

6. Hamza Dar, Tahreem Zaheer, Muhammad Talha Rehman, Amjad Ali, Aneela Javed, Gohar Ayub Khan, Mustafeez Babar, Yasir Waheed. Prediction of promiscuous T-cell epitopes in the Zika virus polyprotein: An in silico approach Asian Pac J Trop Med. 2016 412-420: doi:10.1016/j.apjtm.2016.07.004

7. Syed Aun Muhammad , Amjad Ali*, Anam Naz, Afreenish Hassan, Naeem Riaz, Syed Saeed-ul-Hassan, Saadia andleeb, Debmalya Barh A new broad-spectrum peptide antibiotic produced by Bacillus brevis strain MH9 isolated from Margalla Hills of Islamabad, Pakistan. Int J Pept Res Ther 2016.doi:10.1007/s10989-015-9508-2 

8. Zurah Bibi,  Amjad Ali, Amnah Siddiqa, Samar HK Tareen; Shaheen Shahzad, Hussnain A. Janjua; Shah Khusro; Jamil Ahmad. On the Modeling and Analysis of the Biological Regulatory Network of NF-kB Activation in HIV-1 Infection. Complex Adapt. Syst Model (2016) 4:1 DOI: 10.1186/s40294-015-0013-4.

9. Amnah Siddiqa, Jamil Ahmad, Amjad Ali, Rehan Zafar Paracha, Zurah Shafi, Babar Aslam. Structural Characterization of ANGPTL8 (Betatrophin) With its Interacting Partner Lipoprotein Lipase. Comput Biol Chem. 201, 6 61 (2016) 210–220.

10. Amania Anwar, Sheeba Murad, Summer Gul, Rehan Zafar Paracha, Amjad Ali, Peter Bloodsworth. Identification of novel mutations in the CDKN1B gene in invasive carcinoma of breast cancer. International Journal of Engineering Applied Science and Technology (IJEAST).  
2015

11.     Faryal M. Awan, Anam Naz, Ayesha Obai1, Amjad Ali, Jamil Ahmad, Sadia Anjum, Hussnain A. Janjua. Identification of Circulating Biomarker Candidates for Hepatocellular Carcinoma (HCC): An Integrated Prioritization Approach. PLoS ONE 2015.DOI:10.1371/ journal.pone.0138913.

12.    2.  Muhammad Ikram Ullah, Arsalan Ahmad, Syed Irfan Raza, Ali Amar, Amjad Ali, Attya Bhatti, Peter John, Aisha Mohyuddin, Wasim Ahmad, Muhammad Jawad Hassan. in silico analysis of SIGMAR1 variant (rs4879809) segregating in a consanguineous Pakistani family showing amyotrophic lateral sclerosis without frontotemporal lobar dementia. Neurogenetics 2015, DOI: 10.1007/s10048-015-0453-1.

13.     Leandro G Radusky, Syed Shah Hassan, Esteban Lanzarotti, Sandeep Tiwari,  Syed Babar Jamal, Javed Ali, Amjad Ali, Rafaela Salgado Ferreira, Debmalya Barh, Artur Silva, Adrián G Turjanski, Vasco Azevedo. An Integrated Structural Proteomics Approach Along The Druggable Genome of Corynebacterium Pseudotuberculosis Species For Putative Druggable Targets. BMC Genomics 2015, 16(Suppl 5):S9; DOI: 10.1186/1471-2164-16-S5-S9.

14.    Ayesha Obaid, Jamil Ahmad, Anam Naz, Faryal M Awan, Rehan Z Paracha, Samar H K Tareen, Sadia Anjum, Abida Raza, Jan Baumbach 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. DOI: 10.1039/C4IB00285G.

15.    Anam Naz, Ayesha Obaid, PhD; Syed A Muhammad, Rehan Z Paracha, Jamil Ahmad, Amjad Ali. Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: A reverse vaccinology based approach. Infection, Genetics and Evolution 2015.  http://dx.doi.org/10.1016/j.meegid.2015.03.027.

16.    Amjad Ali, Anam Naz, Siomar C Soares, Bakhtiar SM, Sandeep T, Hassan S, Hanan F, Ramos R, Pereira U, Barh D, Figueiredo HP, Ussery DW, Miyoshi A, Silva A Vasco Azevedo. Pangenome 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; 2015:139580.  DOI: 10.1155/2015/139580.

17.    Amjad Ali, Syeda Marriam Bakhtiar and Vasco Azevedo. Autism Spectrum Disorders (ASD): From Diagnosis to Management (invited article). J Mol Genet Med.  2015. 9:154. doi: 10.4172/1747-0862.1000154

18. B. Aslam, J. Ahmad, A. Ali , R.Z. Paracha, S.H.K. Tareen,  S. Khusro, T. Ahmad, S.A. Muhammad, U. Niazi  and V. Azevedo. Structural modeling and analysis of dengue-mediated inhibition of interferon signaling pathway.  Genetics and Molecular Research: 14 (2): 4215-4237. 

19. 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. 22(4):661-664.DOI:10.5604/12321966.1185903.


2014

20.    Babar Aslam, Jamil Ahmad, Amjad Ali*, Rehan Zafer, Sammar Tareen Umar Niazi, Tariq Saeed.On the Modelling and Analysis of the Regulatory Network of Dengue Virus Pathogenesis and Clearance. Accepted in J. comp. Bio. & Chem (Oct 2014

21.    Hassan SS, Sandeep Tiwari, Luís Guimarães, Jamal SB, Edson Folador, Neha Sharma, Siomar Soares, Síntia Almeida, Amjad Ali, Arshad Islam, Fabiana Póvoa, Vinicius , Antaripa Bhattacharya, Lucky Juneja, Anderson Miyoshi, Artur Silva, Debmalya Barh, Adrian Gustavo Turjanski, Vasco Azevedo, Rafaela Ferreira. Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. BMC Genomics 2014; 15(7):S3.

22.    Rehan Zafer, Jamil Ahmad, Amjad Ali*, Sammar Tareen, Babar Aslam. Formal modelling of toll like receptor 4 and jak/stat signalling pathways: insight into the roles of socs-1, interferon-β and pro-inflammatory cytokines in sepsis. Plos One 2014: 9(9): e108466


23.    Faryal M. Awan, Sadia Anjum, Ayesha Obaid, 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 (2014) Infection, Genetics and Evolution, Oct; 27:355-65. doi: 10.1016/j.meegid.2014.07.022.

24.    Marriam SM, Amjad Ali, SM Baig, Barh D, Miyoshi A, V. Azevedo. Identifying human disease genes: advances in molecular biology and computer approaches (2014). Genet. Mol. Res. 13 3) 5073-5087

25.    Muhammad SA, Safia  Ahmed, Amjad Ali*, Hui  Huang, Xiaogang  Wu, , X. Frank  Yang, Anam  Naz, Jake  Chen. Prioritizing Drug Targets in Clostridium botulinum with a Computational Systems-Level Analysis (2014) Genomics. Jul;104(1):24-35

26.    Rehan Zafar, Amjad Ali*, Jamil Ahmad, Riaz Hussain, Umar Niazi, Aun Muhammad. Structural evaluation of BTK and PKCδ mediated phosphorylation of MAL at positions Tyr86 and Tyr10 (2014), CBAC. Aug;51:22-35


27.    Muhammad SA, Amjad Ali*, Tariq Ismail, Rehan Zafar, Umair Ilyas, Jamil Ahmad. Insilico study of anti-carcinogenic lysyl oxidase-like 2 inhibitors. (2014) CBAC. Aug. 2014, Pages 71–82


2013

28.    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 May; 342(1):10-7. doi: 10.1111/1574-6968.12111.

29.    Amjad Ali, Siomar C Soares, Anderson R Santos, Eudes Barbos, Debmalya Barh,Syeda M. Bakhtiar, Syed S. Hassan, Anderson Miyoshi,Vasco Azevedo, Microbial Comparative Genomics: An Overview of Tools and Insights into the Genus Corynebacterium. J Bacteriol Parasitol. 2013.doi:10.4172/2155-9597.1000167

30.    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

31.    Barh D, Gupta K, Jain N, Khatri G, León-Sicairos N, Canizalez-Roman A, Tiwari S, Verma A, Rahangdale S, Shah Hassan S, Rodrigues Dos Santos A, Amjad Ali, Carlos Guimarães L, Thiago Jucá Ramos R, Devarapalli P, Barve N, Bakhtiar SM, Kumavath R, Ghosh P, Miyoshi A, Silva A, Kumar A, Narayan Misra A, Blum K, Baumbach J, Azevedo V. 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. Integr. Biol., 2013,5, 495-509 DOI: 10.1039/C2IB20206A.

32.    Ulisses P. Pereira, Anderson R. Santos, Syed S. Hassan, Flávia F. Aburjaile, Siomar C. Soares, Rommel T. Ramos, Adriana R. Carneiro, Luís Guimarães, Sintia Almeida, Carlos Diniz, Maria Barbosa, Pablo, Amjad Ali, Syeda Marriam, Fernanda Dorella, AdhemarAraújo, Laura Leite, Guilherme Oliveira, Anderson Miyoshi, Artur Silva, Vasco Azevedo, Henrique Figueiredo.  Complete genome sequence of Streptococcus agalactiae strain SA20-06, a fish pathogen associated to meningoencephalitis outbreaks. Stand Genomic Sci. 2013;8(2):188-97. doi:10.4056/sigs.3687314.


2012

33.    Amjad Ali, Siomar C Soares, Anderson R Santos, Luis C Guimarães, Eudes Barbosa, Sintia S Almeida, Vinícius AC Abreu, Adriana, R Carneiro, Rommel TJ Ramos, Syeda M Bakhtiar, Syed S Hassan, David W Ussery, Stephen On, Artur Silva, Maria P Schneider,Andrey P Lage, Anderson Miyoshi, Vasco Azevedo. Campylobacter fetus subspecies: Comparative Genomics and Prediction of Potential Virulence Targets. Gene  2012 vol. 508 (2) p. 156-145; http://dx.doi.org/10.1016/j.gene.2012.07.070.

34.    Hassan SS, Guimarães Luis, Pereira Ulisses, Islam A, Amjad Ali, Syeda Marriam, Dayana Ribeiro, Anderson Santos, Siomar Soares, Fernanda Dorella, Anne Pinto, Maria Schneider, Maria Barbosa, Síntia Almeida, Vinícius Abreu, Flávia Aburjaile, Flávia Aburjaile, Adriana Carneiro, Debmalya Barh, Anderson Barh, Anderson Miyoshi, Borna Miller, Artur Silva, Vasco Azevedo. Complete genome sequence of Corynebacterium pseudotuberculosis biovar ovis strain P54B96 isolated from antelope in South Africa obtained by Rapid Next Generation Sequencing Technology. SEGS 2012. doi:10.4056/sigs.3066455.

35.    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 Nov 28.

36.    Adriana R Carneiro, Rommel T Ramos, HivanaDall'Agnol, Anne CPinto, Siomar C Soares, Anderson R Santos, Luis C Guimarães, Sintia S Almeida, Rafael A Baraúna, Diego A Graças, Luciano C Franco, Amjad Ali, Syeda M Bakhtiar, DaniellaVilela, Felipe Nóbrega, Adriana L Santos,Marta Sofia P. Carepo, Vasco Azevedo, Maria Paula Cruz Schneider, Vivian Helena Pellizari,and Artur Silva. Genome Sequence of Exiguo bacteriumantarcticum B7, Isolated from a Biofilm in Ginger Lake, King George Island, Antarctica. J. Bacteriol. 2012. doi:10.1128/JB.01791-12.

37.    Hassan SS, Schneider MP, Ramos RT, Carneiro AR, Ranieri A, Guimarães LC, Amjad Ali, Bakhtiar SM, Pereira Ude P, Dos Santos AR, Soares Sde C, Dorella F, Pinto AC, Ribeiro D, Barbosa MS, Almeida S, Abreu V, Aburjaile F, Fiaux K, Barbosa E, Diniz C, Rocha FS, Saxena R, Tiwari S, Zambare V, Ghosh P, 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. J Bacteriol. 2012 Oct;194 (20):5718-9.

38.    Pethick. PE, Lainson. AF Raja Yaga, Flockhart A, Smith DGE, Donachie W,  Louise T. Cerdeira, Silva A, Bol E, Thiago S. Lopes, Maria S. Barbosa, Pinto AC, dos Santos AR, Soares SC, Almeida SS, Guimarães LC, Aburjaile, EF Abreu VAC, Ribeiro D,Amjad Ali, Bakhtiar SM, Dorella FA, Carneiro AR, Ramos RTJ, 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. J. Bacteriol. 2012 194:4736-4737; doi:10.1128/JB.00918-12.

39.    Pethick. PE, Lainson. AF Raja Yaga, Flockhart A, Smith DGE,Donachie W,  Louise T. Cerdeira, Silva A, Bol E, Thiago S. Lopes, Maria S. Barbosa, Pinto AC, dos Santos AR, Soares SC, Almeida SS,Guimarães LC, Aburjaile, EF Abreu VAC, Ribeiro D, Karina K. Fiaux,d Carlos A. A. Diniz, 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. J. Bacteriol. 2012 vol. 194 no. 16. doi: 10.1128/ JB.00922-12. 

40.    Lopes T, Silva A, Thiago R, Carneiro A, Dorella FA, Rocha FS, Dos Santos AR, Lima AR, Guimarães LC, Barbosa EG, Ribeiro D, Fiaux KK, Diniz CA, de Abreu VA, de Almeida SS, Hassan SS, Amjad Ali, Bakhtiar SM, Aburjaile FF, Pinto AC, Soares Sde C, Pereira Ude P, Schneider MP, Miyoshi A, Edman J, Spier S, Azevedo V.J Bacteriol. 2012 Jul;194(13):3567-8. Complete Genome Sequence of Corynebacterium pseudotuberculosis Strain Cp267, Isolated from a Llama. J Bacteriol. 2012 Jul;194(13):3567-8.

41.    D'Afonseca V, Soares SC, Amjad Ali, Santos AR, Pinto AC, Magalhães AAC, Faria CJ, Barbosa E, Guimarães LC, Eslabão M, Almeida SS, Abreu VAC, Zerlotini A, Carneiro AR, Cerdeira LT, Ramos RTJ, Hirata Jr R, Mattos-Guaraldi AL, Trost E, Tauch A, Silva A, Schneider MP, 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 v:4 P 1 -13.


2011

42.    R. T. J, Carneiro., D'Afonseca, V., Silva, A, Amjad Ali, Pinto, A. C., A.R. Santos, R, Aryanne A. M. C. Rocha, De ́bora O. Lopes4, Dorella, F. A, Luis G. C. Pacheco, Marcı ́lia P. Costa, Meritxell Z. Turk, Nubia Seyffert, Pablo M. R. O. Moraes, Soares, S. C, Almeida, S. S, Thiago L. P. Castro, Abreu, V. A. C, Eva Trost, Jan Baumbach, Andreas Tauch6, Maria Paula C. Schneider, John McCulloch, Louise T. Cerdeira, Rommel T. J. Ramos, Zerlotini A, Dominitini A, Resende DM, Elisaˆngela M. Coser, Luciana M. Oliveira Ferro, Ortega JM, Luciano V. Paiva17, Luiz R. Goulart, Almeida JF, Maria Ineˆs T. Ferro, 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 April 2011; 6: e18551. doi:10.1371/journal.pone.0018551.

43.    Cerdeira LT, Schneider MP, Pinto AC, de Almeida SS, Dos Santos AR, Barbosa EG, Amjad Ali, Aburjaile FF, de Abreu VA, Guimarães LC, Soares Sde C, Dorella FA, Rocha FS, Bol E, Gomes de Sá PH, Lopes TS, Barbosa MS, Carneiro AR, Jucá Ramos RT, Coimbra NA, Lima AR, Barh D, Jain N, Tiwari S, 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. J Bacteriol. 2011 Dec;193 (24):7025-6.

44.    Barh D,  Tiwari S, Jain N, Amjad Ali, Santos AR, Amarendra Narayan Misra, Vasco Azevedo, and Anil Kumar, In Silico Subtractive Genomics for Target Identification in Human Bacterial Pathogens. Drug Development Research 72 (2011).

45.    Anderson Santos, Amjad Ali, Eudes Barbosa, Artur Silva, Anderson Miyoshi, Debmalya Barh, Vasco Azevedo. The reverse Vaccinology, a contextual overview. IIOABJ, Vol. 2; Issue 4; 2011: 8␣15

46.    Soares, S.C, Rocha, Aryanne A. M. C. . Barbosa EG, Guimarães LC. ; Almeida, S.S ; Miyoshi, A. Azevedo, V ; Silva, A. ; Ramos, R.T.J ; Carneiro., A. R. ; Cerdeira, L. ; Ali, Amjad; SANTOS, A. ; Abreu, Vinicius A. C. ; Pinto, A.C . Plasticidade genômica e evolução bacteriana. Microbiologia in Foco, 2011 v. 4, p. 31-38,

47.    Cerdeira LT, Pinto AC, Schneider MP, de Almeida SS, Dos Santos AR, Barbosa EG, Ali Amjad, Barbosa MS, Carneiro AR, Ramos RT, de Oliveira RS, Barh D, Barve N, Zambare V, Belchior SE, Guimarães LC, 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. J. Bacteriol. 2011;193 6420-6421.

48.    Barh D, Neha Jain, Sandeep Tiwari, Vivian D’Afonseca,Liwei Li, Amjad Ali, Anderson Rodrigues Santos, Luís Carlos Guimarães, Siomar de Castro Soares3, Anderson Miyoshi, Atanu Bhattacharjee5, Amarendra Narayan Misra, Artur Silva, 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.

2010

49.    *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 2010 doi: 10.1038/nn.2694

50.    Silva, A.  Schneider, M. P. C. Cerdeira, L. Barbosa, M. S. Ramos, R. T. J, Carneiro, A.R. Santos, R. Lima, M.  D'Afonseca, V. Almeida, S. S., Santos, A. R. Soares, S. C.  Pinto, A. C., Amjad, Ali., Dorella, F. A. ; Rocha, F. Abreu, V. A. C. ; 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, 2010.

51.    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 Jan 13.

2008

52.    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 Aug 9.

Book Chapters
________________________________________
53.    Vasco Azevedo, Vinicius Abreu, Sintia Almeida, Anderson Santos, Siomar Soares, Amjad Ali, Anne Pinto, Aryane Magalhães, Eudes Barbosa, Rommel Ramos, Louise Cerdeira, Adriana Carneiro, Paula Schneider, Artur Silva and Anderson Miyoshi (2011). Whole Genome Annotation: In Silico Analysis, Bioinformatics - Trends and Methodologies, Mahmood A. Mahdavi (Ed.), ISBN: 978-953-307-282-1, InTech,  Available from: http://www.intechopen.com/articles/show/title/whole-genome-annotation-in-silico-analysis.

54.    Syeda Marriam Bakhtiar, Amjad Ali, and Debmalya Barh (2014) Epigenetics in Head and Neck Cancer. Spriger: Cancer Epigenetics ISBN 978-1-4939-1803-4.

Conferences/Proceedings/Participations
________________________________________
•    Amjad Ali, Tariq Saeed, Shazina Kanwal and Jamil Ahmad. Participation and Awarded with grant for the “EACR-OECI Conference on “Precision Medicine for Cancer” in Luxembourg, 1-4 March 2015. Formal Analysis of Normal and Induced Apoptosis Pathway for Identification of Therapeutic targets against Cancer.  1-4 March 2015.
•    Anam Naz, Faryal Mehwish Awan, Ayesha Obaid, 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 2014: 34.10 6079-6080

•    Kashif Asghar, Jamil Ahmad, Amjad Ali, Hussnain Janjua. Qualitative Modeling and Analysis of the Indoleamine 2,3-dioxygenase Regulatory Network in Homeostasis and Disease, 11th International Conference on Fuzzy Systems and Knowledge Discovery (FSKD 2014) China.

•    Faiz Q., Zarif S. Nadeem A., Ali A., Bakhtiar S.M. Graphical Representation of Biological Regulatory Network Involved In Wnt Signaling. 1st Student Research Conference on Biological sciences, NIBGE, Faislabad. March 2014.

•    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.

•     D’afonseca V, Ali A, 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.

•     Organizer of IBRO-APRC Associate School of Neuroscience: From Basic Neuroscience to Advanced Applications. September 30 - October 4, 2013 Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology Islamabad, Pakistan

   Training/Workshops and Courses
________________________________________
1.    Omics of Begomoviruses and its Impact on National Economy,  Atta-ur-Rahman School of Applied Biosciences (ASAB), NUST, Islamabad, March 25-27, 2015 (Resource Person).
2.    EACR-OECI Conference on “Precision Medicine for Cancer”, Luxembourg 1-4 March, 2015.
3.    Two days hands-on workshop on “How to Use and Program Supercomputers” at Research Centre for Modeling and Simulation, NUST, Islamabad  2-3 Oct 2013.
4.    From Bench to Bedside: Bacterial Pathogenesis and its Impact on the Clinical Outcome of Infections. School of Veterinary Sciences, UFMG, Brazil 2011.
5.    Comparative Microbial Genomic Course/Training, CBS, Technical University of Denmark (2011).
6.    Perl for Bioinformatics Short Course, Brazilian Association for Bioinformatics Ouro Preto (2011).
7.    Platform for Next Generation Sequencing "NGS-SOLiD" Sequencing, Assembly and Annotation of Bacterial Genomes (90hrs). Aug 30 to Sep 10, 2010, UFPA, Belem, Brazil.
8.    Research Ethic Certificate Course (96hrs) Aga Khan University /John Hopkins USA (Aug. 2009).
9.    Nuclear and other Advance Techniques in Agricultural & Biological Sciences, NIAB, Faisalabad (2006).
10.    Molecular Detection and Genotyping of HCV/ HBV by PCR Methods and Quality Assurance Issues. NIBGE, Faisalabad (2004).

Awards/Grants and Scholarships
________________________________________
1.    TWAS-CNPq PhD Fellowship (2010-2013)
2.    European Molecular Biology Organisation (EMBO) Fellowship
3.    Moroccan Agency for Int. Cooperation (AMCI) Research Fellowship Award (2009)
4.    Higher Education Commission Post Graduate Fellowship (2008) (not availed).
5.    Participation Grant for EACR-OECI Conference “Precision Medicine for Cancer”, Luxembourg 2015

Teaching UG/PG
________________________________________
1.    Genomics, Proteomics and Bioinformatics (PG)
2.    Advances in Computational Biology (PG)
3.    Introduction to Bioinformatics (UG)
PhD Research Fellow
Laboratory of Cellular and Molecular Genetics (LGCM), Dept. of General Biology (ICB),
Federal University of Minas Gerais, Belo Horizonte, Brazil (2010-2013)
Visiting Research Fellow
Comparative Microbial Genomics Group, Centre for Biological Sequence Analysis (CBS),
Technical University of Denmark (2011)
Senior Research Associate
Human Mol. Genetics Laboratory, Health Biotechnology Division, NIBGE, Faisalabad (2009)
Research Associate
Human Mol. Genetics Laboratory, Health Biotechnology Division, NIBGE, Faisalabad (2008)
Technical Support Executive
BIO-RAD Laboratories Inc.; USA, M/S Chemical House Lahore, Pakistan (2006)