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FACULTY PROFILE

Engr. Dr. Raja Hashim Ali

Assistant Professor
Email: hashim.ali@giki.edu.pk
Qualifications: Ph.D. (Kungliga Tekniska Högskolan KTH, Stockholm, Sweden)
Research Interests: Artificial Intelligence, Machine learning, Deep Learning, Computational Intelligence, Bioinformatics
Telephone: +92 938 281026 Ext. 2429
Website: http://sites.google.com/view/dr-raja-hashim-ali

Education and Background


Teaching Experience & Employment


                                                             

 

Ongoing Research and Publications


Research Summary:

Total papers published in IF journals Total Impact Citations Conference Publications Ongoing research - Unpublished manuscripts
8 30 47 2 4
 
Published Research:
  1. Khan A.A., Ali R.H. and Mirza B., (2020) "Evolutionary History of Alzheimer Disease-Causing Protein Family Presenilins with Pathological Implications", Journal of Molecular Evolution88(8), pp.674-688.
  2. Ali R.H., Bogusz M., and Whelan S. (2019) "Identifying clusters of high confidence homologies in multiple sequence alignments", Molecular Biology and Evolution 10(1093):142. 
  3. Mushtaq M., Ali R.H., Kashuba V., Klein G. and Kashuba E. (2016) "S18 family of mitochondrial ribosomal proteins: evolutionary history and Gly132 polymorphism in colon carcinoma", Oncotarget 7(34):55649.
  4. Mohammad D.K., Ali R.H., Turunen J.J., Nore B.F. and Smith C.I.E. (2016), “B Cell Receptor Activation Predominantly Regulates AKT-mTORC1/2 Substrates Functionally Related to RNA Processing”, PloS One 11(8):e0160255.
  5. Ali R.H., Muhammad S.A. and Arvestad L. (2016) “GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm”, BMC Evolutionary Biology 16(1):120.
  6. Ali R.H., Bark M., Jorge M., Muhammad S.A., Sjöstrand J., Zubair S.M., Abbas R.M. and Arvestad L. (2014) “VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces”, BMC Bioinformatics 18(1):97.
  7. Ali R.H. and Khan A.A. (2014) “Tracing the evolution of FERM domain of Kindlins”, Molecular Phylogenetics and Evolution 80(1):193.
  8. Ali R.H., Muhammad S.A. and Arvestad L. (2013) “Quantitative synteny scoring improves homology inference and partitioning of gene families”, BMC Bioinformatics 14(15):S2.

Thesis:

  • DOCTORAL THESIS (PhD) from Kungliga Tekniska Hogskolan (KTH), Stockholm, Sweden [available here].
    • Developed and implemented a new statistical convergence assessment and burn-in estimation technique based on Estimated Sample Size (ESS) for multiple Markov chain Monte Carlo parameters for phylogenetic tree.
    • Developed software “VMCMC”, a visualization and statistical tool for Markov chain Monte Carlo analysis of phylogenetic trees.
    • Designed and implemented a synteny based algorithm “GenFamClust” that quantifies gene synteny and combines it with protein similarity to infer gene homology.
    • Compared and validated the accuracy, cluster size, similarity and differences between GenFamClust and other homology inference algorithms using Chordatic, Fungi and simulated datasets.
    • Applied “GenFamClust” algorithm on a large dataset consisting of whole genome species and inferred gene families and synteny conservation. The results are available in the database “GenFam”.
  • MASTERS THESIS (M.Sc.) from Chalmers University, Gothenburg, Sweden [available here].
    • Determining the relationship between age and the degree of a gene class network graph.
    • Extended the original work to determine the relationship for pathway class graph as well.
    • Worked on a new notion of gene class and pathway class graphs.
  • SENIOR YEAR DESIGN PROJECT (B.S.) from Ghulam Ishaq Khan Institute of Engineering Sciences and Technology, Topi, Pakistan [available here].
    • Lip Synchronization with Speech signal, a mixture of many different domains of Computer Science.
    • Reflects my command of diverse Computer Science fields such as Digital Signal Processing, Computer Graphics, Artificial Intelligence and Artificial Neural Networks.

Conference Papers:

  1. Ali N., Ansari S., Halim Z., Ali R.H., Khan M.F. and Khan M., (2019). "Breast Cancer Classification and Proof of Key Artificial Neural Network Terminologies." In 13th International Conference on Mathematics, Actuarial Science, Computer Science and Statistics (MACS) (pp. 1-6). IEEE.
  2. Mushtaq M., Ali R.H., Kashuba V., Klein G., Kashuba E. (2015) "A link between the evolutionary history of mitochondrial ribosomal proteins of S18 family and GLY132 polymorphism in colon cancer", In Journal of World Mitochondria Society 2(1).

Unpublished Manuscripts:

  • Ali R.H., Boguzs M., Whelan S. “Evaluating the quality of multiple sequence alignment benchmarks for evolutionary analysis” [Manuscript].
  • Ali R.H., Arvestad L., “Normalized and standardized estimated sample size: two novel techniques for convergence assessment and burn-in estimation for multi-parameter Markov chain Monte Carlo traces” [Manuscript].
  • Ali R.H., Arvestad L., “GenFam: a gene family and homology database for Eukaryotes based on quantitative synteny and neighborhood correlation similarity scores” [Manuscript].
  • Khan A.A., Strömblad S., Zhang H., Kumar V., Ali R.H. “A study of Kindlin family promoter evolution reveals the synergy between promoter evolution, protein evolution and evolution of transcription regulation” [Manuscript].

 

Courses, Program & Curriculum Design


 

Research Interests and Projects


  1. Homology inference - Role of synteny

               

a) Pipeline for GenFamClust - The pipeline of the synteny aware method I and my collaborators have proposed for inferring homology.

b) Accuracy of GenFamClust (GFC) - When compared with other existing homology inferring software on a benchmark homology dataset, GFC is certainly the BEST!

  1. MCMC Tree analysis - Post-processing the results of Bayesian phylogeny.

Snapshots of 3 panes of VMCMC - When a standard run of Bayesian phylogeny (containing around a million samples) needs to be processed within a few seconds, whose convergence needs to be assured before any analysis, whose mixing is an enigma for all and whose results need to be summed up as a single tree out of a million trees, VMCMC comes to your rescue. Simple, clean and concise analysis, isn't it?

  1. Multiple Sequence Alignment - Issues, errors and accuracy.

                                                   

Two panes showing the Divvier methodology and its results in comparison with various filtering methods - When there are a lot of errors in an MSA from any MSA method, whereby some of the sequence regions can have extremely unlikely correct alignment, no MSA method will give you the correct solution. The only way out is filtering these regions, and that is where Divvier is the most optimal solution out there!

  1. Domain Phylogeny and Evolution - Evolutionary history of Kindlin and S18

                              

a) Evolutionary relatedness of FDCPs - A phylogenetic tree showing the reconciled evolutionary history of Ferm Domain containing proteins (FDCPs) of which Kindlin is a member, a beauty in colors and display, aint it?  

b) Evolutionary history of S18 gene family - The phylogenetic gene tree grown inside a species tree showing the evolutionary history along with possible duplication and loss events for S18 family of genes in various taxonomic groups.

  1. Molecular Biology - Role of certain motifs in B-cell receptor activation

                                                         

Mapping of motif onto a phylogeny and constructing the neighborhood graph of interacting proteins - Some times a large data set might result in lots of clustered, ugly graphs but when handled correctly by an expert, they reveal beautiful images. But "beauty lies in the eye of the beholder".

 

Research Collaborators


I have had research collaborations with researchers from a wide variety of backgrounds and nations. Some are still in contact with me and some I have lost contact of. Here is a list of most important collaborators, and their most recent profiles! They are listed in no specific order!

  1. Dr. Lars Arvestad, Sweden - Currently an associate professor at Stockholm University, Sweden.
  2. Dr. Simon Whelan, Great Britain (UK) - Works in industry after completing his stint as Assistant professor at Uppsala University, Sweden.
  3. Dr. Sayyed Auwn Muhammad, Pakistan -Works at Ericcson after succesfully completed his post-doc from Karolinska Institute, Sweden.
  4. Dr. Marcin Bogusz, Poland - Will soon be defending his thesis from Uppsala University, Sweden.
  5. Dr. Ammad Aslam Khan, Pakistan - Currently assistant professor of Biochemistry at Virtual Univeristy, Lahore.
  6. Dr. Joel Sjöstrand (Late), Sweden - Died by committing suicide in 2017, was a post-doctoral researcher at SciLifeLab, Stockholm Sweden.
  7. Dr. Muhammad Mushtaq, Pakistan - Currently at Karolinska Institute, Sweden as a post-doctoral researcher..
  8. Dr. Dara K. Muhammad, Iraq - Was a post-doctoral researcher at Karolinska Institute, Sweden, until 2016.
  9. Dr. Beston F. Nore, Iraq - Professor at Suleimani University, Iraq and an associate professor at Karolinska Institute, Sweden.
  10. Dr. George Klein (Late), Hungarian-Swedish - Died at 91 years old, was a professor emiratus at Karolinska Institute, Sweden at the time of his death in 2016.
  11. Dr. Sajid Anwar (Late), Pakistan - A great friend and colleague who was an expert in AI and Computer Hardware, lost to blood cancer at the peak of his career on 2nd Sep 2020.

Supervision of Master’s Thesis & Bachelor’s FYPs


  • Mr. Muhammad Riaz-ul-Haq, Mr. Kashan Iqbal, and Mr. Ans Bin Tariq, "Bluetooth indoor navigation system (BINS)" (Advisor - Bachelor's FYP - Completed in June 2021)
  • Mr. Abdul Raheem Zaidi, Mr. Ahmed Shamas, and Mr. Faizan Ali Khan, "Graph Coloring using Deep Learning" (Advisor - Bachelor's FYP - Completed in June 2021)
  • Ms. Palvashe Wajid, Ms. Tabina Zaheer, and Mr. Umar Luqman, "Ready interiors virtual designing using AWS" (Advisor - Bachelor's FYP - Completed in June 2021) 
  • Mr. Abdulhaq Asad, Mr. Ahmed Habib, and Mr. Wajahat Amjad, "Autonomous Shopping Cart" (Co-Advisor - Bachelor's FYP - Completed in June 2021)
  • Ms. Areeba Shah, “Filtering multiple sequence alignment using Recurrent Neural Networks” (Supervisor - Master’s thesis - Completed in February 2021)
  • Mr. Muhammad Owais, "Shape analysis of subcortical regions in ADHD using spherical Harmonics" (Co-supervisor - Master's thesis - Completed in February 2021) 
  • Mr. Muhammad Faizan, “Fixed-Point optimization of Fully Convolutional Network” (Co-supervisor - Master’s thesis – Completed in June 2020)
  • Mr. Ibrahim Arain, Ms. Marzia Ali, Mr. Umer Waseem, and Mr. Urwa Akmal, “Geo-fence safety for kids” (Advisor - Bachelor’s FYP – Completed in June 2020)
  • Mr. Adil Waqar, Ms. Fatima Rahman, and Mr. Sadiq Shah, “DocOnTap – Intelligent disease diagnostics and appointment system” (Advisor - Bachelor’s FYP – Completed in June 2020)
  • Mr. Husnain Iqbal Khan, Mr. Uzair Baig, and Mr. Shahzeb, “Centimeter – Detecting the emotions of a person using Deep Learning” (Advisor - Bachelor’s FYP – Completed in June 2020)
  • Ms. Fatima Ali, Mr. Muhammad Abdul Basit, and Mr. Bilal Nazir Raja, “Dry-Aware – A system to monitor household water consumption” (Co-Advisor - Bachelor’s FYP – Completed in June 2020)

Honors


  • Got Carl Tryggers Stiftelse (CTS) scholarship worth 500,000 SEK (approximately 9.5 million PKR) for pursuing post-doctorate degree from Evolutionary Biology Center (EBC) at Uppsala University, Uppsala, Sweden with scholarship by Carl Tryggers Stiftelse för Vetenskaplig Forskning, Stockholm, Sweden.
  • Got Higher Education Commission Overseas Scholarship worth 1,008,000 SEK (approximately 19.3 million pkr) for pursuing Masters and Doctoral studies from Sweden under HEC Overseas Scholarships Batch 2 Phase II. 

                                                               



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