Engr. Dr. Raja Hashim Ali

+92 938 281026 Ext. 2429
Faculty Lobby

Engr. Dr. Raja Hashim Ali

Assistant Professor

Qualifications: Ph.D. (Kungliga Tekniska Högskolan KTH, Stockholm, Sweden)
Research Interests: Artificial Intelligence, Machine learning, Computational Biology, Bioinformatics

Education and Background

Sr. # Degree Department Institution City, Country Year Completed Specialization CGPA
1 Post-Doctorate Department of Evolutionary Genetics, Evolutionary Biology Center Uppsala University Uppsala, Sweden 2018 Bioinformatics  
2 Doctorate of Philosophy (Ph.D.) School of Computer Science and Communication (CSC) Kungliga Tekniska Hogskolan (KTH) Stockholm, Sweden 2016 Computational Biology  
3 Master of Science (M.S.) Department of Mathematical Sciences Chalmers University of Technology Goteborg, Sweden 2009 Bioinformatics and Systems Biology 4.00/5.00
4 Bachelor of Science (B.S.) Faculty of Computer Science and Engineering (FCS&E) Ghulam Ishaq Khan (GIK) Institute of Engineering Sciences and Technology Topi, Pakistan 2006 Computer Systems Engineering 3.35/4.00


Supervision of Master’s Thesis & Bachelor’s FYPs

Sr. # Students Title Role Detail Status
1 Mr. Ramzan Shahid Khan Generating sequences of proteins for protein families using Generative Adversarial Networks Supervisor Master’s Thesis In Progress
2 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
3 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
4 Ms. Palvashe Wajid, Ms. Tabina Zaheer, and Mr. Umar Luqman Ready interiors virtual designing using AWS Advisor Bachelor’s FYP Completed in June 2021
5 Mr. Abdulhaq Asad, Mr. Ahmed Habib, and Mr. Wajahat Amjad Autonomous Shopping Cart Co-Advisor Bachelor’s FYP Completed in June 2021
6 Ms. Areeba Shah Filtering multiple sequence alignment using Recurrent Neural Networks Supervisor Master’s Thesis Completed in February 2021
7 Mr. Muhammad Owais Shape analysis of subcortical regions in ADHD using spherical Harmonics Co-supervisor Master’s Thesis Completed in February 2021
8 Mr. Muhammad Faizan Fixed-Point optimization of Fully Convolutional Network Co-supervisor Master’s Thesis Completed in June 2020
9 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
10 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
11 Mr. Husnain Iqbal Khan, Mr. Uzair Baig, and Mr. Shahzeb Sentimeter – Detecting the emotions of a person using Deep Learning Advisor Bachelor’s FYP Completed in June 2020
12 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


Ongoing Research and Publications

Research Summary:

Total papers published in IF journals Total Impact Citations Conference Publications Ongoing research – Unpublished manuscripts
8 30 ~70 2 8
  • Journal Publications:
Sr. # Year of Publ. Title Journal 2020 Impact Factor
1 2020 Evolutionary History of Alzheimer Disease-Causing Protein Family Presenilins with Pathological Implications Journal of Molecular Evolution 2.395
2 2019 Identifying clusters of high confidence homologies in multiple sequence alignments Molecular Biology and Evolution 16.240
3 2016 S18 family of mitochondrial ribosomal proteins: evolutionary history and Gly132 polymorphism in colon carcinoma Oncotarget 3.331
4 2016 B Cell Receptor Activation Predominantly Regulates AKT-mTORC1/2 Substrates Functionally Related to RNA Processing PloS One 3.240
5 2016 GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm BMC Evolutionary Biology 3.027
6 2014 VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo traces BMC Bioinformatics 3.242
7 2014 Tracing the evolution of FERM domain of Kindlins Molecular Phylogenetics and Evolution 3.496
8 2013 Quantitative synteny scoring improves homology inference and partitioning of gene families BMC Bioinformatics 3.242
  • Thesis Published:
Sr. # Thesis Year of Publication University Title
1 DOCTORAL 2016 Kungliga Tekniska Hogskolan (KTH), Stockholm, Sweden. From genome to post-processing of Bayesian inference of Phylogeny
2 MASTERS 2009 Chalmers University, Gothenburg, Sweden. Determining the relationship between gene class network graph and gene age
3 BACHELORS 2006 Ghulam Ishaq Khan Institute of Engineering Sciences and Technology, Topi, Pakistan. LIPSYNC – Lip synchornisation with speech
  • Conference Papers:
Sr. # Year of Publication Conference Paper Title
1 2019 13th International Conference on Mathematics, Actuarial Science, Computer Science and Statistics (MACS) Breast Cancer Classification and Proof of Key Artificial Neural Network Terminologies
2 2015 Journal of World Mitochondria Society A link between the evolutionary history of mitochondrial ribosomal proteins of S18 family and GLY132 polymorphism in colon cancer
  • Unpublished Manuscripts:
Sr. # Title Current Status Target Journal Target Impact Factor (2020)
1 Fixed-Point Optimization of Fully Convolutional Networks Under Review IEEE Transactions on Pattern Analysis and Machine Intelligence 16.389
2 Semantic Segmentation Using Fully Convolutional Network (FCN) Under Review Conference  
3 Graph coloring using Deep Learning Manuscripts Forum of Mathematics, Pi 7.859
4 Evaluating the quality of multiple sequence alignment benchmarks for evolutionary analysis Manuscript Molecular Biology and Evolution 16.24
5 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 Bioinformatics 6.937
6 Importance of Synteny in Homology Inference Under Review Conference  
7 DNA methylation profiling for identifying biomarkers for renal clear cell carcinoma Manuscript BMC Evolutionary Biology 3.027
8 GenFam: a gene family and homology database for Eukaryotes based on quantitative synteny and neighborhood correlation similarity scores In Progress BMC Bioinformatics 3.242


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!

Sr. # Collaborator Citizen of Current Job (2020)
1 Dr. Lars Arvestad Sweden Associate professor at Stockholm University, Sweden
2 Dr. Simon Whelan Great Britain (UK) In SwedBank after completing his stint as Assistant professor at Uppsala University, Sweden
3 Dr. Marcin Bogusz Poland Folksam FutureLab
4 Dr. Sayyed Auwn Muhammad Pakistan Senior Data Scientist at Ericsson
5 Dr. Ammad Aslam Khan Pakistan 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 Post-Doctoral Researcher at Karolinska Institute, Sweden
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 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


Teaching Experience & Employment


Sr. # Scholarship Title Amount Funding Agency Reason
1 Carl Tryggers Stiftelse (CTS) scholarship 500,000 SEK (approximately 9.5 million PKR) Carl Tryggers Stiftelse för Vetenskaplig Forskning, Stockholm, Sweden post-doctorate degree from Evolutionary Biology Center (EBC) at Uppsala University, Uppsala, Sweden
2 Higher Education Commission Overseas Scholarship 1,008,000 SEK (approximately 19.3 million pkr)  HEC Overseas Scholarships Batch 2 Phase II Masters and Doctoral studies from Sweden