Engr. Dr. Raja Hashim Ali

Dr. Raja Hashim Ali, Assistant Professor, Artificial Intelligence
+92 938 281026 Ext. 2429
S-19 New Academic Block

Engr. Dr. Raja Hashim Ali

Associate professor

Ph.D. (Kungliga Tekniska Högskolan KTH, Stockholm, Sweden)

Research Interests:

Artificial Intelligence, Machine learning, Computational Biology, Bioinformatics

Education and Background

Sr. #DegreeDepartmentInstitutionCity, CountryYear CompletedSpecializationCGPA
1Post-DoctorateDepartment of Evolutionary Genetics, Evolutionary Biology CenterUppsala UniversityUppsala, Sweden2018Bioinformatics 
2Doctorate of Philosophy (Ph.D.)School of Computer Science and Communication (CSC)Kungliga Tekniska Hogskolan (KTH)Stockholm, Sweden2016Computational Biology 
3Master of Science (M.S.)Department of Mathematical SciencesChalmers University of TechnologyGoteborg, Sweden2009Bioinformatics and Systems Biology4.00/5.00
4Bachelor of Science (B.S.)Faculty of Computer Science and Engineering (FCS&E)Ghulam Ishaq Khan (GIK) Institute of Engineering Sciences and TechnologyTopi, Pakistan2006Computer Systems Engineering3.35/4.00


Supervision of Master’s Thesis & Bachelor’s FYPs

Sr. #StudentsTitleRoleDetailStatus
1Mr. Ramzan Shahid KhanGenerating sequences of proteins for protein families using Generative Adversarial NetworksSupervisorMaster’s ThesisIn Progress
2Mr. Muhammad Riaz-ul-Haq, Mr. Kashan Iqbal, and Mr. Ans Bin TariqBluetooth indoor navigation system (BINS)AdvisorBachelor’s FYPCompleted in June 2021
3Mr. Abdul Raheem Zaidi, Mr. Ahmed Shamas, and Mr. Faizan Ali KhanGraph Coloring using Deep LearningAdvisorBachelor’s FYPCompleted in June 2021
4Ms. Palvashe Wajid, Ms. Tabina Zaheer, and Mr. Umar LuqmanReady interiors virtual designing using AWSAdvisorBachelor’s FYPCompleted in June 2021
5Mr. Abdulhaq Asad, Mr. Ahmed Habib, and Mr. Wajahat AmjadAutonomous Shopping CartCo-AdvisorBachelor’s FYPCompleted in June 2021
6Ms. Areeba ShahFiltering multiple sequence alignment using Recurrent Neural NetworksSupervisorMaster’s ThesisCompleted in February 2021
7Mr. Muhammad OwaisShape analysis of subcortical regions in ADHD using spherical HarmonicsCo-supervisorMaster’s ThesisCompleted in February 2021
8Mr. Muhammad FaizanFixed-Point optimization of Fully Convolutional NetworkCo-supervisorMaster’s ThesisCompleted in June 2020
9Mr. Ibrahim Arain, Ms. Marzia Ali, Mr. Umer Waseem, and Mr. Urwa AkmalGeo-fence safety for kidsAdvisorBachelor’s FYPCompleted in June 2020
10Mr. Adil Waqar, Ms. Fatima Rahman, and Mr. Sadiq ShahDocOnTap – Intelligent disease diagnostics and appointment systemAdvisorBachelor’s FYPCompleted in June 2020
11Mr. Husnain Iqbal Khan, Mr. Uzair Baig, and Mr. ShahzebSentimeter – Detecting the emotions of a person using Deep LearningAdvisorBachelor’s FYPCompleted in June 2020
12Ms. Fatima Ali, Mr. Muhammad Abdul Basit, and Mr. Bilal Nazir RajaDry-Aware – A system to monitor household water consumptionCo-AdvisorBachelor’s FYPCompleted in June 2020


Ongoing Research and Publications

Research Summary:

Total papers published in IF journalsTotal ImpactCitationsConference PublicationsOngoing research – Unpublished manuscripts
  • Journal Publications:
Sr. #Year of Publ.TitleJournal2020 Impact Factor
12020Evolutionary History of Alzheimer Disease-Causing Protein Family Presenilins with Pathological ImplicationsJournal of Molecular Evolution2.395
22019Identifying clusters of high confidence homologies in multiple sequence alignmentsMolecular Biology and Evolution16.240
32016S18 family of mitochondrial ribosomal proteins: evolutionary history and Gly132 polymorphism in colon carcinomaOncotarget3.331
42016B Cell Receptor Activation Predominantly Regulates AKT-mTORC1/2 Substrates Functionally Related to RNA ProcessingPloS One3.240
52016GenFamClust: an accurate, synteny-aware and reliable homology inference algorithmBMC Evolutionary Biology3.027
62014VMCMC: a graphical and statistical analysis tool for Markov chain Monte Carlo tracesBMC Bioinformatics3.242
72014Tracing the evolution of FERM domain of KindlinsMolecular Phylogenetics and Evolution3.496
82013Quantitative synteny scoring improves homology inference and partitioning of gene familiesBMC Bioinformatics3.242
  • Thesis Published:
Sr. #ThesisYear of PublicationUniversityTitle
1DOCTORAL2016Kungliga Tekniska Hogskolan (KTH), Stockholm, Sweden.From genome to post-processing of Bayesian inference of Phylogeny
2MASTERS2009Chalmers University, Gothenburg, Sweden.Determining the relationship between gene class network graph and gene age
3BACHELORS2006Ghulam Ishaq Khan Institute of Engineering Sciences and Technology, Topi, Pakistan.LIPSYNC – Lip synchornisation with speech
  • Conference Papers:
Sr. #Year of PublicationConferencePaper Title
1201913th International Conference on Mathematics, Actuarial Science, Computer Science and Statistics (MACS)Breast Cancer Classification and Proof of Key Artificial Neural Network Terminologies
22015Journal of World Mitochondria SocietyA link between the evolutionary history of mitochondrial ribosomal proteins of S18 family and GLY132 polymorphism in colon cancer
  • Unpublished Manuscripts:
Sr. #TitleCurrent StatusTarget JournalTarget Impact Factor (2020)
1Fixed-Point Optimization of Fully Convolutional NetworksUnder ReviewIEEE Transactions on Pattern Analysis and Machine Intelligence16.389
2Semantic Segmentation Using Fully Convolutional Network (FCN)Under ReviewConference 
3Graph coloring using Deep LearningManuscriptsForum of Mathematics, Pi7.859
4Evaluating the quality of multiple sequence alignment benchmarks for evolutionary analysisManuscriptMolecular Biology and Evolution16.24
5Normalized and standardized estimated sample size: two novel techniques for convergence assessment and burn-in estimation for multi-parameter Markov chain Monte Carlo tracesManuscriptBioinformatics6.937
6Importance of Synteny in Homology InferenceUnder ReviewConference 
7DNA methylation profiling for identifying biomarkers for renal clear cell carcinomaManuscriptBMC Evolutionary Biology3.027
8GenFam: a gene family and homology database for Eukaryotes based on quantitative synteny and neighborhood correlation similarity scoresIn ProgressBMC Bioinformatics3.242


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. #CollaboratorCitizen ofCurrent Job (2020)
1Dr. Lars ArvestadSwedenAssociate professor at Stockholm University, Sweden
2Dr. Simon WhelanGreat Britain (UK)In SwedBank after completing his stint as Assistant professor at Uppsala University, Sweden
3Dr. Marcin BoguszPolandFolksam FutureLab
4Dr. Sayyed Auwn MuhammadPakistanSenior Data Scientist at Ericsson
5Dr. Ammad Aslam KhanPakistanAssistant professor of Biochemistry at Virtual Univeristy, Lahore
6Dr. Joel Sjöstrand (Late)SwedenDied by committing suicide in 2017, was a post-doctoral researcher at SciLifeLab, Stockholm Sweden
7Dr. Muhammad MushtaqPakistanPost-Doctoral Researcher at Karolinska Institute, Sweden
8Dr. Dara K. MuhammadIraqWas a post-doctoral researcher at Karolinska Institute, Sweden, until 2016
9Dr. Beston F. NoreIraqProfessor at Suleimani University, Iraq and an associate professor at Karolinska Institute, Sweden
10Dr. George Klein (Late)Hungarian-SwedishWas a professor emiratus at Karolinska Institute, Sweden at the time of his death in 2016
11Dr. Sajid Anwar (Late)PakistanA 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 TitleAmountFunding AgencyReason
1Carl Tryggers Stiftelse (CTS) scholarship500,000 SEK (approximately 9.5 million PKR)Carl Tryggers Stiftelse för Vetenskaplig Forskning, Stockholm, Swedenpost-doctorate degree from Evolutionary Biology Center (EBC) at Uppsala University, Uppsala, Sweden
2Higher Education Commission Overseas Scholarship1,008,000 SEK (approximately 19.3 million pkr) HEC Overseas Scholarships Batch 2 Phase IIMasters and Doctoral studies from Sweden


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