|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|
|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|
|Total papers published in IF journals||Total Impact||Citations||Conference Publications||Ongoing research – Unpublished manuscripts|
|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|
|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|
|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|
|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|
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!
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?
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!
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.
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”.
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|
|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|