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Curriculum Vitae

MD ANWARUL KARIM, MBBS, PhD

E-mail: dr.anwarul.karim [at] gmail [dot] com
Google Scholar link
ORCID ID: 0000-0002-5795-6674

Education and Training

Nov 2023 – Present (FT)

Postdoctoral Associate

Department of Neurology, Baylor College of Medicine, Houston, Texas, USA
Major research projects:
  • Investigating how different cell types are affected in spinocerebellar ataxia type 1 (SCA1)
  • Investigating the role of ataxin 1 orthologs in zebrafish using knockout models
Jan 2017 – Nov 2021 (FT)

PhD (Genetics)

Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong

Thesis: Clinico-epidemiological & trio-based genetic analysis of Bangladeshi Hirschsprung disease (HSCR) patients

Thesis abstract and full PDF: https://hub.hku.hk/handle/10722/300424

Outline of my thesis research work:
  • Investigating clinico-epidemiological features of HSCR patients
  • Trio-based Whole Exome Sequencing & Copy Number Variation analysis of HSCR patients
  • Functional analysis (development of the enteric nervous system) of prioritized candidate HSCR genes with CRISPR-Cas9 medicated knockout in zebrafish
Courses taken: Genes and Gene Functions in Diseases; Advanced Cell Biology and Neurobiology; Practical Bioinformatics; Molecular Medicine; Recent Advances in Biomedical Technology; Molecular Genetics and Cytogenetics of Cancer; Introduction to Epidemiology; Research Ethics for Graduate Students; Introduction to Quantitative Research Methods; Introduction to Thesis Writing; Transferable Skills
Nov 2014 – Oct 2015 (FT)

Clinical Internship Training

Chittagong Medical College Hospital, Bangladesh
Nov 2008 – Sep 2014 (FT)

MBBS (Bachelor of Medicine & Surgery)

Chittagong Medical College, Bangladesh

Selected research-related certificate / training courses

Apr 2024

Research Postdoc Training for Responsible Conduct of Research

Baylor College of Medicine, Houston, Texas, USA
Aug 25 – Sept 06, 2019

EMBO Practical Course: Mouse genome engineering

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
July 2018

WGC Advanced Course: Genetic Analysis of Mendelian and Complex Disorders - 2018

Wellcome Genome Campus, Hinxton, Cambridge, UK
Nov 2017

C3BI Hands-on Course on Next Generation Sequencing (NGS) Data Analysis Hong Kong - 2017

Institut Pasteur & The University of Hong Kong

Selected teaching-related certificate / training courses

Dec 2022 – Jan 2023

PBL (Problem-Based Learning) Training Programme for New Tutors

Bau Institute of Medical and Health Sciences Education, LKS Faculty of Medicine, The University of Hong Kong
April 2022

Professional Certificate in Teaching and Learning in Higher Education

Centre for the Enhancement of Teaching and Learning, The University of Hong Kong
March 2022

Teaching in Practice Programme

Centre for the Enhancement of Teaching and Learning, The University of Hong Kong
Feb-March 2018

Certificate of Teaching and Learning in Higher Education

Centre for the Enhancement of Teaching and Learning, The University of Hong Kong

Employment history

Oct 2021 – Nov 2023 (FT)

Senior Research Assistant / Senior E-learning Assistant

School of Clinical Medicine, The University of Hong Kong
Major academic responsibilities/achievements as part of job portfolio
Teaching and e-learning
  • Conducting Problem-Based Learning sessions for MBBS students
  • Co-moderating Active Learning Workshops (ALW) for MBBS students
  • Teaching gross anatomy to MBBS students through cadaveric dissection
  • Developing e-learning modules and case studies for MBBS students
Pedagogical innovation and research

Presented poster about pathology interactive worksheets that I developed in collaboration with pathology department of HKU for pathology teaching.

Conference: Tripartite Medical Education Conference 2023, Hong Kong (January 14-15, 2023).

Collaborative research as personal endeavor
  • Published three research papers (in eLife, Frontiers in Molecular Neuroscience, Oxford Open Neuroscience) as co-author
  • Published one research paper (in PLOS One) as co-first author
  • Published one review paper (in Pediatric Surgery International) as co-author
Jun 2021 – Oct 2021 (FT)
Feb 2021 – Apr 2021 (PT)

Computational Biologist I (Senior Technical Officer)

Centre for PanorOmic Sciences (CPOS), Li Ka Shing Faculty of Medicine, The University of Hong Kong
Major accomplishments:
  • Developed core service bioinformatic pipeline for variant calling from whole exome and target panel NGS data
  • Updated the team about the latest developments in the clinical NGS and application through weekly journal club presentations
Jan 2016 – Dec 2016 (FT)

Lecturer (Anatomy)

Department of Anatomy, Chattogram International Medical College, Bangladesh

Selected voluntary research experiences

Mar 2020 – May 2020

Lead investigator of a COVID-19 study in Bangladesh

Led a large survey with a team of 30 members during the initial COVID-19 spread in Bangladesh to investigate the knowledge and attitudes of Bangladeshi adults towards COVID-19.

Nov 2015 – Dec 2016

Research Assistant (Volunteer, part time)

Department of Pediatric Surgery, Chittagong Medical College Hospital, Bangladesh

Project-1: Epidemiology and genetics of birth defects
Collected clinical data and samples from patients with birth defects including anorectal malformations and Hirschsprung disease

Project-2: Investigating cancer epidemiology in Chattogram, Bangladesh
Led a team of 28 members to collect epidemiological data of more than 500 cancer patients from Chittagong Medical College Hospital, Bangladesh.

May 2015 – Oct 2015

Research Assistant (Volunteer, part time)

Care Investigation Histopathology Laboratory, Chattogram, Bangladesh

Project: Molecular Diagnosis of Breast Cancer
Investigated clinicopathological characteristics and receptor status (ER, PR, HER2) of 59 invasive breast carcinoma patients.

Selected technical skills

Genetics & molecular biology
DNA and RNA extraction and quantification; Gel electrophoresis; Qubit; TapeStation; PCR & Primer designing; RT-qPCR and Primer designing; PCR product purification; Sanger sequencing reaction; Chromatogram interpretation; TaqMan CNV validation; Heteroduplex mobility assay; CRISPR gRNA design; CRISPR-Cas9 knockout experiment in Zebrafish; Nuclei extraction for snRNA seq; Barcoding and sequencing library preparation using Parse Bioscience snRNA-seq technology; Microscopy
Animal models
Zebrafish; Mice
Computational biology
Bash scripting; HPCF use; Pipeline development for NGS data analysis on HPCF; Skilled in using many bioinformatic tools (including FastQC, BWA, SAMtools, Picard, GATK, VerifyBamID, PLINK, KGGSeq, Annovar, GenomeStudio & CNVPartition, PennCNV, QuantiSNP, Rvtests); NGS data analysis, quality control, and interpretation for downstream hypothesis generation and experiments; Network visualization with Cytoscape; Trailmaker for single cell transcriptomics data analysis; Seurat for single cell/nuclei data analysis, Xenium spatial data analysis
Statistics
Prism; R; SPSS
Teaching / E-learning
Moodle; H5P; Articulate Storyline; Mentimeter; Padlet; Kahoot
Computer
MS Office; Inkscape
Language
English; Bengali

Scholarships / awards

  • Travel grant from European Molecular Biology Organization and Travel support award from HKU to attend EMBO Practical Course: Mouse genome engineering at Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany (2019)
  • Certificate of Merit for outstanding poster presentation at 23rd Research Postgraduate Symposium of Li Ka Shing Faculty of Medicine, HKU (6th December 2018)
  • Pilot scheme on international experience for RPg students from HKU to attend “Genetic analysis of mendelian and complex disorders” course at Wellcome Genome Campus, Cambridge (2018)
  • Travel award from HKU to attend and present poster at 5th International Symposium on Development of the ENS at Boston, MA, USA (2018)
  • Full postgraduate scholarship for PhD study at HKU (2017-2020)

Professional certification / membership

BMDC (Bangladesh Medical and Dental Council) registered medical doctor since 2015

Selected Publications

PhD thesis:
•
Clinico-epidemiological and trio-based genetic analysis of Bangladeshi Hirschsprung disease patients.
University of Hong Kong, Pokfulam, Hong Kong SAR.
Persistent identifier: http://hdl.handle.net/10722/300424
Journal articles:
•
Karim A, Keerthisinghe P, Sarasamma S, Ciaburri NA, Giraldez MG, Naidoo K, Orengo JP. Zebrafish knockout models of atxn1a, atxn1b, and atxn1l reveal distinct and shared phenotypic and transcriptomic alterations.
Preprint: bioRxiv (2026). https://doi.org/10.64898/2026.03.05.709450
•
Keerthisinghe P, Karim A, Basak A, Orengo JP. Protocol for quantitative analysis of adult zebrafish swimming behavior using DeepLabCut.
STAR protocols (2026). https://doi.org/10.1016/j.xpro.2026.104374
•
Akter M, Fu Z, Zheng X, Iqbal Z, Zhang N, Karim A, Li Y. Astrocytic GPCR signaling in the anterior cingulate cortex modulates decision making in rats.
Oxford Open Neuroscience (2024). http://doi.org/10.1093/oons/kvae010
•
Akter M, Hasan M, Ramkrishnan AS, Zheng X, Iqbal Z, Fu Z, Lei Z, Karim A, Li Y. Astrocyte and L-lactate in the anterior cingulate cortex modulate schema memory and neuronal mitochondrial biogenesis.
eLife (2023). http://doi.org/10.7554/eLife.85751
Preprint: bioRxiv (2023). http://doi.org/10.1101/2023.01.08.523156
•
Sarasamma S, Karim A, Orengo JP. Zebrafish models of rare neurological diseases like spinocerebellar ataxias (SCAs): Advantages and limitations.
Biology (2023). https://doi.org/10.3390/biology12101322
•
Ahmed S#, Karim A#, Chowdhury TK, Pulock OS, Tamanna N, Akter M, Biswas P, Afroz F, Pinky SD, Alabbi AN, Jamil TR, Tasnim Z, Dev D, Marma M, Aziz TT, Hakim HAN, Basher AKMK, Shahin NHB, Banu T. Patients’ characteristics and 30-day mortality for those undergoing elective surgeries during COVID-19 pandemic in Bangladesh.
# Equal contribution.
PLOS One (2023). https://doi.org/10.1371/journal.pone.0289878
•
Advanced M, Ma H, Hasan M, Karim A, Zhu X, Zhang L, Li Y. Exogenous L-lactate administration in rat hippocampus increases expression of key regulators of mitochondrial biogenesis and antioxidant defense.
Frontiers in Molecular Neuroscience (2023). https://doi.org/10.3389/fnmol.2023.1117146
•
Tang CS, Karim A, Zhong Y, Chung PH, Tam PK. Genetics of Hirschsprung’s disease.
Pediatric Surgery International (2023). https://doi.org/10.1007/s00383-022-05358-x
•
Karim A, Tang CS, Tam PK. The emerging genetic landscape of Hirschsprung disease and its potential clinical applications.
Frontiers in Pediatrics (2021). https://doi.org/10.3389/fped.2021.638093
•
Kuil LE, MacKenzie KC, Tang CS, Windster JD, Le TL, Karim A, de Graaf BM, van der Helm R, van Bever Y, Sloots CEJ, Meeussen C, Tibboel D, de Klein A, Wijnen RMH, Amiel J, Lyonnet S, Garcia-Barcelo MM, Tam PKH, Alves MM, Brooks AS, Hofstra RMW, Brosens E. Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development.
PLOS Genetics (2021). https://doi.org/10.1371/journal.pgen.1009698
Preprint: medRxiv (2020). https://doi.org/10.1101/2020.11.02.20221481
•
Zhuang X, Ye R, So MT, Lam WY, Karim A, Yu M, Ngo ND, Cherny SS, Tam PK, Garcia-Barcelo MM, Tang CS, Sham PC. A random forest-based framework for genotyping and accuracy assessment of copy number variations.
NAR Genomics and Bioinformatics (2020). https://doi.org/10.1093/nargab/lqaa071
•
Karim A, Akter M, Mazid T, Pulock OS, Aziz Harrison TT, Hayee S, Tamanna N, Chuwdhury GS, Haque A, Yeasmin F, Mitu MA, Yeasmin F, Rashid H, Kuri AK, Das A, Majumder K, Barua D, Rahaman M, Akter S, Munia NN, Sultana J, Usaila F, Sifat S, Nourin NA, Uddin F, Bhowmik M, Ahammed T, Sharik N, Mehnaz Q, Bhuiyan NH, Banu T. Knowledge and attitude towards COVID-19: A cross sectional study in Bangladesh through phone and online survey.
J Clin Exp Invest (2020). https://doi.org/10.29333/jcei/9143
Preprint: medRxiv (2020). https://doi.org/10.1101/2020.05.26.20104497
•
Banu T, Karim A, Adel MG, Lakhoo K, Aziz TT, Das A, Sharmeen N, Yapo B, Ferdous KMN, Kabir KA, Zahid MK, Ford K, Ahsan MQ, Akter M, Alam MA. Hoque, M. Multicenter Study of 342 Anorectal Malformation Patients: Age, Gender, Krickenbeck Subtypes, and Associated Anomalies.
Eur J Pediatr Surg (2019). https://doi.org/10.1055/s-0039-1695789
•
Banu T, Chowdhury TK, Aziz TT, Das A, Tamanna N, Pulock OS, Imam MS, Karim A, Akter M, Walid A. Cost Incurred by the Family for Surgery in Their Children: A Bangladesh Perspective.
World Journal of Surgery (2018). https://doi.org/10.1007/s00268-018-4700-0
•
Karim A, Akter M, Aziz TT, Hoque M, Chowdhury TK, Imam MS, Walid A, Kabir M, So M, Lam WY, Tang CS, Wong KK, Tam PKH, Garcia-Barcelo MM, Banu T. Epidemiological characteristics of Hirschsprung’s disease (HSCR): Results of a case series of fifty patients from Bangladesh.
Journal of Pediatric Surgery (2018). https://doi.org/10.1016/j.jpedsurg.2017.12.029
•
Hsu JSJ, So M, Tang CSM, Karim A, Porsch RM, Wong C, Yu M, Yeung F, Xia H, Zhang R, Cherny SS, Chung PHY, Wong KKY, Sham PC, Ngo ND, Li M, Tam PKH, Lui VCH, Garcia-Barcelo MM. De novo mutations in Caudal Type Homeo Box Transcription Factor 2 (CDX2) in patients with persistent cloaca.
Human Molecular Genetics (2017). https://doi.org/10.1093/hmg/ddx406

Selected Symposium / conference presentation (first author)

•
Karim A, et al. Unraveling cell-type-specific transcriptomic changes in the spinal cord of spinocerebellar ataxia type 1 (SCA1) (Poster).
6th Annual GCC Single Cell & Spatial Omics Symposium, Houston, TX, USA (October 22, 2025)
•
Karim A, et al. Zebrafsh knockout models of atxn1a, atxn1b, and atxn1l (Poster).
UTHealth Houston Annual Neuroscience Poster Session 2024, Houston, TX, USA (December 7, 2024)
•
Karim A, et al. Redesigning pathology teaching and learning with online interactive worksheets (Poster).
Tripartite Medical Education Conference 2023, Hong Kong (January 14-15, 2023)
•
Karim A, et al. Genetic profiles of Bangladeshi Hirschsprung disease (HSCR) patients obtained by trio-based whole exome sequencing (WES) (Poster).
23rd Research Postgraduate Symposium, Li Ka Shing Faculty of Medicine, HKU (December 5-6, 2018)
(Received outstanding poster presentation award)
•
Karim A, et al. Epidemiological and genetic analysis of Bangladeshi Hirschsprung disease patients (Poster).
The 5th International Symposium on Development of the Enteric Nervous System: cells, signals, genes and therapy, Boston, MA, USA (April 8-11, 2018)
•
Karim A, et al. Epidemiological characteristics of Hirschsprung’s disease (HSCR): Results of a case series of fifty patients from Bangladesh (Poster).
22nd Research Postgraduate Symposium, Li Ka Shing Faculty of Medicine, HKU (December 6-7, 2017)

Seminar talk

•
Beyond the stethoscope: Venturing into research
Chittagong Medical College, Bangladesh (October 10, 2025)
Presentation link (in Bangla):
https://youtu.be/BFWMGNL5EMI
•
Uncovering genetic basis of disease with next-generation sequencing
Chittagong Research Institute for Children Surgery, Bangladesh (April 17, 2019)