Publications and Presentations

Last Updated: 16 Aug 2026

JOURNAL ARTICLES AND REPORTS

2026:

1. Al Sium SM*, Tonmoy MIQ, Chowdhury SF, et al. (2026). Integrative multi-omics analysis identifies methylation-associated lncRNAs FAM83A-AS2 and AC012213.1 as candidate prognostic markers in lung adenocarcinoma. Bioinformatics Advances, 6(1), vbag096.

2. Seidman JC, Aiemjoy K, ... Al Sium SM, ... Charles RC (2026). Use of Salmonella enterica serovar Typhi hemolysin E and lipopolysaccharide IgA to identify enteric fever cases, South Asia. Emerging Infectious Diseases, 32(8), 1221-1230.

3. Magaña P, Gopalasingam P, ... Al Sium SM, ... Brooksbank C (2026). Towards globally equitable bioinformatics adoption. PLOS Biology, 24(7), e3003839.

4. Asif AM, … Al Sium SM, et al. (2026). Endemic Circulation and Genetic Characterization of Foot-and-Mouth Disease Virus in Buffalo Populations of Bangladesh. Transboundary and Emerging Diseases, 2026 (1):3107202

5. Hossain MM, Cho HS, Al Sium SM, Begum R, Uddin MB (2026). Coding-complete genome sequence of a lumpy skin disease virus isolate from Rajshahi, Bangladesh. Microbiology Resource Announcements, 15(4), e01391-25.

6. Chowdhury SF, Sarkar MH, Al Sium SM, et al. (2026). Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases. Scientific Reports, 16, 11916.

2025:

7. Al Sium SM, Goswami B, Chowdhury SF, et al. (2025). An insight into the genome-wide analysis of bacterial defense mechanisms in a uropathogenic Morganella morganii isolate from Bangladesh. PLOS ONE, 20(1), e0313141.

8. Eranti P, Hegde M, Al Sium SM, Parra RG, Kilpatrick AM, Shome S, Rahman F (2025). Impact of the COVID-19 pandemic on computational biology early career researchers: A global retrospective study. PLOS Computational Biology, 21(10), e1013554.

2024:

9. Ananna NT, Shishir TA, Ahmed A, Al Sium SM, et al. (2024). Characterization of two lytic bacteriophages infecting carbapenem-resistant clinical Klebsiella pneumoniae in Dhaka, Bangladesh. Virus Research, 350, 199491.

10. Al Sium SM, Torrejón E, Chowdhury SF, Ahmed R, Jain A, Treccani M, Veschetti L, Riaz A, Eranti P, Olguín-Orellana GJ (2024). Adapting beyond borders: Insights from the 19th Student Council Symposium (SCS2023), the first hybrid ISCB Student Council global event. Bioinformatics Advances, 4(1), vbae028.

2023:

11. Grover A, Riaz A, Al Sium SM, Dincaslan FB, et al. (2023). 1st ASCS: Expanding the ISCB Student Council Symposia to Asia. F1000Research, 12, 703.

2022:

12. Aiemjoy K, Seidman JC, Saha S, Munira SJ, Islam Sajib MS, Al Sium SM, et al. (2022). Estimating typhoid incidence from community-based serosurveys: A multicohort study. The Lancet Microbe, 3(8), e578-e587.

13. Akram A, Al Sium SM, Islam T, et al. (2022). Genome sequence of SARS-CoV-2 sublineage BA.2.12.1 strain from Bangladesh. New Microbes and New Infections, 49, 101050.

14. Kilpatrick AM, Rahman F, ... Al Sium SM, ... Welch L (2022). Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia. Bioinformatics, 38(Suppl 1), i19-i27.

15. Chowdhury AT, Chowdhury SF, Al Sium SM, Reshad RAI, Mim SK, Miah MF (2022). Nationwide restrictions to combat consecutive COVID-19 waves: Lessons learnt from a developing country like Bangladesh. Journal of Clinical and Experimental Investigations, 13(3), em00799.

2021:

16. Saha S, Tanmoy AM, ... Al Sium SM, et al. (2021). New waves, new variants, old inequity: A continuing COVID-19 crisis. BMJ Global Health, 6(8), e007031.

17. Saha S, Tanmoy AM, Hooda Y, Tanni AA, Goswami S, Al Sium SM, et al. (2021). COVID-19 rise in Bangladesh correlates with increasing detection of B.1.351 variant. BMJ Global Health, 6(5), e006012.

18. Chowdhury SF, Al Sium SM, Anwar S (2021). Research and management of rare diseases in the COVID-19 pandemic era: Challenges and countermeasures. Frontiers in Public Health, 9, 640282.

2020:

19. Islam H, Rahman A, Masud J, Shweta DS, Araf Y, Ullah MA, Sium SMA, Sarkar B (2020). A generalized overview of SARS-CoV-2: Where does the current knowledge stand? Electronic Journal of General Medicine, 17(6), em251.

2019:

20. Habib MA, Rahman A, Khatun F, Hannan MA, Al-Sium MS, Islam MT, Harun-ar-Rashid, Islam MS (2019). Comparative analysis on antioxidant activities of barks from Sonneratia caseolaris grown in three saline zones of Sundarbans. Vedic Research International Biological Medicinal Chemistry, 7(1), 1-6.

PUBLISHED CONFERENCE ABSTRACTS

1. Al Sium SM, et al. (2025). Unraveling epigenetically deregulated lncRNAs FAM83A-AS2 and AC012213.1 as high-risk prognostic markers in lung adenocarcinoma. Briefings in Bioinformatics, 26(Suppl 1), i42-i43.

2. Chowdhury SF, et al. (2025). Metatranscriptomic analysis uncovers microbial and immune signatures underlying COVID-19 severity. Briefings in Bioinformatics, 26(Suppl 1), i14-i15.

PREPRINTS

1. Al Sium SM, Banu TA, et al. (2026). Targeted BRCA1/BRCA2 sequencing in a Bangladeshi clinically referred cohort identifies candidate BRCA1 loss-of-function variants and a multi-exon deletion-like CNV signal. medRxiv. [Preprint; not peer reviewed].

2. Brum E, Saha S, ... Al Sium SM, et al. (2021). Surging COVID-19 in Bangladesh driven by B.1.351 variant. medRxiv. [Preprint; not peer reviewed].

PRESENTATIONS

1. Al Sium SM at el. 2025. Unraveling epigenetically deregulated lncRNAs FAM83A-AS2 and AC012213.1 as high-risk prognostic markers in lung adenocarcinoma. 34th GIW- ISCB Asia, Hong Kong and 4th Asian Student Council Symposium (Best Oral Presentation Award) 

2. Al Sium SM at el. 2025. Epigenetic Deregulation of lncRNAs in Lung Adenocarcinoma: Bridging Multi-omics Insights with Clinical Translation, ICLESSD 2025, Jagannath University (Best Oral Presentation Award) 

3. Al Sium SM at el. 2023. Towards the Record-Breaking Dengue Outbreak in Bangladesh: Understanding the Unprecedented Challenge Amid the COVID-19. GIW - ISCB Asia 2023, Singapore

4. Al Sium SM at el. 2023. Analysis and Mitigation: The Dual Threat of Dengue and COVID-19 in Urban and Rural Areas of Bangladesh. 31th International Conference on Intelligent Systems for Molecular Biology (ISMBECCB2023), France

5. Al Sium SM, Bateman A. 2020. AntiFam 6.0: Are We Close to Getting Rid of Spurious Proteins in Sequence Databases? 6th ISCB European Student Council Symposium - ESCS2020. (Best Poster Award) +  28th International Conference on Intelligent Systems for Molecular Biology (ISMB) + 16th ISCB Student Council Symposium – SCS2020. (Best Poster Award)  

6. Al Sium SM, Chowdhury SF (2018). Production of Agarwood Oil within 3 Months using Biotechnological Approaches. 1st National Biotechnology Fair. (Idea Based Best Poster Award)

DATABASE ENTRIES

• 178 spurious protein families in AntiFam 6.0

• 1000+ SARS CoV-2 sequences in GISAID