Articles

BCL11b interacts with RNA and proteins involved in RNA processing and developmental diseases (PDF)

H. Sobhy*, M. De Rovere*, A. Ait-Ammar*, ... et al... , C. Schwartz, O. Rohr

Biochim Biophys Acta Gene Regul Mech. 2024; doi: 10.1016/j.bbagrm.2024.195065; PMID: 39455000 

• Our data support subsequent grants and publications, including PhD student publications [ e.g., DOI ], proving data utility and reproducibility.

Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins (PDF)

H. Sobhy*, R. Kumar, J. Lewerentz, L. Lizana* and P. Stenberg*

Scientific Reports, 2019; doi: 10.1038/s41598-019-40770-9; PMID: 30872630  

• Our computational analyses subsequently validated by independent experimental studies, examples: Prof. Aziz Sancar's team at UNC - PMID: 33771559; in addition to other articles including PMID: 33057195, PMID: 34598804, PMID: 27851967, and PMID: 28735753

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps (PDF)

R. Kumar, H. Sobhy, L. Lizana and P. Stenberg

Nucleic Acids Research, 2017; doi: 10.1093/nar/gkx644; PMID: 28973466  

Identification of giant Mimivirus protein functions using RNA interference (PDF)

H. Sobhy, B. La Scola, I. Pagnier, D. Raoult, P. Colson

Frontiers in Microbiology, 2015; doi: 10.3389/fmicb.2015.00345; PMID: 25972846

• Our functional genomics methods were independently validated by the Michael Rossmann team (Purdue University) in their concurrent study of viral protein structure (PMID: 25982526). 

• The optimized functional genomics, and protein expression and structure protocols were utilized for first time to study giant viral proteins. the methods were used in Nature (PMID: 26934229), and in JVI (PMID: 29514904) Journals. 

Recombinant expression of Mimivirus L725 ORFan gene product (PDF)

H. Sobhy, G. Gotthard, E. Chabrière, D. Raoult, P. Colson

Acta virologica; 2017; doi: 10.4149/av_2017_01_123; PMID: 28161966

• Our functional genomics methods were independently validated by the Michael Rossmann team (Purdue University) in their concurrent study of viral protein structure (PMID: 25982526). 

• The optimized functional genomics, and protein expression and structure protocols were utilized for first time to study giant viral proteins. the methods were used in Nature (PMID: 26934229), and in JVI (PMID: 29514904) Journals. 

The Potential Functions of Protein Domains during COVID Infection: An Analysis and a Review (PDF)

H. Sobhy*

MDPI COVID Journal 2021; doi: 10.3390/covid1010032

• First report of the presence of a tubulin autoregulation motif in the C-terminal of the COVID  nsp1 protein; later that same year, a Science study showed the involvement of the C-terminus in RNA translation. Our data can support future mechanistic studies and the identification of antiviral therapeutic targets." 

Virophages and their interactions with giant viruses and host cells (PDF)

H. Sobhy*

MDPI Proteomes (invited featured review), 2018; doi: 10.3390/proteomes6020023; PMID: 29786634

• This is an Invited review / feature article

• My work is cited on Wikipedia and featured in educational YouTube videos.

A comparative review of viral entry and attachment during large and giant dsDNA virus infections (PDF)

H. Sobhy*

Archives of Virology, 2017; doi: 10.1007/s00705-017-3497-8; PMID: 28866775

• I am grateful to our colleagues for their positive evaluation of our 2018 review as an ‘outstanding reading’ (PMID: 33647556): "A great review that compares entry and attachment during large and giant dsDNA virus infections, also showing the shape and structure of its viral particles."

A review of functional motifs utilized by viruses (PDF)

H. Sobhy*

MDPI Proteomes, 2016; doi: 10.3390/proteomes4010003; PMID: 28248213

A bioinformatics pipeline to search functional motifs within whole-proteome data: a case study of poxviruses (PDF)

H. Sobhy*

Virus Genes, 2016; doi: 10.1007/s11262-016-1416-9; PMID: 28000080

Shetti, a simple tool to parse, manipulate and search large datasets of sequences (PDF)

H. Sobhy*

SGM Microbial Genomics, 2015; doi: 10.1099/mgen.0.000035; PMID: 28348820

Gemi: PCR primers prediction from multiple alignments (PDF)

H. Sobhy*, P. Colson*

Comparative and Functional Genomics, 2012; doi: 10.1155/2012/783138; PMID: 23316117

• Conceptualized the idea and developed the tool.  The tool is still actively downloaded, reaching up to 25 / day and about 3000 times since 2012 (statistics shown in SourceForge Website, click HERE); attracted commercialization offers, and highlighted by standard methodological books and protocols, including MIMB (Vol. 1275) and a screenshot in Methods in Microbiology (Vol. 57, 2025).  

Social influence and peer review — impact factor and citation (PDF)

H. Sobhy*

EMBO reports, 2016; doi: 10.15252/embr.201642041; PMID: 26882557