Khademul Islam, full name Abul Bashar Mir Mohammad Khademul Islam, defended his Thesis work on Monday. He delivered a 50 minutes presentation followed by 1h and 15 minutes of questions by the committee. He did very well and was awarded the PhD title with maximum distinction. We are all very proud of him! After the defense we had a very nice celebration in the terrace in front on the auditorium.
The Thesis of Khademul has been directed by Elizaveta Benevolenskaya from the University of Illinois at Chicago and myself. The title of the Thesis is “Delineating epigenetic regulatory mechanisms of cell proliferation and differentiation” (see abstract), and focused on the study of the role of KDM5A, also known as RBP2 or JARID1A, in controlling differentiation and cell cycle. The Thesis also includes analysis of the corregulation of Histone-modifying enzymes in cancer and the study of RB/E2F pathway in Drosophila.
The committee remarked that the work by Khademul is a “a very good example of a successful collaboration between an experimental lab and a bioinformatics lab”. Khademul did part of his Thesis in Chicago and worked in collaboration between the two labs during the whole Thesis Project.
I am myself amazed by the capacity of work that Khademul has shown during these years and how he has been able to grasp all the biological and experimental details of the project as well as the more technical aspects of it, including bioinformatics and statistical issues. When Khademul arrived to our lab, back in July 2008, he didn’t know anything about Bioinformatics but he was eager to learn. And indeed, he learned very quickly and was productive in a very short time. The capacity of Khademul is evident by looking at the list of publications he has achieved during the last 4 years of work in our lab (see below).
Khademul will soon go back to Dhaka University. He has a lecturer position at the Department of Genetic Engineering & Biotechnology. I wish him all success in his future career, and I hope to have the opportunity to continue collaborating with him.
1. Khademul before the disertation. 2. Khademul gives the thesis book to Liza. 3. Khademul during the defense. 4. Khademul with Nuria and Liza. 5. The tribunal members. 6. Khademul during the celebration. 7. BG lab members during the celebration with a t-shirt with the image of the cover of the thesis.
List of Publications by Khademul during the last 4 years:
1. Abul Islam, Richter W, Beshiri M, Lopez-Bigas N, and Benevolenskaya E. Overlapping and distinct recruitment of enzymes involved in histone methylation determines epigenetic pattern in human genome. (Manuscript in preparation, 2012).
2. Beshiri M*, Abul Islam*, Lopez-Bigas N, and Benevolenskaya E. KDM5A regulates differentiation through two distinct mechanisms on cell cycle and tissue-specific genes. (Manuscript in preparation, 2012)
3. Beshiri M, Holmes K, Richter W, Hess S, Abul Islam, Yan Q, Plante L, Gévry N, Lopez-Bigas K, Kaelin W and Benevolenskaya E. Demethylation by KDM5A Contributes to Repression of Cell Cycle Genes During Differentiation. (Under Review 2012)
4. Bayarmagnai B, Nicolay B, Abul Islam, Lopez-Bigas N and Frolov M. Functional relationship between GAGA factor and hippo pathways in regulation of cell proliferation. (under review, 2012)
5. Hernando H, Shannon-Lowe C, Abul Islam, Fatima Al-Shahrour, Javier Rodríguez-Ubreva, Virginia C. Rodríguez-Cortez, Biola M. Javierre, Cristina Mangas, Agustin F. Fernandez, Maribel Parra, Henry-Jacques Delecluse, Manel Esteller, Eduardo Lopez-Granados, Mario F. Fraga, Nuria Lopez-Bigas, and Esteban Ballestar. Hypomethylation of B cell specific genes during conversion of resting B cells to proliferating lymphoblasts is an early event in lymphomagenesis. (under review 2012)
6. Mulero C, Ferres-Marco D, Pecoraro M, Abul Islam, Charneco C, Bellora N, Toll A, Gallardo F, Asensio E, López-Arribillaga E, Rodilla V, Iglesias M, Shih V, Alba M, Di Croce L, Hoffmann A, Villà-Freixa J, López-Bigas N, Keyes B, Domínguez M, Bigas A and Espinosa L. Chromatin-bound IκBα is a modulator of PRC2-dependent repression in development and cancer. (under review 2012)
7. Román-González L, Barneda-Zahonero B, Collazo O, Rafati H, Abul Islam, Thomas Graf, Núria López-Bigas, Tokameh Mahmoudi and Maribel Parra. Downregulation of HDAC7, an essential repressor of myeloid-inappropriate genes in B cells is required for transdifferentiation into macrophages. (under review 2012)
8. Abul Islam, Richter WF, Lopez-Bigas N, Benevolenskaya, EV. Selective targeting of histone methylation. Cell Cycle (2011)
9. Abul Islam, Richter WF, Jacobs LA, Lopez-Bigas N and Benevolenskaya EV Coregulation of Histone-modifying Enzymes in Cancer. PLoS One (2011)
10. Truscott M, Abul Islam, Lopez-Bigas N and Frolov MV mir-11 limits the proapoptotic function of its host gene, dE2f1. Genes and Development (2011).
11. Nicolay B, Bayarmagnai B*, Abul Islam*, Lopez-Bigas N and Frolov MV. Cooperation between dE2F1 and Yki/Sd defines a distinct transcriptional program necessary to bypass cell cycle exit. Genes & Development (2011).
12. Beshiri ML, Abul Islam, DeWaal DC, Richter WF, Love J, Lopez-Bigas N, Benevolenskaya EV. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets. JoVE (2010)
13. Ferreiro I, Joaquin M, Abul Islam, Gonzalo Gomez, Montserrat Barragan, Luis Lombardia, Orlando Dominguez, David G. Pisano, Nuria Lopez-Bigas, Angel R. Nebreda and Francesc Posas. Whole genome analysis of p38 SAPK-mediated gene expression upon stress. BMC Genomics, (2010)
14. Aguilar H, Sole X, Bonifaci N, Serra-Musach J, Abul Islam, Lopez-Bigas N, Méndez-Pertuz M, Beijersbergen RL, Lázaro C, Urruticoechea A, Pujana MA. Biological reprogramming in acquired resistance to endocrine therapy of breast cancer. Oncogene. (2010).
15. Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Abul Islam, Deu-Pons J, Furney S and Lopez-Bigas N. IntOGen: Integration and data-mining of multidimensional oncogenomic data. Nature Methods (2010) .
Histone-modifying Enzymes Coregulated in Cancer – a phenomena that can be used for better drug design
miR11 – a protector of cells from e2f induced apoptosis during cell cycle entry
Collaboration with Benevolenskaya lab (Postdoc position available)
Visualized ChIP & ChIPseq protocol