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Items: 18

1.

Creating reproducible pharmacogenomic analysis pipelines.

Mammoliti A, Smirnov P, Safikhani Z, Ba-Alawi W, Haibe-Kains B.

Sci Data. 2019 Sep 3;6(1):166. doi: 10.1038/s41597-019-0174-7.

2.

Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts.

Mer AS, Ba-Alawi W, Smirnov P, Wang YX, Brew B, Ortmann J, Tsao MS, Cescon DW, Goldenberg A, Haibe-Kains B.

Cancer Res. 2019 Sep 1;79(17):4539-4550. doi: 10.1158/0008-5472.CAN-19-0349. Epub 2019 May 29.

PMID:
31142512
3.

ONECUT2 is a driver of neuroendocrine prostate cancer.

Guo H, Ci X, Ahmed M, Hua JT, Soares F, Lin D, Puca L, Vosoughi A, Xue H, Li E, Su P, Chen S, Nguyen T, Liang Y, Zhang Y, Xu X, Xu J, Sheahan AV, Ba-Alawi W, Zhang S, Mahamud O, Vellanki RN, Gleave M, Bristow RG, Haibe-Kains B, Poirier JT, Rudin CM, Tsao MS, Wouters BG, Fazli L, Feng FY, Ellis L, van der Kwast T, Berlin A, Koritzinsky M, Boutros PC, Zoubeidi A, Beltran H, Wang Y, He HH.

Nat Commun. 2019 Jan 17;10(1):278. doi: 10.1038/s41467-018-08133-6.

4.

MYC Interacts with the G9a Histone Methyltransferase to Drive Transcriptional Repression and Tumorigenesis.

Tu WB, Shiah YJ, Lourenco C, Mullen PJ, Dingar D, Redel C, Tamachi A, Ba-Alawi W, Aman A, Al-Awar R, Cescon DW, Haibe-Kains B, Arrowsmith CH, Raught B, Boutros PC, Penn LZ.

Cancer Cell. 2018 Oct 8;34(4):579-595.e8. doi: 10.1016/j.ccell.2018.09.001.

PMID:
30300580
5.

PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies.

Smirnov P, Kofia V, Maru A, Freeman M, Ho C, El-Hachem N, Adam GA, Ba-Alawi W, Safikhani Z, Haibe-Kains B.

Nucleic Acids Res. 2018 Jan 4;46(D1):D994-D1002. doi: 10.1093/nar/gkx911.

6.

DPubChem: a web tool for QSAR modeling and high-throughput virtual screening.

Soufan O, Ba-Alawi W, Magana-Mora A, Essack M, Bajic VB.

Sci Rep. 2018 Jun 14;8(1):9110. doi: 10.1038/s41598-018-27495-x.

7.

Disruption of the anaphase-promoting complex confers resistance to TTK inhibitors in triple-negative breast cancer.

Thu KL, Silvester J, Elliott MJ, Ba-Alawi W, Duncan MH, Elia AC, Mer AS, Smirnov P, Safikhani Z, Haibe-Kains B, Mak TW, Cescon DW.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1570-E1577. doi: 10.1073/pnas.1719577115. Epub 2018 Jan 29.

8.

Statin-Induced Cancer Cell Death Can Be Mechanistically Uncoupled from Prenylation of RAS Family Proteins.

Yu R, Longo J, van Leeuwen JE, Mullen PJ, Ba-Alawi W, Haibe-Kains B, Penn LZ.

Cancer Res. 2018 Mar 1;78(5):1347-1357. doi: 10.1158/0008-5472.CAN-17-1231. Epub 2017 Dec 11.

9.

Integrative cancer pharmacogenomics to establish drug mechanism of action: drug repurposing.

El-Hachem N, Ba-Alawi W, Smith I, Mer AS, Haibe-Kains B.

Pharmacogenomics. 2017 Nov;18(16):1469-1472. doi: 10.2217/pgs-2017-0132. Epub 2017 Oct 23. No abstract available.

10.

DRABAL: novel method to mine large high-throughput screening assays using Bayesian active learning.

Soufan O, Ba-Alawi W, Afeef M, Essack M, Kalnis P, Bajic VB.

J Cheminform. 2016 Nov 10;8:64. eCollection 2016.

11.

DASPfind: new efficient method to predict drug-target interactions.

Ba-Alawi W, Soufan O, Essack M, Kalnis P, Bajic VB.

J Cheminform. 2016 Mar 16;8:15. doi: 10.1186/s13321-016-0128-4. eCollection 2016.

12.

Metabolic traits of an uncultured archaeal lineage--MSBL1--from brine pools of the Red Sea.

Mwirichia R, Alam I, Rashid M, Vinu M, Ba-Alawi W, Anthony Kamau A, Kamanda Ngugi D, Göker M, Klenk HP, Bajic V, Stingl U.

Sci Rep. 2016 Jan 13;6:19181. doi: 10.1038/srep19181.

13.

Mining Chemical Activity Status from High-Throughput Screening Assays.

Soufan O, Ba-alawi W, Afeef M, Essack M, Rodionov V, Kalnis P, Bajic VB.

PLoS One. 2015 Dec 14;10(12):e0144426. doi: 10.1371/journal.pone.0144426. eCollection 2015.

14.

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.

Kulakovskiy IV, Vorontsov IE, Yevshin IS, Soboleva AV, Kasianov AS, Ashoor H, Ba-Alawi W, Bajic VB, Medvedeva YA, Kolpakov FA, Makeev VJ.

Nucleic Acids Res. 2016 Jan 4;44(D1):D116-25. doi: 10.1093/nar/gkv1249. Epub 2015 Nov 19.

15.

Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea.

Kamanda Ngugi D, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang G, Hikmawan T, Guan Y, Antunes A, Siam R, El Dorry H, Bajic V, Stingl U.

ISME J. 2015 Feb;9(2):396-411. doi: 10.1038/ismej.2014.137. Epub 2014 Aug 8.

16.

Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA).

Grötzinger SW, Alam I, Ba Alawi W, Bajic VB, Stingl U, Eppinger J.

Front Microbiol. 2014 Apr 7;5:134. doi: 10.3389/fmicb.2014.00134. eCollection 2014.

17.

Effects of cytosine methylation on transcription factor binding sites.

Medvedeva YA, Khamis AM, Kulakovskiy IV, Ba-Alawi W, Bhuyan MS, Kawaji H, Lassmann T, Harbers M, Forrest AR, Bajic VB; FANTOM consortium.

BMC Genomics. 2014 Mar 26;15:119. doi: 10.1186/1471-2164-15-119.

18.

INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

Alam I, Antunes A, Kamau AA, Ba Alawi W, Kalkatawi M, Stingl U, Bajic VB.

PLoS One. 2013 Dec 6;8(12):e82210. doi: 10.1371/journal.pone.0082210. eCollection 2013.

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