Publications

Highlights

(For a full list of publications see below or at Google Scholar)


Text‑mining‑based feature selection for anticancer drug response prediction

Wu G, Zaker A, Ebrahimi A, Tripathi S, Mer AS

Bioinformatics Advances, 2024

Biological and therapeutic implications of a unique subtype of NPM1 mutated AML

Mer AS, Heath E, Tonekaboni S, Garcia-Prat L, Shlush L, Voisin V, Bader G, Lupien M, Dick J, Minden M, Schimmer A, Haibe-Kains B

Nature Communications, Jan. 2021

Orchestrating and sharing large multimodal data for transparent and reproducible research

Mammoliti A, Smirnov P, Nakano M, Safikhani Z, Eeles C, Seo H, Nair SK, Mer AS, Ho C, Beri G, Kusko R, MAQC Society, Haibe-Kains B

Nature Communications, Oct. 2021

Integrative Pharmacogenomics Analysis of Patient Derived Xenografts

Mer AS, Ba-alawi W, Smirnov P, Wang XY, Brew B, Ortmann J, Tsao MS, Cescon D, Goldenberg A, Haibe-Kains B,

Cancer Research, May 2019

Full List of publications

Publications

Text‑mining‑based feature selection for anticancer drug response prediction
Wu G, Zaker A, Ebrahimi A, Tripathi S, Mer AS
Bioinformatics Advances, 2024
Characterization of the diversity of type IV secretion system‑encoding plasmids in Acinetobacter
Nasser F, Gaudreau A, Lubega S, Zaker A, Xia X, Mer AS, D’Costa VM
Emerging Microbes & Infections, 2024
Large‑scale phenogenomic analysis of human cancers uncovers frequent alterations affecting SMC5/6 complex components in breast cancer
Roy S, Zaker A, Mer AS(co corresponding author) , D’Amours D
NAR Cancer 2023
Spatiotemporal modeling of chemoresistance evolution in breast tumors uncovers dependencies on SLC38A7 and SLC46A1
Audet‑Delage Y, St‑Louis C, Minarrieta L, McGuirk S, Kurreal I, Annis MG, Mer AS, Siegel PM, St‑Pierre J.
Cell reports 2023
Differential DNA damage repair and PARP inhibitor vulnerability of the mammary epithelial lineages
Kim H, Aliar K, Tharmapalan P, McCloskey CW, Kuttanamkuzhi A, Grünwald BT, Palomero L, Mahendralingam MJ, Waas M, Mer AS, Elliott MJ, Zhang B, Al‑Zahrani KN, Langille ER, Parsons M, Narala S, Hofer S, Waterhouse PD, Hakem R, Haibe‑Kains B, Kislinger T, Schramek D, Cescon DW, Pujana MA, Berman HK, Khokha R.
Cell reports 2023
Bimodal gene expression in cancer patients provides interpretable biomarkers for drug sensitivity
Ba-Alawi W, Nair SK, Li B., Mammoliti A., Smirnov P, Mer AS, Linda PZ, Haibe-Kains B
Cancer Research, 2022
IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells
Nachmias B, Khan DH, Voisin V, Mer AS, Thomas GE, Segev N, St-Germain J et al.
Leukemia Feb. 2022
PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis
Feizi N, Nair SK, Smirnov P, Beri G, Eeles C, Esfahani PN, Nakano M, Tkachuk D, Mammoliti A, Gorobets E, Mer AS, Lin E, Yu Y, Martin S, Hafner M, Haibe-Kains B
Nucleic Acids Res. 2022 Jan 7
Ontogeny and Vulnerabilities of Drug-Tolerant Persisters in HER2+ Breast Cancer
Chang CA, Jen J, Jiang S, Sayad A, Mer AS, Brown KR, Nixon AM, Dhabaria A, Tang KH, Venet D, Sotiriou C, Deng J, Wong KK, Adams S, Meyn P, Heguy A, Skok JA, Tsirigos A, Ueberheide B, Moffat J, Singh A, Haibe-Kains B, Khodadadi-Jamayran A, Neel BG
Cancer discovery, Dec. 2021
Assessing therapy response in patient-derived xenografts
Ortmann J, Rampášek L, Tai E, Mer AS, Shi R, Stewart EL, Mascaux C, Fares A, Pham N, Beri G, Eeles C, Tkachuk D, Ho S, Sakashita S, Weiss J, Jiang X, Liu G, Cescon D, O’Brien C, Guo S, Tsao M, Haibe-Kains B, Goldenberg A
Science Translational Medicine Nov. 2021
Novel subtypes of NPM1-mutated AML with distinct outcome
Mer AS, Minden M, Haibe-Kains B, Schimmer A
Molecular & Cellular Oncology, 2021
Orchestrating and sharing large multimodal data for transparent and reproducible research
Mammoliti A, Smirnov P, Nakano M, Safikhani Z, Eeles C, Seo H, Nair SK, Mer AS, Ho C, Beri G, Kusko R, MAQC Society, Haibe-Kains B
Nature Communications, Oct. 2021
Proteogenomic characterization of pancreatic ductal adenocarcinoma
Cao L, Huang C, Cui DZ et al. (including Mer AS)
Cell, 2021
Drug Sensitivity Prediction From Cell Line-Based Pharmacogenomics Data: Guidelines for Developing Machine Learning Models
Noghabi HS, Jahangiri ST, Smirnov P, Hon C, Mammoliti A, Nair SK, Mer AS, Ester M, Haibe-Kains B
Briefings in Bioinformatics 2021
Biological and therapeutic implications of a unique subtype of NPM1 mutated AML
Mer AS, Heath E, Tonekaboni S, Garcia-Prat L, Shlush L, Voisin V, Bader G, Lupien M, Dick J, Minden M, Schimmer A, Haibe-Kains B
Nature Communications, Jan. 2021
Colorectal Cancer Cells Enter a Diapause-like DTP State to Survive Chemotherapy
Rehman S, Haynes J, Collignon E, Brown K, Wang Y, Nixon A, Bruce J, Wintersinger J, Mer AS, Lo E, Leung C, Lima-Fernandes E, Pedley N, Soares F, McGibbon S, He H, Pollet A, Pugh T, Haib-Kains B, Morris Q, Ramalho-Santos M, Goyal S, Moffat J, O’Brien C
Cell, 2021
Integrative Pharmacogenomics Analysis of Patient Derived Xenografts
Mer AS, Ba-alawi W, Smirnov P, Wang XY, Brew B, Ortmann J, Tsao MS, Cescon D, Goldenberg A, Haibe-Kains B,
Cancer Research, May 2019
Machine Learning for Biomarker Discovery in Cancer Pharmacogenomics Data
Mer AS, Smirnov P, Haibe-Kains B
Proceedings of 10th ACM BCB 2019
Organoid cultures as preclinical models of non-small cell lung cancer
Shi R, Radulovich N, Ng C, Liu N, Notsuda H, Cabanero M, Martins-Filho SN, Raghavan V, Li Q, Mer AS, Rosen J, Li M, Wang Y, Tamblyn L, Pham N, Haibe-Kains B, Liu G, Moghal N, Tsao MS
Clinical Cancer Research, 2019
Expression levels of long non-coding RNAs are prognostic for AML outcome
Mer AS, Lindberg L, Nilsson C, Klevebring D, Wang M, Grönberg H, Lehmann S, Rantalainen M
Journal of Hematology & Oncology 11(1), 2018
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 and Mak TW
PNAS, 2018
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, Nov. 2017
Software for the integration of multi-omics experiments in Bioconductor
Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L
Cancer Research Nov., 2017
Validation of risk stratification models in acute myeloid leukemia using sequencing-based molecular profiling
Wang M, Lindberg J, Klevebring D, Nilsson C, Mer AS, Rantalainen M, Lehmann S, Grönberg H
Leukemia, Feb. 2017
Study design requirements for RNA sequencing-based breast cancer diagnostics
Mer AS, Klevebring D, Gronberg H, Rantalainen M
Scientific Reports, 2016
CellWhere: graphical display of interactome networks organized on subcellular localizations
Zhu L, Malatras A, Thorley M, Aghoghogbe I, Mer AS, Duguez S, Butler-Browne G, Voit T, Duddy W
Nucleic acids research 2015
mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data
Gebhardt ML, Mer AS, Andrade-Navarro MA
BMC Research Notes, April 2015
A novel approach for protein subcellular location prediction using amino acid exposure
Mer AS, Andrade-Navarro MA
BMC Bioinformatics. 2013 Nov 28;14(1):342
MicroRNAs Modulate the Dynamics of the NF-𝜅B Signaling Pathway
Vaz C, Mer AS, Bhattacharya A, Ramaswamy R
PloS one, 6(11), 2011

Book Chapters

Applications of Computational Systems Biology in Cancer Signaling Pathways. In Unravelling Cancer Signaling Pathways: A Multidisciplinary Approach
Sandhu V, Manem VS, Mer AS, Kure EH, Haibe-Kains B
Springer Nature Singapore, 2019
PRC1-mediated gene silencing in pluripotent ES cells: function and evolution. Epigenetic Mechanisms in Cellular Reprogramming. In Epigenetic Mechanisms in Cellular Reprogramming (pp. 141-166)
Becker M, Mah N, Zdzieblo D, Li X, Mer AS, Andrade-Navarro MA, Müller AM
Springer Berlin Heidelberg 2015