IMPROVE Project

You can view the documentation for the IMPROVE project here.

A cross-model benchmark dataset for drug discovery in cancer.
In preparation
Jacobson J, Koussa N, Jones SE, Mahlich Y, Fore R, Im A, Zhu Y, Weil R, Gosline S.

Benchmarking community drug response prediction models: datasets, models, tools, and metrics for cross-dataset generalization analysis.
Briefings in Bioinformatics, In revision
Partin A, Vasanthakumari P, Narykov O, Wilke A, Koussa N, Jones SE, Zhu Y, Overbeek JC, Jain R, Fernando GD, Sanchez-Villalobos C, Garcia-Cardona C, Mohd-Yusof J, Chia N, Wozniak JM, Ghosh S, Pal R, Brettin TS, Weil R, Stevens RL.
Arxiv

The Hallmarks of Predictive Oncology
Cancer Discovery, 2025
Singhal A, Zhao X, Wall P, So E, Calderini G, Partin A, Koussa N, Vasanthakumari P, Narykov O, Zhu Y, Jones SE, Abbas-Aghababazadeh F, Kadambat Nair S, Bélisle-Pipon JC, Jayaram A, Parker BA, Yeung KT, Griffiths JI, Weil R, Nath A, Haibe-Kains B, Ideker T.
Pubmed

Nussenzweig Lab

Comprehensive mapping of cell fates in microsatellite unstable cancer cells support dual targeting of WRN and ATR.
Genes & Development, 2023
Zong D, Koussa NC, Cornwell JA, Pankajam AVA, Kruhlak MJ, Wong N, Chari R, Cappell SD, Nussenzweig A.
Pubmed

S1-END-seq reveals DNA secondary structures in human cells.
Molecular Cell, 2022
Matos-Rodrigues G, van Wietmarschen N, Wu W, Tripathi V, Koussa NC, Pavani R, Nathan WJ, Callen E, Belinky F, Mohammed A, Napierala M, Usdin K, Ansari AZ, Mirkin SM, Nussenzweig A.
Pubmed

Smith Lab

Post-replicative nick translation occurs on the lagging strand during prolonged depletion of DNA ligase I in Saccharomyces cerevisiae.
G3 Genes|Genomes|Genetics, 2021
Koussa NC, Smith DJ.
Pubmed

Limiting DNA polymerase delta alters replication dynamics and leads to a dependence on checkpoint activation and recombination-mediated DNA repair.
PLoS Genetics, 2021
Koussa NC, Smith DJ.
Pubmed

Separable, Ctf4-mediated recruitment of DNA Polymerase α for initiation of DNA synthesis at replication origins and lagging-strand priming during replication elongation.
PLoS Genetics, 2020
Porcella SY, Koussa NC, Tang CP, Kramer DN, Srivastava P, Smith DJ.
Pubmed

Baselga Lab

Pten loss promotes MAPK pathway dependency in HER2/neu breast carcinomas.
Proceedings of the National Academy of Sciences, 2016
Ebbesen SH, Scaltriti M, Bialucha CU, Morse N, Kastenhuber ER, Wen HY, Dow LE, Baselga J, Lowe SW.
Pubmed

Taselisib (GDC-0032), a Potent beta-Sparing Small Molecule Inhibitor of PI3K, Radiosensitizes Head and Neck Squamous Carcinomas Containing Activating PIK3CA Alterations.
Clinical Cancer Research, 2016
Zumsteg ZS, Morse N, Krigsfeld G, Gupta G, Higginson DS, Lee NY, Morris L, Ganly I, Shiao SL, Powell SN, Chung CH, Scaltriti M, Baselga J.
Pubmed

AXL mediates resistance to PI3Kα inhibition by activating the EGFR/PKC/mTOR axis in head and neck and esophageal squamous cell carcinomas.
Cancer Cell, 2015
Elkabets M, Pazarentzos E, Juric D, Sheng Q, Pelossof RA, Brook S, Benzaken AO, Rodon J, Morse N, Yan JJ, Liu M, Das R, Chen Y, Tam A, Wang H, Liang J, Gurski JM, Kerr DA, Rosell R, Teixido C, Huang A, Ghossein RA, Rosen N, Bivona TG, Scaltriti M, Baselga J.
Pubmed

PI3K inhibition results in enhanced estrogen receptor function and dependence in hormone receptor-positive breast cancer.
Science Translational Medicine, 2015
Bosch A, Li Z, Bergamaschi A, Ellis H, Toska E, Prat A, Tao JJ, Spratt DE, Viola-Villegas NT, Castel P, Minuesa G, Morse N, Rodón J, Ibrahim Y, Cortes J, Perez-Garcia J, Galvan P, Grueso J, Guzman M, Katzenellenbogen JA, Kharas M, Lewis JS, Dickler M, Serra V, Rosen N, Chandarlapaty S, Scaltriti M, Baselga J.
Pubmed

Antagonism of EGFR and HER3 enhances the response to inhibitors of the PI3K-Akt pathway in triple-negative breast cancer.
Science Signaling, 2014
Tao JJ, Castel P, Radosevic-Robin N, Elkabets M, Auricchio N, Aceto N, Weitsman G, Barber P, Vojnovic B, Ellis H, Morse N, Viola-Villegas NT, Bosch A, Juric D, Hazra S, Singh S, Kim P, Bergamaschi A, Maheswaran S, Ng T, Penault-Llorca F, Lewis JS, Carey LA, Perou CM, Baselga J, Scaltriti M.
Pubmed

mTORC1 inhibition is required for sensitivity to PI3K p110α inhibitors in PIK3CA-mutant breast cancer.
Science Translational Medicine, 2013
Elkabets M, Vora S, Juric D, Morse N, Mino-Kenudson M, Muranen T, Tao J, Campos AB, Rodon J, Ibrahim YH, Serra V, Rodrik-Outmezguine V, Hazra S, Singh S, Kim P, Quadt C, Liu M, Huang A, Rosen N, Engelman JA, Scaltriti M, Baselga J.*
Pubmed