Publications

2016

Naeini MP, Cooper GF. Binary classifier calibration using an ensemble of piecewise linear regression models. Proc SIAM Int Conf Data Min. 2016 May;2016:261-269. doi: 10.1137/1.9781611974348.30. PMCID: PMC5367639

Ruffalo M, Bar-Joseph Z. Genome-wide predictions of miRNA regulation by transcription factors. Bioinformatics 2016 Sep 1;32(17):i746-i754. doi: 10.1093/bioinformatics/btw452. PMID: 27587697

2017

Schwartz R, Schäffer AA. The evolution of tumour phylogenetics: Principles and practice. Nature Reviews Genetics. 2017 Apr;18(4):213-229. doi: 10.1038/nrg.2016.170. Epub 2017 Feb 13.

Chen V, Paisley J, Lu X. Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling. 2017 Mar 14;18(Suppl 2):105. doi: 10.1186/s12864-017-3494-z. PMCID: PMC5374647

Lee S, Jiang X. Modeling miRNA-mRNA interactions that cause phenotypic abnormality in breast cancer patients. PLoS One. 2017 Aug 9;12(8):e0182666. doi: 10.1371/journal.pone.0182666. eCollection 2017. PMCID: PMC5549916.

Ruffalo M, Stojanov P, Pillutla VK, Varma R, Bar-Joseph Z. Reconstructing cancer drug response networks using multitask learning. BMC Syst Biol. 2017 Oct 10;11(1):96. doi: 10.1186/s12918-017-0471-8. PMCID: PMC5635550

Roman T, Xie L, Schwartz R. Automated deconvolution of structured mixtures from bulk tumor genomic data. PLoS computational biology. 2017 Oct 23;13(10):e1005815. PMID: 29059177; PMCID: PMC5695636.

Ding J, Bar-Joseph Z. MethRaFo: MeDIP-seq methylation estimate using a Random Forest Regressor. Bioinformatics. 2017 Nov 1;33(21):3477-3479. doi: 10.1093/bioinformatics/btx449. PMCID: PMC5860172

Ding MQ, Chen L, Cooper GF, Young JD, Lu X. Precision Oncology beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics. Molecular Cancer Research. 2017 Nov 13.

2018

Naeini MP, Cooper GF. Binary classifier calibration using an ensemble of piecewise linear regression models. Knowl Inf Syst. 2018 Jan;54(1):151-170. doi: 10.1007/s10115-017-1133-2. Epub 2017 Nov 17. PMCID: PMC5875942 [Available on 2019-01-01.

Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, Pauley MA, Rosenwald A, Rustici G, Sierk M, Warnow T, Welch L. The development and application of bioinformatics core competencies to improve bioinformatics training and education. PLoS Comput Biol. 2018 Feb 1;14(2):e1005772. doi: 10.1371/journal.pcbi.1005772. eCollection 2018 Feb. PMCID: PMC5794068.

Ding J, Hagood JS, Ambalavanan N, Kaminski N, Bar-Joseph Z. iDREM: Interactive visualization of dynamic regulatory networks. PLoS Comput Biol. 2018 Mar 14;14(3):e1006019. doi: 10.1371/journal.pcbi.1006019. eCollection 2018 Mar.PMID: 29538379; PMCID: PMC5868853.

Oltmann J, Heselmeyer-Haddad K, Hernandez LS, Meyer R,Torres I, Hu Y, Doberstein N, Killian JK, Petersen D, Zhu YJ, Edelman DC, Meltzer PS, Schwartz R, Gertz EM, Schäffer AA, Auer G, Haberman JK, Ried T. Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients.Genes Chromosomes Cancer. 2018 Apr;57(4):165-175. doi: 10.1002/gcc.22515. Epub 2018 Jan 9. PMCID: PMC5807164.

Ma C, Shao M, Kingsford C. SQUID: Transcriptomic Structural Variation Detection from RNA-seq. Genome Biol. 2018 Apr 12;19(1):52. doi: 10.1186/s13059-018-1421-5. DOI: 10.1186/s13059-018-1421-5. PMID: 29650026; PMCID: PMC5896115.

Du T, Zhu L, Levine KM, Tasdemir N, Lee AV, Vignali DAA, Houten BV, Tseng GC, Oesterreich S. Invasive lobular and ductal breast carcinoma differ in immune response, protein translation efficiency and metabolism. Sci Rep. 2018 May 8;8(1):7205. doi: 10.1038/s41598-018-25357-0. PMID: 29739984; PMCID: PMC5940770.

Thomas M, Schwartz R. A method for efficient Bayesian optimization of self-assembly systems from scattering data. BMC Syst Biol. 2018 Jun 8;12(1):65. doi: 10.1186/s12918-018-0592-8. PMID: 29884203; PMCID: PMC5994016.

Wangsa D, Braun R, Schiefer M, Gertz EM, Bronder D, Quintanilla I, Padilla-Nash HM, Torres I, Hunn C, Warner L, Buishand FO, Hu Y, Hirsch D, Gaiser T, Camps J, Schwartz R, Schäffer AA, Heselmeyer-Haddad K, Reid T. The evolution of single cell-derived colorectal cancer cell lines is dominated by the continued selection of tumor-specific genomic imbalances, despite random chromosomal instability. Carcinogenesis, 39 (8) August 2018, Pages 993–1005, https://doi.org/10.1093/carcin/bgy068. PMID: 29800151; PMCID: PMC6067130 [Available on 2019-07-30]

Kang J, Rancati T, Lee S, Oh JH, Kerns SL, Scott JG, Schwartz R, Kim S, Rosenstein BS. Machine Learning and Radiogenomics: Lessons Learned and Future Directions. Front. Oncol., 21 June 2018 | https://doi.org/10.3389/fonc.2018.00228. PMID: 29977864; PMCID: PMC6021505

Eaton J, Wang J, Schwartz R. Deconvolution and phylogeny inference of structural variations in tumor genomic samples. Bioinformatics. 2018 Jul 1;34(13):i357-i365. doi: 10.1093/bioinformatics/bty270. DOI: 10.1093/bioinformatics/bty270 PMID: 29950001; PMCID: PMC6022719.

Andrews, B., Ramsey, J. Cooper, G.F. Scoring Bayesian networks of mixed variables. Int J Data Sci Anal. 2018 Aug;6(1):3-18. doi: 10.1007/s41060-017-0085-7. Epub 2018 Jan 11. PMID: 30140730; PMCID: PMC6101981 [Available on 2019-08-01]

Jabbari F, Visweswaran S, Cooper GF. Instance-Specific Bayesian Network Structure Learning. Proceedings of the Ninth International Conference on Probabilistic Graphical Models, PMLR 72:169-180, 2018. PMID: 30775723; PMCID: PMC6376975.

Tasdemir N, Bossart EA, Li Z, Zhu L, Sikora MJ, Levine KM, Jacobsen BM, Tseng GC, Davidson NE, Oesterreich S. Comprehensive Phenotypic Characterization of Human Invasive Lobular Carcinoma Cell Lines in 2D and 3D Cultures. Cancer Res. 2018 Nov 1;78(21):6209-6222. doi: 10.1158/0008-5472.CAN-18-1416. Epub 2018 Sep 18.PMID: 30228172; PMC-in process.

Alavi A, Ruffalo M, Parvangada A, Huang Z, Bar-Joseph Z. A web server for comparative analysis of single-cell RNA-seq data. Nat Commun. 9(1):4768, 2018 PMID: 30425249; PMCID: PMC6233170.

2019

Ruffalo M, Thomas R, Lee A, Oesterreich S, Bar-Joseph Z. Network-guided prediction of aromatase inhibitor response in breast cancer. PLoS Comput Biol. 2019 Feb 11;15(2):e1006730. doi: 10.1371/journal.pcbi.1006730. eCollection 2019 Feb. PMID: 30742607; PMCID: PMC6386390.

Ruffalo M, Bar-Joseph Z. Protein interacation disruption in cancer. BMC Cancer 19:370, 2019 PMID: 31014259; DOI: 10.1186/s12885-019-5532-5

Ray M, Ruffalo MM, Bar-Joseph Z. Construction of integrated microRNA and mRNA immune cell signatures to predict survival of patients with breast and ovarian cancer. Genes Chromosomes Cancer. 58(1):34-42, 2019. PMID: 30285311; DOI:10.1002/gcc.22688.

Lei H. et al. (2019) Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data. In: Cowen L. (eds) Research in Computational Molecular Biology. RECOMB 2019. Lecture Notes in Computer Science, vol 11467. Springer, Cham

Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Yu L, Hochheiser HS, Jiang X, Wang JQ, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLOS Comput Biol, 2019 Jul 15(7):e1007088. doi: 10.1371/journal.pcbi.1007088. [Epub ahead of print] PMID: 31276486

Book Chapter

Schwartz R. (2019) Computational Models for Cancer Phylogenetics. In: Warnow T. (eds) Bioinformatics and Phylogenetics. Computational Biology, vol 29. Springer, Cham. First online Apr 2019

Pre-Prints

Ma C, Kingsford C. Detecting anomalies in RNA-seq quantification. bioRxiv preprint first posted online Feb. 5, 2019. http://dx.doi.org/10.1101/541714.

Tao Y, Cai C, Cohen WW, Lu X. From genome to phenome: Predicting multiplecancer phenotypes based on somatic genomic alterations via the genomic impact transformer. arXiv.org > q-bio > arXiv:1902.00078. Feb 9 2019. To appear in Oxford Systems Biology.