• 2237 Citations (Scopus)
  • 23 h-Index
20042019

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Scholarly Research

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2019

Evaluating the consistency of large-scale pharmacogenomic studies

Rahman, R., Dhruba, S. R., Matlock, K., Negron, C. D. N. P., Ghosh, S. & Pal, R., May 2019, In : Briefings in Bioinformatics. p. 1734–1753

Research output: Contribution to journalArticle

Functional Random Forests with applications in dose response predictions

Rahman, R., Dhruba, S. R., Ghosh, S. & Pal, R., Feb 2019, In : Scientific reports.

Research output: Contribution to journalArticle

Functional random forest with applications in dose-response predictions

Rahman, R., Dhruba, S. R., Ghosh, S. & Pal, R., Dec 1 2019, In : Scientific reports. 9, 1, 1628.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations

Potential Active Shooter Detection Based on Radar Micro-Doppler and Range-Doppler Analysis Using Artificial Neural Network

Li, Y., Peng, Z., Pal, R. & Li, C., Feb 1 2019, In : IEEE Sensors Journal. 19, 3, p. 1052-1063 12 p., 8519763.

Research output: Contribution to journalArticle

14 Scopus citations

Preclinical rationale for entinostat in embryonal rhabdomyosarcoma

Bharathy, N., Berlow, N. E., Wang, E., Abraham, J., Settelmeyer, T. P., Hooper, J. E., Svalina, M. N., Bajwa, Z., Goros, M. W., Hernandez, B. S., Wolff, J. E., Pal, R., Davies, A. M., Ashok, A., Bushby, D., Mancini, M., Noakes, C., Goodwin, N. C., Ordentlich, P., Keck, J. & 7 others, Hawkins, D. S., Rudzinski, E. R., Mansoor, A., Perkins, T. J., Vakoc, C. R., Michalek, J. E. & Keller, C., May 21 2019, In : Skeletal Muscle. 9, 1, 12.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Preclinical rationale for entinostat in embryonal rhabdomyosarcoma.

Bharathy, N., Berlow, N., Wang, E., Abraham, J., Settelmeyer, T. P., Hooper, J. E., Svalina, M. N., Bajwa, Z., Goros, M. W., Hernandez, B. S., Wolff, J. E., Pal, R., Davies, A. M., Ashok, A., Bushby, D., Mancini, M., Noakes, C., Goodwin, N. C., Ordentlich, P., Keck, J. & 7 others, Hawkins, D. S., Rudzinski, E. R., Mansoor, A., Perkins, T. J., Vakoc, C. R., Michalek, J. E. & Keller, C., May 21 2019, In : Default journal. p. 12

Research output: Contribution to journalArticle

Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

Berlow, N. E., Rikhi, R., Geltzeiler, M., Abraham, J., Svalina, M. N., Davis, L. E., Wise, E., Mancini, M., Noujaim, J., Mansoor, A., Quist, M. J., Matlock, K. L., Goros, M. W., Hernandez, B. S., Doung, Y. C., Thway, K., Tsukahara, T., Nishio, J., Huang, E. T., Airhart, S. & 9 others, Bult, C. J., Gandour-Edwards, R., Maki, R. G., Jones, R. L., Michalek, J. E., Milovancev, M., Ghosh, S., Pal, R. & Keller, C., Jun 17 2019, In : BMC Cancer. 19, 1, 593.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma.

Berlow, N., Rikhi, R., Geltzeiler, M., Abraham, J., Svalina, M. N., Davis, L. E., Wise, E., Mancini, M., Noujaim, J., Mansoor, A., Quist, M. J., Matlock, K., Goros, M. W., Hernandez, B. S., Doung, Y. C., Thway, K., Tsukahara, T., Nishio, J., Huang, E. T., Airhart, S. & 9 others, Bult, C. J., Gandour-Edwards, R., Maki, R. G., Jones, R. L., Michalek, J. E., Milovancev, M., Ghosh, S., Pal, R. & Keller, C., Jun 17 2019, In : Default journal. p. 593

Research output: Contribution to journalArticle

Recursive model for dose-time responses in pharmacological studies

Dhruba, S. R., Rahman, A., Rahman, R., Ghosh, S. & Pal, R., Jun 20 2019, In : BMC Bioinformatics. 20, 317.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Recursive model for dose-time responses in pharmacological studies.

Dhruba, S. R., Rahman, A., Rahman, R., Ghosh, S. & Pal, R., Jun 20 2019, In : BMC Bioinformatics.

Research output: Contribution to journalArticle

Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).

Yoon, B. J., Qian, X., Kahveci, T. & Pal, R., Jun 20 2019, In : Default journal. p. 316

Research output: Contribution to journalArticle

Sstack: An R package for stacking with applications to scenarios involving sequential addition of samples and features

Matlock, K., Rahman, R., Ghosh, S. & Pal, R., Sep 1 2019, In : Bioinformatics. 35, 17, p. 3143-3145 3 p.

Research output: Contribution to journalArticle

Sstack: An R Package for Stacking with Applications to Scenarios Involving Sequential Addition of Samples and Features

Matlock, K., Rahman, R., Ghosh, S. & Pal, R., Jan 2019, In : Bioinformatics. p. btz010

Research output: Contribution to journalArticle

2018

Application of transfer learning for cancer drug sensitivity prediction

Dhruba, S. R., Rahman, R., Matlock, K., Ghosh, S. & Pal, R., Dec 2018, In : BMC Bioinformatics. p. 497

Research output: Contribution to journalArticle

Application of transfer learning for cancer drug sensitivity prediction

Dhruba, S. R., Rahman, R., Matlock, K., Ghosh, S. & Pal, R., Dec 28 2018, In : BMC Bioinformatics. 19, 497.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Deep Sequencing Data Analysis

Ghosh, B., Datta, A. & Pal, R., Mar 1 2018, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Research output: Contribution to journalArticle

Deep Sequencing Data Analysis

Ghosh, B., Datta, A. & Pal, R., Mar 1 2018, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. p. 482-483

Research output: Contribution to journalArticle

Investigation of model stacking for drug sensitivity prediction

Matlock, K., De Niz, C., Rahman, R., Ghosh, S. & Pal, R., Mar 21 2018, In : BMC Bioinformatics. 19, 71.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Investigation of Model Stacking for Drug Sensitivity Prediction

Matlock, K., Negron, C. D. N. P., Rahman, R., Ghosh, S. & Pal, R., Mar 2018, In : BMC Bioinformatics. p. 71

Research output: Contribution to journalArticle

Modeling of drug diffusion in a solid tumor leading to tumor cell death

Rahman, A., Ghosh, S. & Pal, R., Dec 18 2018, In : Physical Review E. 98, 6, 062408.

Research output: Contribution to journalArticle

Modeling of drug diffusion in a solid tumor leading to tumor cell death.

Rahman, A., Ghosh, S. & Pal, R., Dec 2018, In : Physical Review E.

Research output: Contribution to journalArticle

Potential Active Shooter Detection Based on Radar Micro-Doppler and Range-Doppler Analysis Using Artificial Neural Network

Li, Y., Peng, Z., Pal, R. & Li, C., Nov 2018, In : IEEE Sensor Journal. p. 1052 - 1063

Research output: Contribution to journalArticle

Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Yoon, B-J., Qian, X., Kahveci, T. & Pal, R., Mar 21 2018, In : BMC Bioinformatics. p. 69

Research output: Contribution to journalArticle

Sequential Feature Selection and Inference using Multivariate Random Forests

Mayer, J., Rahman, R., Ghosh, S. & Pal, R., Apr 2018, In : Bioinformatics. p. 1336–1344

Research output: Contribution to journalArticle

Sequential feature selection and inference using multi-variate random forests

Mayer, J., Rahman, R., Ghosh, S. & Pal, R., Apr 15 2018, In : Bioinformatics. 34, 8, p. 1336-1344 9 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma

Wolff, J. E., Rudek, M. A., Xu, L., Anders, N. M., Pal, R., Harrold, A. P., Davies, A. M., Ashok, A., Bushby, D., Mancini, M., Noakes, C., Goodwin, N. C., Ordentlich, P., Keck, J., Hawkins, D. S., Rudzinski, E. R., Chatterjee, B., Bächinger, H. P., Barr, F. G., Liddle, J. & 6 others, Garcia, B. A., Mansoor, A., Perkins, T. J., Vakoc, C. R., Michalek, J. E. & Keller, C., Nov 20 2018, In : Default journal.

Research output: Contribution to journalArticle

The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma

Bharathy, N., Berlow, N. E., Wang, E., Abraham, J., Settelmeyer, T. P., Hooper, J. E., Svalina, M. N., Ishikawa, Y., Zientek, K., Bajwa, Z., Goros, M. W., Hernandez, B. S., Wolff, J. E., Rudek, M. A., Xu, L., Anders, N. M., Pal, R., Harrold, A. P., Davies, A. M., Ashok, A. & 18 others, Bushby, D., Mancini, M., Noakes, C., Goodwin, N. C., Ordentlich, P., Keck, J., Hawkins, D. S., Rudzinski, E. R., Chatterjee, B., Bächinger, H. P., Barr, F. G., Liddle, J., Garcia, B. A., Mansoor, A., Perkins, T. J., Vakoc, C. R., Michalek, J. E. & Keller, C., Nov 20 2018, In : Science Signaling. 11, 557, aau7632.

Research output: Contribution to journalArticle

11 Scopus citations
2017

Combination therapy design for maximizing sensitivity and minimizing toxicity

Matlock, K., Berlow, N., Keller, C. & Pal, R., Mar 22 2017, In : BMC Bioinformatics. 18, 116.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

Combination therapy design for maximizing sensitivity and minimizing toxicity

Matlock, K., Berlow, N., Keller, C. & Pal, R., Mar 2017, In : BMC Bioinformatics. p. 116

Research output: Contribution to journalArticle

Heterogeneity aware random forest for drug sensitivity prediction

Rahman, R., Matlock, K., Ghosh, S. & Pal, R., Dec 1 2017, In : Scientific reports. 7, 1, 11347.

Research output: Contribution to journalArticle

Open Access
11 Scopus citations

Heterogeneity Aware Random Forest for Drug Sensitivity Prediction

Rahman, R., Matlock, K., Ghosh, S. & Pal, R., Sep 2017, In : Scientific reports. p. 11347

Research output: Contribution to journalArticle

IntegratedMRF: Random forest-based framework for integrating prediction from different data types

Rahman, R., Otridge, J. & Pal, R., May 1 2017, In : Bioinformatics. 33, 9, p. 1407-1410 4 p.

Research output: Contribution to journalArticle

23 Scopus citations

IntegratedMRF: Random Forest based framework for integrating prediction from different data types

Rahman, R., Otridge, J. & Pal, R., 2017, In : Bioinformatics.

Research output: Contribution to journalArticle

2016

Algorithms for Drug Sensitivity Prediction

Negron, C. D. N. P., Rahman, R., Zhao, X. & Pal, R., 2016, In : Default journal. p. 77

Research output: Contribution to journalArticle

Design of probabilistic random forests with applications to anticancer drug sensitivity prediction

Rahman, R., Haider, S., Ghosh, S. & Pal, R., Mar 31 2016, In : Cancer Informatics. 15, p. 57-73 17 p.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

Design of Probabilistic Random Forests with applications to anti-cancer Drug Sensitivity Prediction

Rahman, R., Haider, S., Ghosh, S. & Pal, R., Mar 2016, In : Cancer Informatics. p. 57-73

Research output: Contribution to journalArticle

Inferring causal molecular networks: Empirical assessment through a community-based effort

Hill, S. M., Heiser, L. M., Cokelaer, T., Linger, M., Nesser, N. K., Carlin, D. E., Zhang, Y., Sokolov, A., Paull, E. O., Wong, C. K., Graim, K., Bivol, A., Wang, H., Zhu, F., Afsari, B., Danilova, L. V., Favorov, A. V., Lee, W. S., Taylor, D., Hu, C. W. & 115 others, Long, B. L., Noren, D. P., Bisberg, A. J., Mills, G. B., Gray, J. W., Kellen, M., Norman, T., Friend, S., Qutub, A. A., Fertig, E. J., Guan, Y., Song, M., Stuart, J. M., Spellman, P. T., Koeppl, H., Stolovitzky, G., Saez-Rodriguez, J., Mukherjee, S., Al-Ouran, R., Anton, B., Arodz, T., Sichani, O. A., Bagheri, N., Berlow, N., Bohler, A., Bonet, J., Bonneau, R., Budak, G., Bunescu, R., Caglar, M., Cai, B., Cai, C., Carlon, A., Chen, L., Ciaccio, M. F., Cooper, G., Coort, S., Creighton, C. J., Daneshmand, S. M. H., De La Fuente, A., Di Camillo, B., Dutta-Moscato, J., Emmett, K., Evelo, C., Fassia, M. K. H., Finotello, F., Finkle, J. D., Gao, X., Garcia-Garcia, J., Ghosh, S., Giaretta, A., Großeholz, R., Guinney, J., Hafemeister, C., Hahn, O., Haider, S., Hase, T., Hodgson, J., Hoff, B., Hsu, C. H., Hu, Y., Huang, X., Jalili, M., Jiang, X., Kacprowski, T., Kaderali, L., Kang, M., Kannan, V., Kikuchi, K., Kim, D. C., Kitano, H., Knapp, B., Komatsoulis, G., Krämer, A., Kursa, M. B., Kutmon, M., Li, Y., Liang, X., Liu, Z., Liu, Y., Lu, S., Lu, X., Manfrini, M., Matos, M. R. A., Meerzaman, D., Min, W., Müller, C. L., Neapolitan, R. E., Oliva, B., Opiyo, S. O., Pal, R., Palinkas, A., Planas-Iglesias, J., Poglayen, D., Sambo, F., Sanavia, T., Sharifi-Zarchi, A., Slawek, J., Streck, A., Strunz, S., Tegnér, J., Thobe, K., Toffolo, G. M., Trifoglio, E., Unger, M., Wan, Q., Welch, L., Wu, J. J., Xue, A. Y., Yamanaka, R., Yan, C., Zairis, S., Zengerling, M., Zenil, H. & Zi, Z., Mar 30 2016, In : Nature Methods. 13, 4, p. 310-322 13 p.

Research output: Contribution to journalArticle

104 Scopus citations
2015

A copula based approach for design of multivariate random forests for drug sensitivity prediction

Haider, S., Rahman, R., Ghosh, S. & Pal, R., Dec 2015, In : PLoS ONE. p. e0144490

Research output: Contribution to journalArticle

A copula based approach for design of multivariate random forests for drug sensitivity prediction

Haider, S., Rahman, R., Ghosh, S. & Pal, R., Dec 1 2015, In : PloS one. 10, 12, e0144490.

Research output: Contribution to journalArticle

Open Access
18 Scopus citations

A high-throughput in Vitro drug screen in a genetically engineered mouse model of diffuse intrinsic pontine glioma identifies BMS-754807 as a promising therapeutic agent

Halvorson, K. G., Barton, K. L., Schroeder, K., Misuraca, K. L., Hoeman, C., Chung, A., Crabtree, D. M., Cordero, F. J., Singh, R., Spasojevic, I., Berlow, N., Pal, R. & Becher, O. J., Mar 6 2015, In : PloS one. 10, 3, e0118926.

Research output: Contribution to journalArticle

Open Access
31 Scopus citations

Functionally defined therapeutic targets in diffuse intrinsic pontine glioma

Grasso, C. S., Tang, Y., Truffaux, N., Berlow, N. E., Liu, L., Debily, M. A., Quist, M. J., Davis, L. E., Huang, E. C., Woo, P. J., Ponnuswami, A., Chen, S., Johung, T. B., Sun, W., Kogiso, M., Du, Y., Qi, L., Huang, Y., Hütt-Cabezas, M., Warren, K. E. & 20 others, Le Dret, L., Meltzer, P. S., Mao, H., Quezado, M., Van Vuurden, D. G., Abraham, J., Fouladi, M., Svalina, M. N., Wang, N., Hawkins, C., Nazarian, J., Alonso, M. M., Raabe, E. H., Hulleman, E., Spellman, P. T., Li, X. N., Keller, C., Pal, R., Grill, J. & Monje, M., Jun 9 2015, In : Nature Medicine. 21, 6, p. 555-559 5 p.

Research output: Contribution to journalArticle

236 Scopus citations

Functionally defined therapeutic targets in diffuse intrinsic pontine glioma

Grasso, C. S., Berlow, N., Pal, R. & al, E., May 4 2015, In : NATURE MEDICINE. p. 555–559

Research output: Contribution to journalArticle

On the fast convergence modeling and accurate calculation of PV output energy for operation and planning studies

Navabi, R., Abedi, S., Hosseinian, S. H. & Pal, R., Jan 1 2015, In : Energy Conversion and Management. 89, p. 497-506 10 p.

Research output: Contribution to journalArticle

25 Scopus citations

On the fast convergence modeling and accurate calculation of PV output energy for operation and planning studies

Navabi, R., Abedi, S., Hosseinian, S. H. & Pal, R., Jan 2015, In : Energy Conversion and Management. p. 497–506

Research output: Contribution to journalArticle

2014

A community effort to assess and improve drug sensitivity prediction algorithms

NCI DREAM Community, Dec 1 2014, In : Nature Biotechnology. 32, 12, p. 1202-1212 11 p.

Research output: Contribution to journalArticle

Open Access
291 Scopus citations

A diverse stochastic search algorithm for combination therapeutics

Caglar, M. U. & Pal, R., 2014, In : BioMed Research International. 2014, 873436.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

A Diverse Stochastic Search Algorithm for Combination Therapeutics

Caglar, U. & Pal, R., 2014, In : BioMed Research International. p. doi 10.1155/2014/873436

Research output: Contribution to journalArticle

An ensemble based top performing approach for NCI - DREAM drug sensitivity prediction challenge

Wan, Q. & Pal, R., 2014, In : PLoS ONE. p. e101183

Research output: Contribution to journalArticle