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Publications 2007 2019

2019

DrugComb: an integrative cancer drug combination data portal

Zagidullin, B., Aldahdooh, J. M. F., Zheng, S., Wang, W., Wang, Y., Saad, J., Malyutina, A., Jafari, M., Tanoli, Z-R., Pessia, A. & Tang, J., 8 May 2019, In : Nucleic Acids Research.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Making Sense of the Epigenome Using Data Integration Approaches

Cazaly, E., Saad, J., Wang, W., Heckman, C., Ollikainen, M. & Tang, J., 19 Feb 2019, In : Frontiers in Pharmacology. 10, 15 p., 126.

Research output: Contribution to journalReview ArticleScientificpeer-review

Open Access
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Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search

Younsi, R., Tang, J. & Holm, L. U. T., 29 Jan 2019, (Unpublished) In : arXiv.org .

Research output: Contribution to journalArticleGeneral public

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2018

Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling

Andersson, E. I., Pützer, S., Yadav, B., Dufva, O., Khan, S., He, L., Sellner, L., Schrader, A., Crispatzu, G., Oleś, M., Zhang, H., Adnan-Awad, S., Lagström, S., Bellanger, D., Mpindi, J. P., Eldfors, S., Pemovska, T., Pietarinen, P., Lauhio, A., Tomska, K. & 19 othersCuesta-Mateos, C., Faber, E., Koschmieder, S., Brümmendorf, T. H., Kytölä, S., Savolainen, E-R., Siitonen, T., Ellonen, P., Kallioniemi, O., Wennerberg, K., Ding, W., Stern, M-H., Huber, W., Anders, S., Tang, J., Aittokallio, T., Zenz, T., Herling, M. & Mustjoki, S., 2018, In : Leukemia. 32, 3, p. 774-787 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions

Tang, J., Tanoli, Z-R., Ravikumar, B., Alam, Z., Rebane, A., Vähä-Koskela, M., Peddinti, G., van Adrichem, A. J., Wakkinen, J., Jaiswal, A., Karjalainen, E., Gautam, P., He, L., Parri, E., Khan, S., Gupta, A., Ali, M., Yetukuri, L., Gustavsson, A-L., Seashore-Ludlow, B. & 6 othersHersey, A., Leach, A. R., Overington, J. P., Repasky, G., Wennerberg, K. & Aittokallio, T., 15 Feb 2018, In : Cell chemical biology. 25, 2, p. 224-+ 8 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Open Access
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Eltrombopag Promotes Megakaryocyte Survival and Signaling in the Presence of Specific Cytotoxic Agents

Javarappa, K. K., Tsallos, D., Zagidullin, B., Saad, J., Tang, J., Ramos, P. M., Pallaud, C. & Heckman, C. A., 2018, In : Blood. 132

Research output: Contribution to journalMeeting AbstractResearchpeer-review

Integrative bioinformatics of functional and genomic profiles for cancer systems medicine

Jaiswal, A., 2018, Helsinki: Helsingin yliopisto. 80 p.

Research output: ThesisDoctoral ThesisCollection of Articles

Loss-of-function mutations with circadian rhythm regulator Per1/Per2 lead to premature ovarian insufficiency\

Zheng, Y., Liu, C., Li, Y., Jiang, H., Yang, P., Tang, J., Xu, Y., Wang, H. & He, Y., 1 Nov 2018, In : Biology of Reproduction. 100, 4, p. 1066-1072 7 p.

Research output: Contribution to journalArticleScientificpeer-review

Methods for High-throughput Drug Combination Screening and Synergy Scoring

He, L., Kulesskiy, E., Saarela, J. S., Turunen, L. L., Wennerberg, J. K., Aittokallio, T. A. & Tang, J., 2018, Cancer Systems Biology. von Stechow, L. (ed.). New York: Humana Press, p. 351-398 48 p. (Methods in molecular biology; no. 1711).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

Multi-Parametric Single Cell Profiling Defines Distinct Drug Responses in Healthy Hematological Cell Lineages That Are Retained in Corresponding Malignant Cell Types

Majumder, MM., Leppä, A-M., Hellesøy, M., Dowling, P., Malyutina, A., Bazou, D., Andersson, E. I., Parsons, A., Tang, J., Kallioniemi, O-P., Mustjoki, S. M., O'Gorman, P., Wennerberg, J. K., Porkka, K. V. K., Gjertsen, B-T. & Heckman, C. A., 2018, In : Blood. 132

Research output: Contribution to journalMeeting AbstractResearchpeer-review

Open Access

Patient-Customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients

He, L., Tang, J., Andersson, E. I., Timonen, S., Koschmieder, S., Wennerberg, K., Mustjoki, S. & Aittokallio, T., 1 May 2018, In : Cancer Research. 78, 9, p. 2407-2418 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Precision Treatment of Acute Myeloid Leukemia: Predictive Response Biomarkers for BET inhibitor JQ1

Saad, J., 27 Sep 2018, 63 p.

Research output: ThesisMaster's thesisTheses

Open Access
2017

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

Gönen, M., Weir, B. A., Cowley, G. S., Vazquez, F., Guan, Y., Jaiswal, A., Karasuyama, M., Uzunangelov, V., Wang, T., Tsherniak, A., Howell, S., Marbach, D., Hoff, B., Norman, T. C., Airola, A., Bivol, A., Bunte, K., Carlin, D., Chopra, S., Deran, A. & 26 othersEllrott, K., Gopalacharyulu, P., Graim, K., Kaski, S., Khan, S. A., Newton, Y., Ng, S., Pahikkala, T., Paull, E., Sokolov, A., Tang, H., Tang, J., Wennerberg, K., Xie, Y., Zhan, X., Zhu, F., Aittokallio, T., Mamitsuka, H., Stuart, J. M., Boehm, J. S., Root, D. E., Xiao, G., Stolovitzky, G., Hahn, W. C., Margolin, A. A. & Broad-DREAM Community, 22 Nov 2017, In : Cell Systems. 5, 5, p. 485-+ 16 p.

Research output: Contribution to journalArticleScientificpeer-review

Informatics Approaches for Predicting, Understanding, and Testing Cancer Drug Combinations

Tang, J., 2017, Kinase Signaling Networks. Tan, A-C. & Huang, P. H. (eds.). 1st ed. ed. New York: Humana Press, p. 485-506 22 p. ( Methods in Molecular Biology; vol. 1636).

Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

JAK1/2 and BCL2 inhibitors synergize to counteract bone marrow stromal cell-induced protection of AML

Karjalainen, R., Pemovska, T., Popa, M., Liu, M., Javarappa, K. K., Majumder, M. M., Yadav, B., Tamborero, D., Tang, J., Bychkov, D., Kontro, M., Parsons, A., Suvela, M., Safont, M. M., Porkka, K., Aittokallio, T., Kallioniemi, O., McCormack, E., Gjertsen, B. T., Wennerberg, K. & 2 othersKnowles, J. & Heckman, C. A., 10 Aug 2017, In : Blood. 130, 6, p. 789-802 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access

Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells

Jaiswal, A., Peddinti, G., Akimov, Y., Wennerberg, K., Kuznetsov, S., Tang, J. & Aittokallio, T., 1 Jun 2017, In : Genome medicine. 9, 15 p., 51.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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SynergyFinder: a web application for analyzing drug combination dose-response matrix data

Ianevski, A., He, L., Aittokallio, T. & Tang, J., 1 Aug 2017, In : Bioinformatics. 33, 15, p. 2413-2415 3 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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The inconvenience of data of convenience: computational research beyond post-mortem analyses

Azencott, C-A., Aittokallio, T., Roy, S., Norman, T., Friend, S., Stolovitzky, G., Goldenberg, A., DREAM Idea Challenge Consortium & Tang, J., Oct 2017, In : Nature methods. 14, 10, p. 937-938 2 p.

Research output: Contribution to journalArticleScientific

Treatment of novel IL17A inhibitor in glioblastoma implementing 3rd generation co-culture cell line and patient-derived tumor model

Khan, M. S. S., Asif, M., Basheer, M. K. A., Kang, C. W., Al-Suede, F. S., Ein, O. C., Tang, J., Majid, A. S. A. & Majid, A. M. S. A., 15 May 2017, In : European Journal of Pharmacology. 803, p. 24-38 15 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2016

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Sieberts, S. K., Zhu, F., Garcia-Garcia, J., Stahl, E., Pratap, A., Pandey, G., Pappas, D., Aguilar, D., Anton, B., Bonet, J., Eksi, R., Fornes, O., Guney, E., Li, H., Marin, M. A., Panwar, B., Planas-Iglesias, J., Poglayen, D., Cui, J., Falcao, A. O. & 31 othersSuver, C., Hoff, B., Balagurusamy, V. S. K., Dillenberger, D., Neto, E. C., Norman, T., Aittokallio, T., Ammad-ud-din, M., Azencott, C-A., Bellon, V., Boeva, V., Bunte, K., Chheda, H., Cheng, L., Corander, J., Dumontier, M., Goldenberg, A., Gopalacharyulu, P., Hajiloo, M., Hidru, D., Jaiswal, A., Kaski, S., Khalfaoui, B., Khan, S. A., Kramer, E. R., Marttinen, P., Pirinen, M., Saarela, J., Tang, J., Wennerberg, K. & Rheumatoid Arth Challenge, Aug 2016, In : Nature Communications. 7, 9 p., 12460.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2015

A Bayesian Predictive Model for Clustering Data of Mixed Discrete and Continuous Type

Blomstedt, P., Tang, J., Xiong, J., Granlund, C. & Corander, J., Mar 2015, In : IEEE Transactions on Pattern Analysis and Machine Intelligence. 37, 3, p. 489-498 10 p.

Research output: Contribution to journalArticleScientificpeer-review

From drug response profiling to target addiction scoring in cancer cell models

Yadav, B., Gopalacharyulu, P., Pemovska, T., Khan, S. A., Szwajda, A., Tang, J., Wennerberg, K. & Aittokallio, T., Oct 2015, In : Disease Models & Mechanisms. 8, 10, p. 1255-1264 10 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Network pharmacology applications to map the unexplored target space and therapeutic potential of natural products

Kibble, M., Saarinen, N., Tang, J., Wennerberg, K., Makela, S. & Aittokallio, T., 2015, In : Natural Product Reports. 32, 8, p. 1249-1266 18 p.

Research output: Contribution to journalReview ArticleScientificpeer-review

Open Access
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Systematic Mapping of Kinase Addiction Combinations in Breast Cancer Cells by Integrating Drug Sensitivity and Selectivity Profiles

Szwajda, A., Gautam, P., Karhinen, L., Jha, S. K., Saarela, J., Shakyawar, S., Turunen, L., Yadav, B., Tang, J., Wennerberg, K. & Aittokallio, T., 20 Aug 2015, In : Chemistry & Biology. 22, 8, p. 1144-1155 12 p.

Research output: Contribution to journalArticleScientificpeer-review

TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples

He, L., Wennerberg, K., Aittokallio, T. & Tang, J., 1 Jun 2015, In : Bioinformatics. 31, 11, p. 1866-1868 3 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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Toward more realistic drug-target interaction predictions

Pahikkala, T., Airola, A., Pietila, S., Shakyawar, S., Szwajda, A., Tang, J. & Aittokallio, T., Mar 2015, In : Briefings in Bioinformatics. 16, 2, p. 325-337 13 p.

Research output: Contribution to journalArticleScientificpeer-review

What is synergy? The Saariselka agreement revisited

Tang, J., Wennerberg, K. & Aittokallio, T., 1 Sep 2015, In : Frontiers in Pharmacology. 6, 5 p., 181.

Research output: Contribution to journalReview ArticleScientificpeer-review

Open Access
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2014

Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis

Tang, J., Szwajda, A., Shakyawar, S., Xu, T., Hintsanen, P., Wennerberg, K. & Aittokallio, T., Mar 2014, In : Journal of Chemical Information and Modeling. 54, 3, p. 735-743 9 p.

Research output: Contribution to journalArticleScientificpeer-review

Network Pharmacology Strategies Toward Multi-Target Anticancer Therapies: From Computational Models to Experimental Design Principles

Tang, J. & Aittokallio, T., Jan 2014, In : Current Pharmaceutical Design. 20, 1, p. 23-36 14 p.

Research output: Contribution to journalArticleScientificpeer-review

2013

Genomic, Transcriptomic, and Lipidomic Profiling Highlights the Role of Inflammation in Individuals With Low High-density Lipoprotein Cholesterol

Laurila, P-P., Surakka, I., Sarin, A-P., Yetukuri, L., Hyotylainen, T., Söderlund, S., Naukkarinen, J., Tang, J., Kettunen, J., Mirel, D. B., Soronen, J., Lehtimaki, T., Ruokonen, A., Ehnholm, C., Eriksson, J. G., Salomaa, V., Jula, A., Raitakari, O. T., Jarvelin, M-R., Palotie, A. & 5 othersPalotie, L., Oresic, M., Jauhiainen, M., Taskinen, M-R. & Ripatti, S., Apr 2013, In : Arteriosclerosis, Thrombosis, and Vascular Biology. 33, 4, p. 847-U510 39 p.

Research output: Contribution to journalArticleScientificpeer-review

Target Inhibition Networks: Predicting Selective Combinations of Druggable Targets to Block Cancer Survival Pathways

Tang, J., Karhinen, L., Xu, T., Szwajda, A., Yadav, B., Wennerberg, K. & Aittokallio, T., Sep 2013, In : PLoS Computational Biology. 9, 9, p. Article Number: e1003226 16 p.

Research output: Contribution to journalArticleScientificpeer-review

2012

Phospholipids and insulin resistance in psychosis: a lipidomics study of twin pairs discordant for schizophrenia

Oresic, M., Seppänen-Laakso, T., Sun, D., Tang, J., Therman, S., Viehman, R., Mustonen, U., van Erp, T. G. M., Hyötyläinen, T., Thompson, P., Toga, A. W., Huttunen, M. O., Suvisaari, J., Kaprio, J., Lönnqvist, J. & Cannon, T. D., 2012, In : Genome medicine. 4, 1, 11 p.

Research output: Contribution to journalArticleScientificpeer-review

Open Access
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2011

Association of Lipidome Remodeling in the Adipocyte Membrane with Acquired Obesity in Humans

Pietiläinen, K. H., Rog, T., Seppanen-Laakso, T., Virtue, S., Gopalacharyulu, P., Tang, J., Rodriguez-Cuenca, S., Maciejewski, A., Naukkarinen, J., Ruskeepaa, A-L., Niemela, P. S., Yetukuri, L., Tan, C. Y., Velagapudi, V., Castillo, S., Nygren, H., Hyotylainen, T., Rissanen, A., Kaprio, J., Yki-Järvinen, H. & 3 othersVattulainen, I., Vidal-Puig, A. & Oresic, M., 2011, In : PLoS Biology. 9, 6, p. - 14 p.

Research output: Contribution to journalArticleScientificpeer-review

Metabolome in schizophrenia and other psychotic disorders: a general population study.

Orešič, M., Tang, J., Seppänen-Laakso, T., Mattila, I., Saarni, S. E. M., Saarni, S. I., Lönnqvist, J., Sysiaho, M., Hyotylainen, T., Perala, J. & Suvisaari, J., 2011, In : Genome medicine. 3, 19, 14 p.

Research output: Contribution to journalArticleScientificpeer-review

2009

Bayesian clustering of fuzzy feature vectors using a quasi-likelihood approach

Marttinen, P., Tang, J., De Baets, B., Dawyndt, P. & Corander, J., 2009, In : IEEE Transactions on Pattern Analysis and Machine Intelligence. 31, 1, p. 74-85 12 p.

Research output: Contribution to journalArticleScientificpeer-review

Hyper-Recombination, Diversity, and Antibiotic Resistance in Pneumococcus

Hanage, W. P., Fraser, C., Tang, J., Connor, T. R. & Corander, J., 2009, In : Science. 324, 5933, p. 1454-1457 4 p.

Research output: Contribution to journalArticleScientificpeer-review

Identifying currents in the gene pool for bacterial populations using an integrative approach

Tang, J., Hanage, W., Fraser, C. & Corander, J., 2009, In : PLoS Computational Biology. 5, 8, p. e1000455 18 p.

Research output: Contribution to journalArticleScientificpeer-review

Integrating post-genomic approaches as a strategy to advance our understanding of health and disease

Tang, J., Tan, C., Oresic, M. & Vidal-Puig, A., 2009, In : Genome medicine. 1, 3, p. 35 1 p.

Research output: Contribution to journalArticleScientificpeer-review

2008

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

Corander, J., Marttinen, P., Siren, J. & Tang, J., 2008, In : BMC Bioinformatics. 9, 14 p.

Research output: Contribution to journalArticleScientificpeer-review

2007

Bayesian analysis of population structure based on linked molecular information

Corander, J. & Tang, J., 2007, In : Mathematical Biosciences. 205, 1, p. 19-31 13 p.

Research output: Contribution to journalArticleScientificpeer-review