Suleiman Ali Khan

Publications

Research output per year 2012 2016 2017 2019 2021 2023

• 17 Article
• 4 Conference contribution
• 3 Meeting Abstract
• 1 Chapter
• 2 More
  • 1 Conference article
  • 1 Review Article

Research output per year

Research output per year

Search results

• 2023

  A Generalized Deep Learning Model for Multi-disease Chest X-Ray Diagnostics

  Bajwa, N., Bajwa, K., Shakeel, M. F., Rana, A., Haqqi, K. & Khan, S., 2023, Advances in Computational Intelligence - 17th International Work-Conference on Artificial Neural Networks, IWANN 2023, Proceedings. Rojas, I., Joya, G. & Catala, A. (eds.). Springer Science and Business Media Deutschland GmbH, p. 541-552 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 14134 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

• Drug response profiles in patient-derived cancer cells across histological subtypes of ovarian cancer: real-time therapy tailoring for a patient with low-grade serous carcinoma

  Murumägi, A., Ungureanu, D., Khan, S., Arjama, M., Välimäki, K., Ianevski, A., Ianevski, P., Bergstrom, R., Dini, A., Kanerva, A., Koivisto-Korander, R., Tapper, J., Lassus, H., Loukovaara, M., Mägi, A., Hirasawa, A., Aoki, D., Pietiäinen, V., Pellinen, T. & Butzow, R. & 2 others, Aittokallio, T. & Kallioniemi, O., 16 Feb 2023, In: British Journal of Cancer. 128, 4, p. 678–690 13 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2022

  Adaptive Weight Aggregation in Federated Learning for Brain Tumor Segmentation

  Khan, M. I., Jafaritadi, M., Alhoniemi, E., Kontio, E. & Khan, S. A., 2022, Lecture Notes in Computer Science. Springer International Publishing AG, Vol. 12963. p. 455-469 15 p. (Lecture Notes in Computer Science).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review
• 2021

  Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia

  White, B. S., Khan, S. A., Mason, M. J., Ammad-ud-din, M., Potdar, S., Malani, D., Kuusanmäki, H., Druker, B. J., Heckman, C., Kallioniemi, O., Kurtz, S. E., Porkka, K., Tognon, C. E., Tyner, J. W., Aittokallio, T., Wennerberg, K. & Guinney, J., 23 Jul 2021, In: npj precision oncology. 5, 1, 11 p., 71.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• COVID-19 Detection via Image Classification using Deep Learning on Chest X-Ray

  Azeem, M. A., Khan, M. I. & Khan, S. A., 2021, 2021 Ethics and Explainability for Responsible Data Science (EE-RDS). IEEE

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review

• Modeling Public Sentiments About JUUL Flavors on Twitter Through Machine Learning

  Malik, A., Khan, M. I., Karbasian, H., Nieminen, M., Ammad-Ud-Din, M. & Khan, S. A., Nov 2021, In: Nicotine & Tobacco Research. 23, 11, p. 1869-1879 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review
• 2020

  An integrative machine learning approach to discovering multi-level molecular mechanisms of obesity using data from monozygotic twin pairs

  Kibble, M., Khan, S. A., Ammad-ud-din, M., Bollepalli, S., Palviainen, T., Kaprio, J., Pietiläinen, K. H. & Ollikainen, M., 21 Oct 2020, In: Royal Society Open Science. 7, 10, 21 p., 200872.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2019

  Clinical implementation of precision systems oncology in the treatment of ovarian cancer based on ex-vivo drug testing and molecular profiling

  Murumagi, A., Ungureanu, D., Khan, S., Hirasawa, A., Arjama, M., Valimaki, K., Mikkonen, P., Niininen, W., Kumar, A., Eldfors, S., Pellinen, T., Pietiainen, V., Magi, A., Koivisto-Korander, R., Tapper, J., Loukovaara, M., Aittokallio, T., Butzow, R. & Kallioniemi, O., Jul 2019, In: Cancer Research. 79, 13, 2 p.

  Research output: Contribution to journal › Meeting Abstract › peer-review

• Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

  Menden, M. P., Wang, D., Mason, M. J., Szalai, B., Bulusu, K. C., Guan, Y., Yu, T., Kang, J., Jeon, M., Wolfinger, R., Nguyen, T., Zaslavskiy, M., Abante, J., Abecassis, B. S., Aben, N., Aghamirzaie, D., Aittokallio, T., Akhtari, F. S., Al-lazikani, B. & Alam, T. & 280 others, Allam, A., Allen, C., de Almeida, M. P., Altarawy, D., Alves, V., Amadoz, A., Anchang, B., Antolin, A. A., Ash, J. R., Aznar, V. R., Ba-alawi, W., Bagheri, M., Bajic, V., Ball, G., Ballester, P. J., Baptista, D., Bare, C., Bateson, M., Bender, A., Bertrand, D., Wijayawardena, B., Boroevich, K. A., Bosdriesz, E., Bougouffa, S., Bounova, G., Brouwer, T., Bryant, B., Calaza, M., Calderone, A., Calza, S., Capuzzi, S., Carbonell-Caballero, J., Carlin, D., Carter, H., Castagnoli, L., Celebi, R., Cesareni, G., Chang, H., Chen, G., Chen, H., Chen, H., Cheng, L., Chernomoretz, A., Chicco, D., Cho, K.-H., Cho, S., Choi, D., Choi, J., Choi, K., Choi, M., Cock, M. D., Coker, E., Cortes-Ciriano, I., Cserzö, M., Cubuk, C., Curtis, C., Daele, D. V., Dang, C. C., Dijkstra, T., Dopazo, J., Draghici, S., Drosou, A., Dumontier, M., Ehrhart, F., Eid, F.-E., ElHefnawi, M., Elmarakeby, H., van Engelen, B., Engin, H. B., de Esch, I., Evelo, C., Falcao, A. O., Farag, S., Fernandez-Lozano, C., Fisch, K., Flobak, A., Fornari, C., Foroushani, A. B. K., Fotso, D. C., Fourches, D., Friend, S., Frigessi, A., Gao, F., Gao, X., Gerold, J. M., Gestraud, P., Ghosh, S., Gillberg, J., Godoy-Lorite, A., Godynyuk, L., Godzik, A., Goldenberg, A., Gomez-Cabrero, D., Gonen, M., de Graaf, C., Gray, H., Grechkin, M., Guimera, R., Guney, E., Haibe-Kains, B., Han, Y., Hase, T., He, D., He, L., Heath, L. S., Hellton, K. H., Helmer-Citterich, M., Hidalgo, M. R., Hidru, D., Hill, S. M., Hochreiter, S., Hong, S., Hovig, E., Hsueh, Y.-C., Hu, Z., Huang, J. K., Huang, R. S., Hunyady, L., Hwang, J., Hwang, T. H., Hwang, W., Hwang, Y., Isayev, O., Don’t Walk, O. B., Jack, J., Jahandideh, S., Ji, J., Jo, Y., Kamola, P. J., Kanev, G. K., Karacosta, L., Karimi, M., Kaski, S., Kazanov, M., Khamis, A. M., Khan, S. A., Kiani, N. A., Kim, A., Kim, J., Kim, J., Kim, K., Kim, K., Kim, S., Kim, Y., Kim, Y., Kirk, P. D. W., Kitano, H., Klambauer, G., Knowles, D., Ko, M., Kohn-Luque, A., Kooistra, A. J., Kuenemann, M. A., Kuiper, M., Kurz, C., Kwon, M., van Laarhoven, T., Laegreid, A., Lederer, S., Lee, H., Lee, J., Lee, Y. W., Lepp_aho, E., Lewis, R., Li, J., Li, L., Liley, J., Lim, W. K., Lin, C., Liu, Y., Lopez, Y., Low, J., Lysenko, A., Machado, D., Madhukar, N., Maeyer, D. D., Malpartida, A. B., Mamitsuka, H., Marabita, F., Marchal, K., Marttinen, P., Mason, D., Mazaheri, A., Mehmood, A., Mehreen, A., Michaut, M., Miller, R. A., Mitsopoulos, C., Modos, D., Moerbeke, M. V., Moo, K., Motsinger-Reif, A., Movva, R., Muraru, S., Muratov, E., Mushthofa, M., Nagarajan, N., Nakken, S., Nath, A., Neuvial, P., Newton, R., Ning, Z., Niz, C. D., Oliva, B., Olsen, C., Palmeri, A., Panesar, B., Papadopoulos, S., Park, J., Park, S., Park, S., Pawitan, Y., Peluso, D., Pendyala, S., Peng, J., Perfetto, L., Pirro, S., Plevritis, S., Politi, R., Poon, H., Porta, E., Prellner, I., Preuer, K., Pujana, M. A., Ramnarine, R., Reid, J. E., Reyal, F., Richardson, S., Ricketts, C., Rieswijk, L., Rocha, M., Rodriguez-Gonzalvez, C., Roell, K., Rotroff, D., de Ruiter, J. R., Rukawa, P., Sadacca, B., Safikhani, Z., Safitri, F., Sales-Pardo, M., Sauer, S., Schlichting, M., Seoane, J. A., Serra, J., Shang, M.-M., Sharma, A., Sharma, H., Shen, Y., Shiga, M., Shin, M., Shkedy, Z., Shopsowitz, K., Sinai, S., Skola, D., Smirnov, P., Soerensen, I. F., Soerensen, P., Song, J.-H., Song, S. O., Soufan, O., Spitzmueller, A., Steipe, B., Suphavilai, C., Tamayo, S. P., Tamborero, D., Tang, J., Tanoli, Z.-U.-R., Tarres-Deulofeu, M., Tegner, J., Thommesen, L., Tonekaboni, S. A. M., Tran, H., Troyer, E. D., Truong, A., Tsunoda, T., Turu, G., Tzeng, G.-Y., Verbeke, L., Videla, S. & Consortium, A.-S. D. C. D., 17 Jun 2019, In: Nature Communications. 10, 1, 17 p., 2674.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Matrix and Tensor Factorization Methods for Toxicogenomic Modeling and Prediction

  Khan, S. A., Aittokallio, T., Scherer, A., Grafström, R. C. & Kohonen, P., May 2019, Advances in Computational Toxicology: Methodologies and Applications in Regulatory Science. Hong, H. (ed.). Cham: Springer International Publishing AG, p. 57-74 18 p. (Challenges and Advances in Computational Chemistry and Physics; vol. 30).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter › Scientific › peer-review

  Open Access

  File

• Novel Screening Method Identifies PI3K alpha, mTOR, and IGF1R as Key Kinases Regulating Cardiomyocyte Survival

  Elmadani, M., Khan, S., Tenhunen, O., Magga, J., Aittokallio, T., Wennerberg, K. & Kerkelä, R., 5 Nov 2019, In: Journal of the American Heart Association. 8, 21, 51 p., 013018.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 2018

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

  Tang, J., Tanoli, Z.-U.-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 others, Hersey, 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 journal › Article › Scientific › peer-review

  Open Access

  File

• Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach

  Ali, M., Khan, S. A., Wennerberg, K. & Aittokallio, T., 15 Apr 2018, In: Bioinformatics. 34, 8, p. 1353-1362 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File
• 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 others, Ellrott, 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 journal › Article › Scientific › peer-review

• Identifying ovarian cancer specific targeted drugs using high-throughput drug sensitivity profiles of primary cancer cells

  Murumagi, A., Hirasawa, A., Khan, S., Ungureanu, D., Arjama, M., Pellinen, T., Eldfors, S., Koivisto-Korander, R., Leminen, A., Butzow, R., Aittokallio, T. & Kallioniemi, O., Jul 2017, In: Cancer Research. 77, Supplement 13, 2 p., 410.

  Research output: Contribution to journal › Meeting Abstract › peer-review

• Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data

  Guinney, J., Wang, T., Laajala, T. D., Winner, K. K., Bare, J. C., Neto, E. C., Khan, S. A., Peddinti, G., Airola, A., Pahikkala, T., Mirtti, T., Yu, T., Bot, B. M., Shen, L., Abdallah, K., Norman, T., Friend, S., Stolovitzky, G., Soule, H. & Sweeney, C. J. & 8 others, Ryan, C. J., Scher, H. I., Sartor, O., Xie, Y., Aittokallio, T., Zhou, F. L., Costello, J. C. & Prostate Canc Challenge DREAM Comm, Jan 2017, In: Lancet Oncology. 18, 1, p. 132-142 11 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression

  Ammad-ud-din, M., Khan, S. A., Wennerberg, K. & Aittokallio, T., 15 Jul 2017, In: Bioinformatics. 33, 14, p. I359-I368 10 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access
• 2016

  Bayesian multi-tensor factorization

  Khan, S. A., Leppaaho, E. & Kaski, S., Nov 2016, In: Machine Learning. 105, 2, p. 233-253 21 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

  File

• 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 others, Suver, 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 journal › Article › Scientific › peer-review

  Open Access

  File

• Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization

  Ammad-ud-din, M., Khan, S. A., Malani, D., Murumägi, A., Kallioniemi, O., Aittokallio, T. & Kaski, S., 1 Sept 2016, In: Bioinformatics. 32, 17, p. 455-463 9 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

• Novel therapeutic possibilities for chemorefractory ovarian cancer patients identified by functional ex vivo drug sensitivity testing of primary cells

  Murumagi, A., Hirasawa, A., Khan, S., Arjama, M., Pellinen, T., Koivisto-Korander, R., Leminen, A., Magi, A., Aittokallio, T., Butzow, R. & Kallioniemi, O., Oct 2016, In: International Journal of Gynecological Cancer. 26, p. 653-653 1 p.

  Research output: Contribution to journal › Meeting Abstract › peer-review

• Transcriptional response networks for elucidating mechanisms of action of multitargeted agents

  Kibble, M., Khan, S. A., Saarinen, N., Iorio, F., Saez-Rodriguez, J., Makela, S. & Aittokallio, T., Jul 2016, In: Drug Discovery Today. 21, 7, p. 1063-1075 13 p.

  Research output: Contribution to journal › Review Article › peer-review

  Open Access

  File
• 2015

  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 journal › Article › Scientific › peer-review

  Open Access

  File
• 2014

  A community effort to assess and improve drug sensitivity prediction algorithms

  Costello, J. C., Heiser, L. M., Georgii, E., Gonen, M., Menden, M. P., Wang, N. J., Bansal, M., Ammad-ud-din, M., Hintsanen, P., Khan, S. A., Mpindi, J.-P., Kallioniemi, O., Honkela, A., Aittokallio, T., Wennerberg, K., Collins, J. J., Gallahan, D., Singer, D., Saez-Rodriguez, J. & Kaski, S. & 3 others, Gray, J. W., Stolovitzky, G. & NCI DREAM Community, Dec 2014, In: Nature Biotechnology. 32, 12, p. 1202-U57 13 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

• Bayesian multi-view tensor factorization

  Khan, S. A. & Kaski, S., 2014, Machine Learning and Knowledge Discovery in Databases: European Conference, ECML PKDD 2014, Nancy, France, September 15-19, 2014. Proceedings. Calders, T., Esposito, F., Hüllermeier, E. & Meo, R. (eds.). Heidelberg: Springer-Verlag, Vol. 1. p. 656-671 16 p. (Lecture Notes in Computer Science; vol. 8724).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Scientific › peer-review
• 2012

  Bayesian Group Factor Analysis

  Virtanen, S., Klami, A., Khan, S. A. & Kaski, S., 2012, In: JMRL : Workshop and Conference Proceedings. 22, p. 1269-1277 9 p.

  Research output: Contribution to journal › Conference article › Scientific › peer-review

• Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

  Khan, S. A., Faisal, A., Mpindi, J. P., Parkkinen, J. A., Kalliokoski, T., Poso, A., Kallioniemi, O. P., Wennerberg, K. & Kaski, S., 30 May 2012, In: BMC Bioinformatics. 13, p. Article Number: 112 14 p.

  Research output: Contribution to journal › Article › Scientific › peer-review

  Open Access

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