Breeze: an integrated quality control and data analysis application for high-throughput drug screening
Potdar, Swapnil, Ianevski, Aleksandr, Mpindi, John-Patrick, Bychkov, Dmitrii, Fiere, Clément, Ianevski, Philipp, Yadav, Bhagwan, Wennerberg, Krister, Aittokallio, Tero, Kallioniemi, Olli, Saarela, Jani, Östling, Päivi
Published in Bioinformatics (01.06.2020)
Published in Bioinformatics (01.06.2020)
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High-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells
Hongisto, Vesa, Jernström, Sandra, Fey, Vidal, Mpindi, John-Patrick, Kleivi Sahlberg, Kristine, Kallioniemi, Olli, Perälä, Merja
Published in PloS one (23.10.2013)
Published in PloS one (23.10.2013)
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A comprehensive panel of three-dimensional models for studies of prostate cancer growth, invasion and drug responses
Härmä, Ville, Virtanen, Johannes, Mäkelä, Rami, Happonen, Antti, Mpindi, John-Patrick, Knuuttila, Matias, Kohonen, Pekka, Lötjönen, Jyrki, Kallioniemi, Olli, Nees, Matthias
Published in PloS one (03.05.2010)
Published in PloS one (03.05.2010)
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A community effort to assess and improve drug sensitivity prediction algorithms
Costello, James C, Heiser, Laura M, Georgii, Elisabeth, Gönen, Mehmet, Menden, Michael P, Wang, Nicholas J, Bansal, Mukesh, Ammad-ud-din, Muhammad, Hintsanen, Petteri, Khan, Suleiman A, Mpindi, John-Patrick, Kallioniemi, Olli, Honkela, Antti, Aittokallio, Tero, Wennerberg, Krister, Collins, James J, Gallahan, Dan, Singer, Dinah, Saez-Rodriguez, Julio, Kaski, Samuel, Gray, Joe W, Stolovitzky, Gustavo
Published in Nature biotechnology (01.12.2014)
Published in Nature biotechnology (01.12.2014)
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A community computational challenge to predict the activity of pairs of compounds
Bansal, Mukesh, Yang, Jichen, Karan, Charles, Menden, Michael P, Costello, James C, Tang, Hao, Xiao, Guanghua, Li, Yajuan, Allen, Jeffrey, Zhong, Rui, Chen, Beibei, Kim, Minsoo, Wang, Tao, Heiser, Laura M, Realubit, Ronald, Mattioli, Michela, Alvarez, Mariano J, Shen, Yao, Gallahan, Daniel, Singer, Dinah, Saez-Rodriguez, Julio, Xie, Yang, Stolovitzky, Gustavo, Califano, Andrea
Published in Nature biotechnology (01.12.2014)
Published in Nature biotechnology (01.12.2014)
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High-throughput RNAi screening for novel modulators of vimentin expression identifies MTHFD2 as a regulator of breast cancer cell migration and invasion
Lehtinen, Laura, Ketola, Kirsi, Mäkelä, Rami, Mpindi, John-Patrick, Viitala, Miro, Kallioniemi, Olli, Iljin, Kristiina
Published in Oncotarget (01.01.2013)
Published in Oncotarget (01.01.2013)
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Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues
Kilpinen, Sami, Autio, Reija, Ojala, Kalle, Iljin, Kristiina, Bucher, Elmar, Sara, Henri, Pisto, Tommi, Saarela, Matti, Skotheim, Rolf I, Björkman, Mari, Mpindi, John-Patrick, Haapa-Paananen, Saija, Vainio, Paula, Edgren, Henrik, Wolf, Maija, Astola, Jaakko, Nees, Matthias, Hautaniemi, Sampsa, Kallioniemi, Olli
Published in Genome biology (19.09.2008)
Published in Genome biology (19.09.2008)
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Arachidonic Acid Pathway Members PLA2G7 , HPGD , EPHX2 , and CYP4F8 Identified as Putative Novel Therapeutic Targets in Prostate Cancer
Vainio, Paula, Gupta, Santosh, Ketola, Kirsi, Mirtti, Tuomas, Mpindi, John-Patrick, Kohonen, Pekka, Fey, Vidal, Perälä, Merja, Smit, Frank, Verhaegh, Gerald, Schalken, Jack, Alanen, Kalle A, Kallioniemi, Olli, Iljin, Kristiina
Published in The American journal of pathology (01.02.2011)
Published in The American journal of pathology (01.02.2011)
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Prediction of human population responses to toxic compounds by a collaborative competition
Eduati, Federica, Mangravite, Lara M, Wang, Tao, Tang, Hao, Bare, J Christopher, Huang, Ruili, Norman, Thea, Kellen, Mike, Menden, Michael P, Yang, Jichen, Zhan, Xiaowei, Zhong, Rui, Xiao, Guanghua, Xia, Menghang, Abdo, Nour, Kosyk, Oksana, Friend, Stephen, Dearry, Allen, Simeonov, Anton, Tice, Raymond R, Rusyn, Ivan, Wright, Fred A, Stolovitzky, Gustavo, Xie, Yang, Saez-Rodriguez, Julio
Published in Nature biotechnology (01.09.2015)
Published in Nature biotechnology (01.09.2015)
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Anagrelide for Gastrointestinal Stromal Tumor
Pulkka, Olli-Pekka, Gebreyohannes, Yemarshet K, Wozniak, Agnieszka, Mpindi, John-Patrick, Tynninen, Olli, Icay, Katherine, Cervera, Alejandra, Keskitalo, Salla, Murumägi, Astrid, Kulesskiy, Evgeny, Laaksonen, Maria, Wennerberg, Krister, Varjosalo, Markku, Laakkonen, Pirjo, Lehtonen, Rainer, Hautaniemi, Sampsa, Kallioniemi, Olli, Schöffski, Patrick, Sihto, Harri, Joensuu, Heikki
Published in Clinical cancer research (01.03.2019)
Published in Clinical cancer research (01.03.2019)
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ITGB1-dependent upregulation of Caveolin-1 switches TGFβ signalling from tumour-suppressive to oncogenic in prostate cancer
Pellinen, Teijo, Blom, Sami, Sánchez, Sara, Välimäki, Katja, Mpindi, John-Patrick, Azegrouz, Hind, Strippoli, Raffaele, Nieto, Raquel, Vitón, Mariano, Palacios, Irene, Turkki, Riku, Wang, Yinhai, Sánchez-Alvarez, Miguel, Nordling, Stig, Bützow, Anna, Mirtti, Tuomas, Rannikko, Antti, Montoya, María C., Kallioniemi, Olli, del Pozo, Miguel A.
Published in Scientific reports (05.02.2018)
Published in Scientific reports (05.02.2018)
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High-throughput transcriptomic and RNAi analysis identifies AIM1, ERGIC1, TMED3 and TPX2 as potential drug targets in prostate cancer
Vainio, Paula, Mpindi, John-Patrick, Kohonen, Pekka, Fey, Vidal, Mirtti, Tuomas, Alanen, Kalle A, Perälä, Merja, Kallioniemi, Olli, Iljin, Kristiina
Published in PloS one (28.06.2012)
Published in PloS one (28.06.2012)
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A functional genetic screen reveals new regulators of β1-integrin activity
Pellinen, Teijo, Rantala, Juha K, Arjonen, Antti, Mpindi, John-Patrick, Kallioniemi, Olli, Ivaska, Johanna
Published in Journal of cell science (01.02.2012)
Published in Journal of cell science (01.02.2012)
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REG4 Is Highly Expressed in Mucinous Ovarian Cancer: A Potential Novel Serum Biomarker
Lehtinen, Laura, Vesterkvist, Pia, Roering, Pia, Korpela, Taina, Hattara, Liisa, Kaipio, Katja, Mpindi, John-Patrick, Hynninen, Johanna, Auranen, Annika, Davidson, Ben, Haglund, Caj, Iljin, Kristiina, Grenman, Seija, Siitari, Harri, Carpen, Olli
Published in PloS one (16.03.2016)
Published in PloS one (16.03.2016)
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A cell spot microarray method for production of high density siRNA transfection microarrays
Rantala, Juha K, Mäkelä, Rami, Aaltola, Anna-Riina, Laasola, Petra, Mpindi, John-Patrick, Nees, Matthias, Saviranta, Petri, Kallioniemi, Olli
Published in BMC genomics (28.03.2011)
Published in BMC genomics (28.03.2011)
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High miR-30 Expression Associates with Improved Breast Cancer Patient Survival and Treatment Outcome
Jamshidi, Maral, Fagerholm, Rainer, Muranen, Taru A., Kaur, Sippy, Potdar, Swapnil, Khan, Sofia, Netti, Eliisa, Mpindi, John-Patrick, Yadav, Bhagwan, Kiiski, Johanna I., Aittomäki, Kristiina, Heikkilä, Päivi, Saarela, Jani, Bützow, Ralf, Blomqvist, Carl, Nevanlinna, Heli
Published in Cancers (10.06.2021)
Published in Cancers (10.06.2021)
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Plasticity of blood- and lymphatic endothelial cells and marker identification
Keuschnigg, Johannes, Karinen, Sirkku, Auvinen, Kaisa, Irjala, Heikki, Mpindi, John-Patrick, Kallioniemi, Olli, Hautaniemi, Sampsa, Jalkanen, Sirpa, Salmi, Marko
Published in PloS one (10.09.2013)
Published in PloS one (10.09.2013)
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Journal Article
Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data
Mpindi, John-Patrick, Swapnil, Potdar, Dmitrii, Bychkov, Jani, Saarela, Saeed, Khalid, Wennerberg, Krister, Aittokallio, Tero, Östling, Päivi, Kallioniemi, Olli
Published in Bioinformatics (Oxford, England) (01.12.2015)
Published in Bioinformatics (Oxford, England) (01.12.2015)
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Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs
Khan, Suleiman A, Faisal, Ali, Mpindi, John Patrick, Parkkinen, Juuso A, Kalliokoski, Tuomo, Poso, Antti, Kallioniemi, Olli P, Wennerberg, Krister, Kaski, Samuel
Published in BMC bioinformatics (30.05.2012)
Published in BMC bioinformatics (30.05.2012)
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