A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection von Fourati, Slim, Talla, Aarthi, Mahmoudian, Mehrad, Burkhart, Joshua G., Klén, Riku, Henao, Ricardo, Yu, Thomas, Aydın, Zafer, Yeung, Ka Yee, Ahsen, Mehmet Eren, Almugbel, Reem, Jahandideh, Samad, Liang, Xiao, Nordling, Torbjörn E. M., Shiga, Motoki, Stanescu, Ana, Vogel, Robert, Pandey, Gaurav, Chiu, Christopher, McClain, Micah T., Woods, Christopher W., Ginsburg, Geoffrey S., Elo, Laura L., Tsalik, Ephraim L., Mangravite, Lara M., Sieberts, Solveig K.

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A Crowdsourcing Approach to Develop Machine Learning Models to Quantify Radiographic Joint Damage in Rheumatoid Arthritis von Sun, Dongmei, Nguyen, Thanh M, Allaway, Robert J, Wang, Jelai, Chung, Verena, Yu, Thomas V, Mason, Michael, Dimitrovsky, Isaac, Ericson, Lars, Li, Hongyang, Guan, Yuanfang, Israel, Ariel, Olar, Alex, Pataki, Balint Armin, Stolovitzky, Gustavo, Guinney, Justin, Gulko, Percio S, Frazier, Mason B, Chen, Jake Y, Costello, James C, Bridges, Jr, S Louis

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Targeted serum proteomics of longitudinal samples from newly diagnosed youth with type 1 diabetes distinguishes markers of disease and C-peptide trajectory von Moulder, Robert, Välikangas, Tommi, Hirvonen, M. Karoliina, Suomi, Tomi, Brorsson, Caroline A., Lietzén, Niina, Bruggraber, Sylvaine F. A., Overbergh, Lut, Dunger, David B., Peakman, Mark, Chmura, Piotr J., Brunak, Soren, Schulte, Anke M., Mathieu, Chantal, Knip, Mikael, Elo, Laura L., Lahesmaa, Riitta

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Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics von Yang, Mi, Petralia, Francesca, Li, Zhi, Li, Hongyang, Ma, Weiping, Song, Xiaoyu, Kim, Sunkyu, Lee, Heewon, Yu, Han, Lee, Bora, Bae, Seohui, Heo, Eunji, Kaczmarczyk, Jan, Stępniak, Piotr, Warchoł, Michał, Yu, Thomas, Calinawan, Anna P., Boutros, Paul C., Payne, Samuel H., Reva, Boris, Aderinwale, Tunde, Afyounian, Ebrahim, Agrawal, Piyush, Ali, Mehreen, Amadoz, Alicia, Azuaje, Francisco, Bachman, John, Bae, Seohui, Bhalla, Sherry, Carbonell-Caballero, José, Chakraborty, Priyanka, Chaudhary, Kumardeep, Choi, Yonghwa, Choi, Yoonjung, Çubuk, Cankut, Dhanda, Sandeep Kumar, Dopazo, Joaquín, Elo, Laura L., Fóthi, Ábel, Gevaert, Olivier, Granberg, Kirsi, Greiner, Russell, Heo, Eunji, Hidalgo, Marta R., Jayaswal, Vivek, Jeon, Hwisang, Jeon, Minji, Kalmady, Sunil V., Kambara, Yasuhiro, Kang, Jaewoo, Kang, Keunsoo, Kaoma, Tony, Kaur, Harpreet, Kazan, Hilal, Kesar, Devishi, Kesseli, Juha, Kim, Daehan, Kim, Keonwoo, Kim, Sang-Yoon, Kim, Sunkyu, Kumar, Sajal, Lee, Bora, Lee, Heewon, Liu, Yunpeng, Luethy, Roland, Mahajan, Swapnil, Mahmoudian, Mehrad, Muller, Arnaud, Nazarov, Petr V., Nguyen, Hien, Nykter, Matti, Okuda, Shujiro, Park, Sungsoo, Pal Singh Raghava, Gajendra, Rajapakse, Jagath C., Rantapero, Tommi, Ryu, Hobin, Salavert, Francisco, Saraei, Sohrab, Sharma, Ruby, Siitonen, Ari, Sokolov, Artem, Subramanian, Kartik, Suni, Veronika, Suomi, Tomi, Tranchevent, Léon-Charles, Usmani, Salman Sadullah, Välikangas, Tommi, Vega, Roberto, Zhong, Hua, Boja, Emily, Rodriguez, Henry, Stolovitzky, Gustavo, Guan, Yuanfang, Kang, Jaewoo, Wang, Pei, Fenyö, David, Saez-Rodriguez, Julio

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Targeted serum proteomics of longitudinal samples from newly diagnosed youth with type 1 diabetes distinguishes markers of disease and C-peptide trajectory von Moulder, Robert, Valikangas, Tommi, Hirvonen, M. Karoliina, Suomi, Tomi A, Brorsson, Caroline A, Lietzen, Niina, Bruggraber, Sylvaine F.A, Overbergh, Lut, Dunger, David B, Peakman, Mark, Chmura, Piotr J, Brunak, Soren, Schulte, Anke M, Mathieu, Chantal, Knip, Mikael, Elo, Laura L, Lahesmaa, Riitta

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A systematic evaluation of normalization methods in quantitative label-free proteomics von Välikangas, Tommi, Suomi, Tomi, Elo, Laura L

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Enhanced differential expression statistics for data-independent acquisition proteomics von Suomi, Tomi, Elo, Laura L.

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ROTS: An R package for reproducibility-optimized statistical testing von Suomi, Tomi, Seyednasrollah, Fatemeh, Jaakkola, Maria K, Faux, Thomas, Elo, Laura L

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A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation von Välikangas, Tommi, Suomi, Tomi, Elo, Laura L

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Computational solutions for spatial transcriptomics von Kleino, Iivari, Frolovaitė, Paulina, Suomi, Tomi, Elo, Laura L.

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Distinct cellular immune responses in children en route to type 1 diabetes with different first-appearing autoantibodies von Starskaia, Inna, Valta, Milla, Pietilä, Sami, Suomi, Tomi, Pahkuri, Sirpa, Kalim, Ubaid Ullah, Rasool, Omid, Rydgren, Emilie, Hyöty, Heikki, Knip, Mikael, Veijola, Riitta, Ilonen, Jorma, Toppari, Jorma, Lempainen, Johanna, Elo, Laura L., Lahesmaa, Riitta

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Statistical and machine learning methods to study human CD4+ T cell proteome profiles von Suomi, Tomi, Elo, Laura L.

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Benchmarking tools for detecting longitudinal differential expression in proteomics data allows establishing a robust reproducibility optimization regression approach von Välikangas, Tommi, Suomi, Tomi, Chandler, Courtney E., Scott, Alison J., Tran, Bao Q., Ernst, Robert K., Goodlett, David R., Elo, Laura L.

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Compressive stress-mediated p38 activation required for ERα + phenotype in breast cancer von Munne, Pauliina M., Martikainen, Lahja, Räty, Iiris, Bertula, Kia, Nonappa, Ruuska, Janika, Ala-Hongisto, Hanna, Peura, Aino, Hollmann, Babette, Euro, Lilya, Yavuz, Kerim, Patrikainen, Linda, Salmela, Maria, Pokki, Juho, Kivento, Mikko, Väänänen, Juho, Suomi, Tomi, Nevalaita, Liina, Mutka, Minna, Kovanen, Panu, Leidenius, Marjut, Meretoja, Tuomo, Hukkinen, Katja, Monni, Outi, Pouwels, Jeroen, Sahu, Biswajyoti, Mattson, Johanna, Joensuu, Heikki, Heikkilä, Päivi, Elo, Laura L., Metcalfe, Ciara, Junttila, Melissa R., Ikkala, Olli, Klefström, Juha

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COVID-19-specific transcriptomic signature detectable in blood across multiple cohorts von Välikangas, Tommi, Junttila, Sini, Rytkönen, Kalle T, Kukkonen-Macchi, Anu, Suomi, Tomi, Elo, Laura L

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Employee Engagement and Internal Branding: Two Sides of the Same Coin? von Suomi, Kati, Saraniemi, Saila, Vähätalo, Mervi, Kallio, Tomi J., Tevameri, Terhi

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SimPhospho: a software tool enabling confident phosphosite assignment von Suni, Veronika, Suomi, Tomi, Tsubosaka, Tomoya, Imanishi, Susumu Y, Elo, Laura L, Corthals, Garry L

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Brief Isoflurane Anesthesia Produces Prominent Phosphoproteomic Changes in the Adult Mouse Hippocampus von Kohtala, Samuel, Theilmann, Wiebke, Suomi, Tomi, Wigren, Henna-Kaisa, Porkka-Heiskanen, Tarja, Elo, Laura L, Rokka, Anne, Rantamäki, Tomi

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Phenotypic profiling of human induced regulatory T cells at early differentiation: insights into distinct immunosuppressive potential von Kattelus, Roosa, Starskaia, Inna, Lindén, Markus, Batkulwar, Kedar, Pietilä, Sami, Moulder, Robert, Marson, Alexander, Rasool, Omid, Suomi, Tomi, Elo, Laura L., Lahesmaa, Riitta, Buchacher, Tanja

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Data-Independent Acquisition Mass Spectrometry in Metaproteomics of Gut MicrobiotaImplementation and Computational Analysis von Aakko, Juhani, Pietilä, Sami, Suomi, Tomi, Mahmoudian, Mehrad, Toivonen, Raine, Kouvonen, Petri, Rokka, Anne, Hänninen, Arno, Elo, Laura L

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