Korchak, Jennifer A.;Jeffery, Erin D.;Bandyopadhyay, Saikat;Jordan, Ben T.;Lehe, Micah D.;Watts, Emily F.;Fenix, Aidan;Wilhelm, Mathias;Sheynkman, Gloria M.
IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection
Journal of the American Society for Mass Spectrometry
2024
35
11
2614-2630

Hoffmann, Markus;Poschenrieder, Julian M;Incudini, Massimiliano;Baier, Sylvie;Fritz, Amelie;Maier, Andreas;Hartung, Michael;Hoffmann, Christian;Trummer, Nico;Adamowicz, Klaudia;Picciani, Mario;Scheibling, Evelyn;Harl, Maximilian V;Lesch, Ingmar;Frey, Hunor;Kayser, Simon;Wissenberg, Paul;Schwartz, Leon;Hafner, Leon;Acharya, Aakriti;Hackl, Lena;Grabert, Gordon;Lee, Sung-Gwon;Cho, Gyuhyeok;Cloward, Matthew E;Jankowski, Jakub;Lee, Hye Kyung;Tsoy, Olga;Wenke, Nina;Pedersen, Anders Gorm;Bønnelykke, Klaus;Mandarino, Antonio;Melograna, Federico;Schulz, Laura;Climente-González, Héctor;Wilhelm, Mathias;Iapichino, Luigi;Wienbrandt, Lars;Ellinghaus, David;Van Steen, Kristel;Grossi, Michele;Furth, Priscilla A;Hennighausen, Lothar;Di Pierro, Alessandra;Baumbach, Jan;Kacprowski, Tim;List, Markus;Blumenthal, David B
Network medicine-based epistasis detection in complex diseases: ready for quantum computing
Nucleic Acids Research
2024
52
17
10144-10160

He, Fuchu;Aebersold, Ruedi;Baker, Mark S.;Bian, Xiuwu;Bo, Xiaochen;Chan, Daniel W.;Chang, Cheng;Chen, Luonan;Chen, Xiangmei;Chen, Yu-Ju;Cheng, Heping;Collins, Ben C.;Corrales, Fernando;Cox, Jürgen;E, Weinan;Van Eyk, Jennifer E.;Fan, Jia;Faridi, Pouya;Figeys, Daniel;Gao, George Fu;Gao, Wen;Gao, Zu-Hua;Goda, Keisuke;Goh, Wilson Wen Bin;Gu, Dongfeng;Guo, Changjiang;Guo, Tiannan;He, Yuezhong;Heck, Albert J. R.;Hermjakob, Henning;Hunter, Tony;Iyer, Narayanan Gopalakrishna;Jiang, Ying;Jimenez, Connie R.;Joshi, Lokesh;Kelleher, Neil L.;Li, Ming;Li, Yang;Lin, Qingsong;Liu, Cui Hua;Liu, Fan;Liu, Guang-Hui;Liu, Yansheng;Liu, Zhihua;Low, Teck Yew;Lu, Ben;Mann, Matthias;Meng, Anming;Moritz, Robert L.;Nice, Edouard;Ning, Guang;Omenn, Gilbert S.;Overall, Christopher M.;Palmisano, Giuseppe;Peng, Yaojin;Pineau, Charles;Poon, Terence Chuen Wai;Purcell, Anthony W.;Qiao, Jie;Reddel, Roger R.;Robinson, Phillip J.;Roncada, Paola;Sander, Chris;Sha, Jiahao;Song, Erwei;Srivastava, Sanjeeva;Sun, Aihua;Sze, Siu Kwan;Tang, Chao;Tang, Liujun;Tian, Ruijun;Vizcaíno, Juan Antonio;Wang, Chanjuan;Wang, Chen;Wang, Xiaowen;Wang, Xinxing;Wang, Yan;Weiss, Tobias;Wilhelm, Mathias;Winkler, Robert;Wollscheid, Bernd;Wong, Limsoon;Xie, Linhai;Xie, Wei;Xu, Tao;Xu, Tianhao;Yan, Liying;Yang, Jing;Yang, Xiao;Yates, John;Yun, Tao;Zhai, Qiwei;Zhang, Bing;Zhang, Hui;Zhang, Lihua;Zhang, Lingqiang;Zhang, Pingwen;Zhang, Yukui;Zheng, Yu Zi;Zhong, Qing;Zhu, Yunping;;Chan, Daniel W.;Tan, Chris Soon Heng;E, Weinan;Van Eyk, Jennifer E.;Gao, Mingxia;Gao, Qiang;Gao, Yushun;Guo, Xuejiang;He, Jie;He, Jun;He, Qing-Yu;Hou, Jinlin;Huang, Canhua;Jia, Chenxi;Kuster, Bernhard;Li, Chaoying;Li, Dong;Li, Yan;Li, Yanchang;Liu, Siqi;Liu, Xiaonan;Liu, Ya;Liu, Zhongyang;Lu, Haojie;Nie, Yongzhan;Okada, Mariko;Qian, Guojun;Qin, Hongqiang;Rao, Yu;Rao, Zihe;Ren, Xianwen;Ren, Yan;Shen, Feng;Shen, Lin;Su, Shicheng;Tan, Minjia;Tang, Ben Zhong;Tao, Sheng-Ce;Wang, Jian;Wang, Tong;Wei, Liming;Wong, Catherine C. L.;Xie, Xiaoliang Sunney;Xu, Li;Xu, Ping;Xu, Tao;Yang, Huanming;Yang, Jianjun;Ye, Mingliang;Ying, Wantao;Yu, Xiaobo;Yuan, Yaxiang;Zeng, Qingcun;Zhan, Qimin;Zhang, Xiaofei;Zhang, Xu;Zhang, Ying;Zhong, Nan-Shan;Zhou, Feng;Zhu, Yi;Zhang, Zemin
π-HuB: the proteomic navigator of the human body
Nature
2024
636
8042
322-331

Abbas, Qussai;Wilhelm, Mathias;Kuster, Bernhard;Poppenberger, Brigitte;Frishman, Dmitrij
Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies
BMC Genomics
2024
25
1

The, Matthew;Picciani, Mario;Jensen, Cecilia;Gabriel, Wassim;Kuster, Bernhard;Wilhelm, Mathias
AI-Assisted Processing Pipeline to Boost Protein Isoform Detection
Methods in Molecular Biology
Springer US
2024

Beltrao, Pedro;Van Den Bossche, Tim;Gabriels, Ralf;Holstein, Tanja;Kockmann, Tobias;Nameni, Alireza;Panse, Christian;Schlapbach, Ralph;Lautenbacher, Ludwig;Mattanovich, Matthias;Nesvizhskii, Alexey;Van Puyvelde, Bart;Scheid, Jonas;Schwämmle, Veit;Strauss, Maximilian;Susmelj, Anna Klimovskaia;The, Matthew;Webel, Henry;Wilhelm, Mathias;Winkelhardt, Dirk;Wolski, Witold E.;Xi, Muyao
Proceedings of the EuBIC-MS developers meeting 2023
Journal of Proteomics
2024
305
105246

Gabriel, Wassim;Picciani, Mario;The, Matthew;Wilhelm, Mathias
Deep Learning-Assisted Analysis of Immunopeptidomics Data
Methods in Molecular Biology
Springer US
2024

Kalhor, Mostafa;Lapin, Joel;Picciani, Mario;Wilhelm, Mathias
Rescoring Peptide Spectrum Matches: Boosting Proteomics Performance by Integrating Peptide Property Predictors into Peptide Identification
Molecular & Cellular Proteomics
2024
100798

Adams, Charlotte;Gabriel, Wassim;Laukens, Kris;Picciani, Mario;Wilhelm, Mathias;Bittremieux, Wout;Boonen, Kurt
Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF
Nature Communications
2024
15
1

Klaproth-Andrade, Daniela;Hingerl, Johannes;Bruns, Yanik;Smith, Nicholas H.;Träuble, Jakob;Wilhelm, Mathias;Gagneur, Julien
Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing
Nature Communications
2024
15
1