Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues.
Nature Communications
Abelin, Jennifer G JG; Bergstrom, Erik J EJ; Rivera, Keith D KD; Taylor, Hannah B HB; Klaeger, Susan S; Xu, Charles C; Verzani, Eva K EK; Jackson White, C C; Woldemichael, Hilina B HB; Virshup, Maya M; Olive, Meagan E ME; Maynard, Myranda M; Vartany, Stephanie A SA; Allen, Joseph D JD; Phulphagar, Kshiti K; Harry Kane, M M; Rachimi, Suzanna S; Mani, D R DR; Gillette, Michael A MA; Satpathy, Shankha S; Clauser, Karl R KR; Udeshi, Namrata D ND; Carr, Steven A SA
Next-generation whole exome sequencing to delineate the genetic basis of primary congenital glaucoma.
Scientific Reports
Rauf, Bushra B; Khan, Shahid Y SY; Jiao, Xiaodong X; Irum, Bushra B; Ashfaq, Ramla R; Zehra, Mubashra M; Khan, Asma A AA; Naeem, Muhammad Asif MA; Shahzad, Mohsin M; Riazuddin, Sheikh S; Hejtmancik, J Fielding JF; Riazuddin, S Amer SA
Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.
Cell
Krug, Karsten K; Jaehnig, Eric J EJ; Satpathy, Shankha S; Blumenberg, Lili L; Karpova, Alla A; Anurag, Meenakshi M; Miles, George G; Mertins, Philipp P; Geffen, Yifat Y; Tang, Lauren C LC; Heiman, David I DI; Cao, Song S; Maruvka, Yosef E YE; Lei, Jonathan T JT; Huang, Chen C; Kothadia, Ramani B RB; Colaprico, Antonio A; Birger, Chet C; Wang, Jarey J; Dou, Yongchao Y; Wen, Bo B; Shi, Zhiao Z; Liao, Yuxing Y; Wiznerowicz, Maciej M; Wyczalkowski, Matthew A MA; Chen, Xi Steven XS; Kennedy, Jacob J JJ; Paulovich, Amanda G AG; Thiagarajan, Mathangi M; Kinsinger, Christopher R CR; Hiltke, Tara T; Boja, Emily S ES; Mesri, Mehdi M; Robles, Ana I AI; Rodriguez, Henry H; Westbrook, Thomas F TF; Ding, Li L; Getz, Gad G; Clauser, Karl R KR; Fenyö, David D; Ruggles, Kelly V KV; Zhang, Bing B; Mani, D R DR; Carr, Steven A SA; Ellis, Matthew J MJ; Gillette, Michael A MA; ,
Distinctive mutational spectrum and karyotype disruption in long-term cisplatin-treated urothelial carcinoma cell lines.
Scientific Reports
Skowron, Margaretha A MA; Petzsch, Patrick P; Hardt, Karin K; Wagner, Nicholas N; Beier, Manfred M; Stepanow, Stefanie S; Drechsler, Matthias M; Rieder, Harald H; Köhrer, Karl K; Niegisch, Günter G; Hoffmann, Michèle J MJ; Schulz, Wolfgang A WA
Publication Date: 2019-10-09
Variant appearance in text: WARS2: A267P; rs3790549
Breast cancer quantitative proteome and proteogenomic landscape.
Nature Communications
Johansson, Henrik J HJ; Socciarelli, Fabio F; Vacanti, Nathaniel M NM; Haugen, Mads H MH; Zhu, Yafeng Y; Siavelis, Ioannis I; Fernandez-Woodbridge, Alejandro A; Aure, Miriam R MR; Sennblad, Bengt B; Vesterlund, Mattias M; Branca, Rui M RM; Orre, Lukas M LM; Huss, Mikael M; Fredlund, Erik E; Beraki, Elsa E; Garred, Øystein Ø; Boekel, Jorrit J; Sauer, Torill T; Zhao, Wei W; Nord, Silje S; Höglander, Elen K EK; Jans, Daniel C DC; Brismar, Hjalmar H; Haukaas, Tonje H TH; Bathen, Tone F TF; Schlichting, Ellen E; Naume, Bjørn B; , ; Luders, Torben T; Borgen, Elin E; Kristensen, Vessela N VN; Russnes, Hege G HG; Lingjærde, Ole Christian OC; Mills, Gordon B GB; Sahlberg, Kristine K KK; Børresen-Dale, Anne-Lise AL; Lehtiö, Janne J
A reference collection of patient-derived cell line and xenograft models of proneural, classical and mesenchymal glioblastoma.
Scientific Reports
Stringer, Brett W BW; Day, Bryan W BW; D'Souza, Rochelle C J RCJ; Jamieson, Paul R PR; Ensbey, Kathleen S KS; Bruce, Zara C ZC; Lim, Yi Chieh YC; Goasdoué, Kate K; Offenhäuser, Carolin C; Akgül, Seçkin S; Allan, Suzanne S; Robertson, Thomas T; Lucas, Peter P; Tollesson, Gert G; Campbell, Scott S; Winter, Craig C; Do, Hongdo H; Dobrovic, Alexander A; Inglis, Po-Ling PL; Jeffree, Rosalind L RL; Johns, Terrance G TG; Boyd, Andrew W AW
Publication Date: 2019-03-20
Variant appearance in text: WARS2: A267P; rs3790549
Organoids as a new model for improving regenerative medicine and cancer personalized therapy in renal diseases.
Cell Death & Disease
Grassi, Ludovica L; Alfonsi, Romina R; Francescangeli, Federica F; Signore, Michele M; De Angelis, Maria Laura ML; Addario, Antonio A; Costantini, Manuela M; Flex, Elisabetta E; Ciolfi, Andrea A; Pizzi, Simone S; Bruselles, Alessandro A; Pallocca, Matteo M; Simone, Giuseppe G; Haoui, Mustapha M; Falchi, Mario M; Milella, Michele M; Sentinelli, Steno S; Di Matteo, Paola P; Stellacci, Emilia E; Gallucci, Michele M; Muto, Giovanni G; Tartaglia, Marco M; De Maria, Ruggero R; Bonci, Désirée D
Publication Date: 2019-02-27
Variant appearance in text: WARS2: 799G>C; Ala267Pro; rs3790549
Development and validation of a targeted next generation DNA sequencing panel outperforming whole exome sequencing for the identification of clinically relevant genetic variants.
Oncotarget
Miller, Eirwen M EM; Patterson, Nicole E NE; Zechmeister, Jenna Marcus JM; Bejerano-Sagie, Michal M; Delio, Maria M; Patel, Kunjan K; Ravi, Nivedita N; Quispe-Tintaya, Wilber W; Maslov, Alexander A; Simmons, Nichelle N; Castaldi, Maria M; Vijg, Jan J; Karabakhtsian, Rouzan G RG; Greally, John M JM; Kuo, Dennis Y S DYS; Montagna, Cristina C
Publication Date: 2017-11-24
Variant appearance in text: WARS2: A267P; rs3790549
Proteogenomics connects somatic mutations to signalling in breast cancer.
Nature
Mertins, Philipp P; Mani, D R DR; Ruggles, Kelly V KV; Gillette, Michael A MA; Clauser, Karl R KR; Wang, Pei P; Wang, Xianlong X; Qiao, Jana W JW; Cao, Song S; Petralia, Francesca F; Kawaler, Emily E; Mundt, Filip F; Krug, Karsten K; Tu, Zhidong Z; Lei, Jonathan T JT; Gatza, Michael L ML; Wilkerson, Matthew M; Perou, Charles M CM; Yellapantula, Venkata V; Huang, Kuan-lin KL; Lin, Chenwei C; McLellan, Michael D MD; Yan, Ping P; Davies, Sherri R SR; Townsend, R Reid RR; Skates, Steven J SJ; Wang, Jing J; Zhang, Bing B; Kinsinger, Christopher R CR; Mesri, Mehdi M; Rodriguez, Henry H; Ding, Li L; Paulovich, Amanda G AG; Fenyö, David D; Ellis, Matthew J MJ; Carr, Steven A SA; ,
Publication Date: 2016-06-02
Variant appearance in text: WARS2: A267P; rs3790549
Whole-genome sequencing of the world's oldest people.
Plos One
Gierman, Hinco J HJ; Fortney, Kristen K; Roach, Jared C JC; Coles, Natalie S NS; Li, Hong H; Glusman, Gustavo G; Markov, Glenn J GJ; Smith, Justin D JD; Hood, Leroy L; Coles, L Stephen LS; Kim, Stuart K SK
Publication Date: 2014
Variant appearance in text: WARS2: A267P; rs3790549
NCI-60 whole exome sequencing and pharmacological CellMiner analyses.
Plos One
Reinhold, William C WC; Varma, Sudhir S; Sousa, Fabricio F; Sunshine, Margot M; Abaan, Ogan D OD; Davis, Sean R SR; Reinhold, Spencer W SW; Kohn, Kurt W KW; Morris, Joel J; Meltzer, Paul S PS; Doroshow, James H JH; Pommier, Yves Y
Common non-synonymous SNPs associated with breast cancer susceptibility: findings from the Breast Cancer Association Consortium.
Human Molecular Genetics
Milne, Roger L RL; Burwinkel, Barbara B; Michailidou, Kyriaki K; Arias-Perez, Jose-Ignacio JI; Zamora, M Pilar MP; Menéndez-Rodríguez, Primitiva P; Hardisson, David D; Mendiola, Marta M; González-Neira, Anna A; Pita, Guillermo G; Alonso, M Rosario MR; Dennis, Joe J; Wang, Qin Q; Bolla, Manjeet K MK; Swerdlow, Anthony A; Ashworth, Alan A; Orr, Nick N; Schoemaker, Minouk M; Ko, Yon-Dschun YD; Brauch, Hiltrud H; Hamann, Ute U; , ; Andrulis, Irene L IL; Knight, Julia A JA; Glendon, Gord G; Tchatchou, Sandrine S; , ; , ; Matsuo, Keitaro K; Ito, Hidemi H; Iwata, Hiroji H; Tajima, Kazuo K; Li, Jingmei J; Brand, Judith S JS; Brenner, Hermann H; Dieffenbach, Aida Karina AK; Arndt, Volker V; Stegmaier, Christa C; Lambrechts, Diether D; Peuteman, Gilian G; Christiaens, Marie-Rose MR; Smeets, Ann A; Jakubowska, Anna A; Lubinski, Jan J; Jaworska-Bieniek, Katarzyna K; Durda, Katazyna K; Hartman, Mikael M; Hui, Miao M; Yen Lim, Wei W; Wan Chan, Ching C; Marme, Federick F; Yang, Rongxi R; Bugert, Peter P; Lindblom, Annika A; Margolin, Sara S; García-Closas, Montserrat M; Chanock, Stephen J SJ; Lissowska, Jolanta J; Figueroa, Jonine D JD; Bojesen, Stig E SE; Nordestgaard, Børge G BG; Flyger, Henrik H; Hooning, Maartje J MJ; Kriege, Mieke M; van den Ouweland, Ans M W AM; Koppert, Linetta B LB; Fletcher, Olivia O; Johnson, Nichola N; dos-Santos-Silva, Isabel I; Peto, Julian J; Zheng, Wei W; Deming-Halverson, Sandra S; Shrubsole, Martha J MJ; Long, Jirong J; Chang-Claude, Jenny J; Rudolph, Anja A; Seibold, Petra P; Flesch-Janys, Dieter D; Winqvist, Robert R; Pylkäs, Katri K; Jukkola-Vuorinen, Arja A; Grip, Mervi M; Cox, Angela A; Cross, Simon S SS; Reed, Malcolm W R MW; Schmidt, Marjanka K MK; Broeks, Annegien A; Cornelissen, Sten S; Braaf, Linde L; Kang, Daehee D; Choi, Ji-Yeob JY; Park, Sue K SK; Noh, Dong-Young DY; Simard, Jacques J; Dumont, Martine M; Goldberg, Mark S MS; Labrèche, France F; Fasching, Peter A PA; Hein, Alexander A; Ekici, Arif B AB; Beckmann, Matthias W MW; Radice, Paolo P; Peterlongo, Paolo P; Azzollini, Jacopo J; Barile, Monica M; Sawyer, Elinor E; Tomlinson, Ian I; Kerin, Michael M; Miller, Nicola N; Hopper, John L JL; Schmidt, Daniel F DF; Makalic, Enes E; Southey, Melissa C MC; Hwang Teo, Soo S; Har Yip, Cheng C; Sivanandan, Kavitta K; Tay, Wan-Ting WT; Shen, Chen-Yang CY; Hsiung, Chia-Ni CN; Yu, Jyh-Cherng JC; Hou, Ming-Feng MF; Guénel, Pascal P; Truong, Therese T; Sanchez, Marie M; Mulot, Claire C; Blot, William W; Cai, Qiuyin Q; Nevanlinna, Heli H; Muranen, Taru A TA; Aittomäki, Kristiina K; Blomqvist, Carl C; Wu, Anna H AH; Tseng, Chiu-Chen CC; Van Den Berg, David D; Stram, Daniel O DO; Bogdanova, Natalia N; Dörk, Thilo T; Muir, Kenneth K; Lophatananon, Artitaya A; Stewart-Brown, Sarah S; Siriwanarangsan, Pornthep P; Mannermaa, Arto A; Kataja, Vesa V; Kosma, Veli-Matti VM; Hartikainen, Jaana M JM; Shu, Xiao-Ou XO; Lu, Wei W; Gao, Yu-Tang YT; Zhang, Ben B; Couch, Fergus J FJ; Toland, Amanda E AE; , ; Yannoukakos, Drakoulis D; Sangrajrang, Suleeporn S; McKay, James J; Wang, Xianshu X; Olson, Janet E JE; Vachon, Celine C; Purrington, Kristen K; Severi, Gianluca G; Baglietto, Laura L; Haiman, Christopher A CA; Henderson, Brian E BE; Schumacher, Fredrick F; Le Marchand, Loic L; Devilee, Peter P; Tollenaar, Robert A E M RA; Seynaeve, Caroline C; Czene, Kamila K; Eriksson, Mikael M; Humphreys, Keith K; Darabi, Hatef H; Ahmed, Shahana S; Shah, Mitul M; Pharoah, Paul D P PD; Hall, Per P; Giles, Graham G GG; Benítez, Javier J; Dunning, Alison M AM; Chenevix-Trench, Georgia G; Easton, Douglas F DF