Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery.
Nature Communications
Havugimana, Pierre C PC; Goel, Raghuveera Kumar RK; Phanse, Sadhna S; Youssef, Ahmed A; Padhorny, Dzmitry D; Kotelnikov, Sergei S; Kozakov, Dima D; Emili, Andrew A
Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age.
Nature Communications
Burkhardt, Birgit B; Michgehl, Ulf U; Rohde, Jonas J; Erdmann, Tabea T; Berning, Philipp P; Reutter, Katrin K; Rohde, Marius M; Borkhardt, Arndt A; Burmeister, Thomas T; Dave, Sandeep S; Tzankov, Alexandar A; Dugas, Martin M; Sandmann, Sarah S; Fend, Falko F; Finger, Jasmin J; Mueller, Stephanie S; Gökbuget, Nicola N; Haferlach, Torsten T; Kern, Wolfgang W; Hartmann, Wolfgang W; Klapper, Wolfram W; Oschlies, Ilske I; Richter, Julia J; Kontny, Udo U; Lutz, Mathias M; Maecker-Kolhoff, Britta B; Ott, German G; Rosenwald, Andreas A; Siebert, Reiner R; von Stackelberg, Arend A; Strahm, Brigitte B; Woessmann, Wilhelm W; Zimmermann, Martin M; Zapukhlyak, Myroslav M; Grau, Michael M; Lenz, Georg G
The genetic heterogeneity and drug resistance mechanisms of relapsed refractory multiple myeloma.
Nature Communications
Vo, Josh N JN; Wu, Yi-Mi YM; Mishler, Jeanmarie J; Hall, Sarah S; Mannan, Rahul R; Wang, Lisha L; Ning, Yu Y; Zhou, Jin J; Hopkins, Alexander C AC; Estill, James C JC; Chan, Wallace K B WKB; Yesil, Jennifer J; Cao, Xuhong X; Rao, Arvind A; Tsodikov, Alexander A; Talpaz, Moshe M; Cole, Craig E CE; Ye, Jing C JC; , ; Bergsagel, P Leif PL; Auclair, Daniel D; Cho, Hearn Jay HJ; Robinson, Dan R DR; Chinnaiyan, Arul M AM
KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas.
Plos One
Rudd, Meghan L ML; Hansen, Nancy F NF; Zhang, Xiaolu X; Urick, Mary Ellen ME; Zhang, Suiyuan S; Merino, Maria J MJ; , ; Mullikin, James C JC; Brody, Lawrence C LC; Bell, Daphne W DW
KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas.
Plos One
Rudd, Meghan L ML; Hansen, Nancy F NF; Zhang, Xiaolu X; Urick, Mary Ellen ME; Zhang, Suiyuan S; Merino, Maria J MJ; , ; Mullikin, James C JC; Brody, Lawrence C LC; Bell, Daphne W DW
Embeddings from protein language models predict conservation and variant effects.
Human Genetics
Marquet, Céline C; Heinzinger, Michael M; Olenyi, Tobias T; Dallago, Christian C; Erckert, Kyra K; Bernhofer, Michael M; Nechaev, Dmitrii D; Rost, Burkhard B
The spliceosome pathway activity correlates with reduced anti-tumor immunity and immunotherapy response, and unfavorable clinical outcomes in pan-cancer.
Computational And Structural Biotechnology Journal
Chen, Zuobing Z; Chen, Canping C; Li, Lin L; Zhang, Tianfang T; Wang, Xiaosheng X
Whole-exome sequencing identified a novel heterozygous mutation of SALL1 and a new homozygous mutation of PTPRQ in a Chinese family with Townes-Brocks syndrome and hearing loss.
Bmc Medical Genomics
Yang, Guangxian G; Yin, Yi Y; Tan, Zhiping Z; Liu, Jian J; Deng, Xicheng X; Yang, Yifeng Y
Integrated molecular drivers coordinate biological and clinical states in melanoma.
Nature Genetics
Conway, Jake R JR; Dietlein, Felix F; Taylor-Weiner, Amaro A; AlDubayan, Saud S; Vokes, Natalie N; Keenan, Tanya T; Reardon, Brendan B; He, Meng Xiao MX; Margolis, Claire A CA; Weirather, Jason L JL; Haq, Rizwan R; Schilling, Bastian B; Stephen Hodi, F F; Schadendorf, Dirk D; Liu, David D; Van Allen, Eliezer M EM
CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications.
Elife
Franch-Expósito, Sebastià S; Bassaganyas, Laia L; Vila-Casadesús, Maria M; Hernández-Illán, Eva E; Esteban-Fabró, Roger R; Díaz-Gay, Marcos M; Lozano, Juan José JJ; Castells, Antoni A; Llovet, Josep Maria JM; Castellví-Bel, Sergi S; Camps, Jordi J
APOBEC3A is a prominent cytidine deaminase in breast cancer.
Plos Genetics
Cortez, Luis M LM; Brown, Amber L AL; Dennis, Madeline A MA; Collins, Christopher D CD; Brown, Alexander J AJ; Mitchell, Debra D; Mertz, Tony M TM; Roberts, Steven A SA
Transcriptomic signature reveals mechanism of flower bud distortion in witches'-broom disease of soybean (Glycine max).
Bmc Plant Biology
Jaiswal, Sarika S; Jadhav, Pravin V PV; Jasrotia, Rahul Singh RS; Kale, Prashant B PB; Kad, Snehal K SK; Moharil, Mangesh P MP; Dudhare, Mahendra S MS; Kheni, Jashminkumar J; Deshmukh, Amit G AG; Mane, Shyamsundar S SS; Nandanwar, Ravindra S RS; Penna, Suprasanna S; Manjaya, Joy G JG; Iquebal, Mir Asif MA; Tomar, Rukam Singh RS; Kawar, Prashant G PG; Rai, Anil A; Kumar, Dinesh D
The prognostic effects of somatic mutations in ER-positive breast cancer.
Nature Communications
Griffith, Obi L OL; Spies, Nicholas C NC; Anurag, Meenakshi M; Griffith, Malachi M; Luo, Jingqin J; Tu, Dongsheng D; Yeo, Belinda B; Kunisaki, Jason J; Miller, Christopher A CA; Krysiak, Kilannin K; Hundal, Jasreet J; Ainscough, Benjamin J BJ; Skidmore, Zachary L ZL; Campbell, Katie K; Kumar, Runjun R; Fronick, Catrina C; Cook, Lisa L; Snider, Jacqueline E JE; Davies, Sherri S; Kavuri, Shyam M SM; Chang, Eric C EC; Magrini, Vincent V; Larson, David E DE; Fulton, Robert S RS; Liu, Shuzhen S; Leung, Samuel S; Voduc, David D; Bose, Ron R; Dowsett, Mitch M; Wilson, Richard K RK; Nielsen, Torsten O TO; Mardis, Elaine R ER; Ellis, Matthew J MJ
Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis.
Nature Communications
Braun, Simon S; Enculescu, Mihaela M; Setty, Samarth T ST; Cortés-López, Mariela M; de Almeida, Bernardo P BP; Sutandy, F X Reymond FXR; Schulz, Laura L; Busch, Anke A; Seiler, Markus M; Ebersberger, Stefanie S; Barbosa-Morais, Nuno L NL; Legewie, Stefan S; König, Julian J; Zarnack, Kathi K
Modeling cancer driver events in vitro using barrier bypass-clonal expansion assays and massively parallel sequencing.
Oncogene
Huskova, H H; Ardin, M M; Weninger, A A; Vargova, K K; Barrin, S S; Villar, S S; Olivier, M M; Stopka, T T; Herceg, Z Z; Hollstein, M M; Zavadil, J J; Korenjak, M M
Genome-wide DNA methylation profile identified a unique set of differentially methylated immune genes in oral squamous cell carcinoma patients in India.
A Landscape of Pharmacogenomic Interactions in Cancer.
Cell
Iorio, Francesco F; Knijnenburg, Theo A TA; Vis, Daniel J DJ; Bignell, Graham R GR; Menden, Michael P MP; Schubert, Michael M; Aben, Nanne N; Gonçalves, Emanuel E; Barthorpe, Syd S; Lightfoot, Howard H; Cokelaer, Thomas T; Greninger, Patricia P; van Dyk, Ewald E; Chang, Han H; de Silva, Heshani H; Heyn, Holger H; Deng, Xianming X; Egan, Regina K RK; Liu, Qingsong Q; Mironenko, Tatiana T; Mitropoulos, Xeni X; Richardson, Laura L; Wang, Jinhua J; Zhang, Tinghu T; Moran, Sebastian S; Sayols, Sergi S; Soleimani, Maryam M; Tamborero, David D; Lopez-Bigas, Nuria N; Ross-Macdonald, Petra P; Esteller, Manel M; Gray, Nathanael S NS; Haber, Daniel A DA; Stratton, Michael R MR; Benes, Cyril H CH; Wessels, Lodewyk F A LFA; Saez-Rodriguez, Julio J; McDermott, Ultan U; Garnett, Mathew J MJ
De novo mutations in histone-modifying genes in congenital heart disease.
Nature
Zaidi, Samir S; Choi, Murim M; Wakimoto, Hiroko H; Ma, Lijiang L; Jiang, Jianming J; Overton, John D JD; Romano-Adesman, Angela A; Bjornson, Robert D RD; Breitbart, Roger E RE; Brown, Kerry K KK; Carriero, Nicholas J NJ; Cheung, Yee Him YH; Deanfield, John J; DePalma, Steve S; Fakhro, Khalid A KA; Glessner, Joseph J; Hakonarson, Hakon H; Italia, Michael J MJ; Kaltman, Jonathan R JR; Kaski, Juan J; Kim, Richard R; Kline, Jennie K JK; Lee, Teresa T; Leipzig, Jeremy J; Lopez, Alexander A; Mane, Shrikant M SM; Mitchell, Laura E LE; Newburger, Jane W JW; Parfenov, Michael M; Pe'er, Itsik I; Porter, George G; Roberts, Amy E AE; Sachidanandam, Ravi R; Sanders, Stephan J SJ; Seiden, Howard S HS; State, Mathew W MW; Subramanian, Sailakshmi S; Tikhonova, Irina R IR; Wang, Wei W; Warburton, Dorothy D; White, Peter S PS; Williams, Ismee A IA; Zhao, Hongyu H; Seidman, Jonathan G JG; Brueckner, Martina M; Chung, Wendy K WK; Gelb, Bruce D BD; Goldmuntz, Elizabeth E; Seidman, Christine E CE; Lifton, Richard P RP