L
Lijun Chen
Researcher at Johns Hopkins University
Publications - 34
Citations - 3215
Lijun Chen is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Glycosylation & Glycoprotein. The author has an hindex of 16, co-authored 28 publications receiving 1816 citations. Previous affiliations of Lijun Chen include Johns Hopkins University School of Medicine.
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Journal ArticleDOI
Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
Hui Zhang,Tao Liu,Zhen Zhang,Samuel H. Payne,Bai Zhang,Jason E. McDermott,Jian-Ying Zhou,Vladislav A. Petyuk,Li Chen,Debjit Ray,Shisheng Sun,Feng Yang,Lijun Chen,Jing Wang,Punit Shah,Seong Won Cha,Paul Aiyetan,Sunghee Woo,Yuan Tian,Marina A. Gritsenko,Therese R. W. Clauss,Caitlin H. Choi,Matthew E. Monroe,Stefani N. Thomas,Song Nie,Chaochao Wu,Ronald J. Moore,Kun-Hsing Yu,David L. Tabb,David Fenyö,Vineet Bafna,Yue Wang,Henry Rodriguez,Emily S. Boja,Tara Hiltke,Robert Rivers,Lori J. Sokoll,Heng Zhu,Ie Ming Shih,Leslie Cope,Akhilesh Pandey,Bing Zhang,Michael Snyder,Douglas A. Levine,Richard D. Smith,Daniel W. Chan,Karin D. Rodland,Steven A. Carr,Michael A. Gillette,Karl R. Klauser,Eric Kuhn,D. R. Mani,Philipp Mertins,Karen A. Ketchum,Ratna R. Thangudu,Shuang Cai,Mauricio Oberti,Amanda G. Paulovich,Jeffrey R. Whiteaker,Nathan Edwards,Peter B. McGarvey,Subha Madhavan,Pei Wang,Gordon Whiteley,Steven J. Skates,Forest M. White,Christopher R. Kinsinger,Mehdi Mesri,Kenna M. Shaw,Stephen E. Stein,Paul A. Rudnick,Michael Snyder,Yingming Zhao,Xian Chen,David F. Ransohoff,Andrew N. Hoofnagle,Daniel C. Liebler,Melinda E. Sanders,Zhiao Shi,Robbert J.C. Slebos,Lisa J. Zimmerman,Sherri R. Davies,Li Ding,Matthew J. Ellis,R. Reid Townsend +84 more
TL;DR: A view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in HGSC is provided.
Journal ArticleDOI
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma.
David J. Clark,Saravana M. Dhanasekaran,Francesca Petralia,Jianbo Pan,Xiaoyu Song,Yingwei Hu,Felipe da Veiga Leprevost,Boris Reva,Tung-Shing M. Lih,Hui Yin Chang,Weiping Ma,Chen Huang,Christopher J. Ricketts,Lijun Chen,Azra Krek,Yize Li,Dmitry Rykunov,Qing Kay Li,Lin Chen,Umut Ozbek,Suhas Vasaikar,Yige Wu,Seungyeul Yoo,Shrabanti Chowdhury,Matthew A. Wyczalkowski,Jiayi Ji,Michael Schnaubelt,Andy T. Kong,Sunantha Sethuraman,Dmitry M. Avtonomov,Minghui Ao,Antonio Colaprico,Song Cao,Kyung-Cho Cho,Selim Kalayci,Shiyong Ma,Wenke Liu,Kelly V. Ruggles,Anna Calinawan,Zeynep H. Gümüş,Daniel J. Geiszler,Emily Kawaler,Guo Ci Teo,Bo Wen,Yuping Zhang,Sarah Keegan,Kai Li,Feng Chen,Nathan Edwards,Phillip M. Pierorazio,Xi Steven Chen,Christian P. Pavlovich,A. Ari Hakimi,Gabriel Bromiński,James J. Hsieh,Andrzej Antczak,Tatiana Omelchenko,Jan Lubinski,Maciej Wiznerowicz,Maciej Wiznerowicz,W. Marston Linehan,Christopher R. Kinsinger,Mathangi Thiagarajan,Emily S. Boja,Mehdi Mesri,Tara Hiltke,Ana I. Robles,Henry Rodriguez,Jiang Qian,David Fenyö,Bing Zhang,Li Ding,Eric E. Schadt,Arul M. Chinnaiyan,Zhen Zhang,Gilbert S. Omenn,Marcin Cieslik,Daniel W. Chan,Alexey I. Nesvizhskii,Pei Wang,Hui Zhang,Abdul Samad Hashimi,Alexander R. Pico,Alla Y. Karpova,Alyssa Charamut,Amanda G. Paulovich,Amy M. Perou,Anna Malovannaya,Annette Marrero-Oliveras,Anupriya Agarwal,Barbara Hindenach,Barbara Pruetz,Beom-Jun Kim,Brian J. Druker,Chelsea J. Newton,Chet Birger,Corbin D. Jones,Cristina E. Tognon,D. R. Mani,Dana R. Valley,Daniel C. Rohrer,Daniel C. Zhou,Darlene Tansil,David Chesla,David I. Heiman,David C. Wheeler,Donghui Tan,Doug W. Chan,Emek Demir,Ewa P. Malc,Francesmary Modugno,Gaddy Getz,Galen Hostetter,George D. Wilson,Gerald W. Hart,Heng Zhu,Hongwei Liu,Houston Culpepper,Hua Sun,Hua Zhou,Jacob J. Day,James Suh,Jasmine Huang,Jason E. McDermott,Jeffrey R. Whiteaker,Jeffrey W. Tyner,Jennifer M. Eschbacher,Jin Chen,John McGee,Jun Zhu,Karen A. Ketchum,Karin D. Rodland,Karl R. Clauser,Karna Robinson,Karsten Krug,Katherine A. Hoadley,Ki Sung Um,Kim Elburn,Kimberly R. Holloway,Liang-Bo Wang,Lili Blumenberg,Linda Hannick,Liqun Qi,Lori J. Sokoll,MacIntosh Cornwell,Marc M. Loriaux,Marcin J. Domagalski,Marina A. Gritsenko,Matthew L. Anderson,Matthew E. Monroe,Matthew J. Ellis,Maureen Dyer,Meenakshi Anurag,Meghan C. Burke,Melissa Borucki,Michael A. Gillette,Michael J. Birrer,Michael T. Lewis,Michael Ittmann,Michael Smith,Michael Vernon,Michelle Chaikin,Milan G. Chheda,Munziba Khan,Nancy Roche,Nathan Edwards,Negin Vatanian,Nicole Tignor,Noam D. Beckmann,Pamela Grady,Patricia Castro,Paul D. Piehowski,Peter B. McGarvey,Piotr A. Mieczkowski,Pushpa Hariharan,Qingsong Gao,Rajiv Dhir,Ramani B. Kothadia,Ratna R. Thangudu,Rebecca I. Montgomery,Reyka G Jayasinghe,Richard D. Smith,Robert Edwards,Robert Zelt,Ross Bremner,Ruiyang Liu,Runyu Hong,Sailaja Mareedu,Samuel H. Payne,Sandra Cottingham,Sanford P. Markey,Scott D. Jewell,Shalin Patel,Shankha Satpathy,Shannon Richey,Sherri R. Davies,Shuang Cai,Simina M. Boca,Snehal Patil,Sohini Sengupta,Sonya Carter,Stacey Gabriel,Stefani N. Thomas,Stephanie De Young,Stephen E. Stein,Steven A. Carr,Steven M. Foltz,Sue Hilsenbeck,Tanya Krubit,Tao Liu,Tara Skelly,Thomas F. Westbrook,Uma Borate,Uma Velvulou,Vladislav A. Petyuk,William Bocik,Xi Chen,Yan Shi,Yifat Geffen,Yihao Lu,Ying Wang,Yosef E. Maruvka,Zhi Li,Zhiao Shi,Zhidong Tu +224 more
TL;DR: A large-scale proteogenomic analysis of ccRCC is reported to discern the functional impact of genomic alterations and provides evidence for rational treatment selection stemming fromccRCC pathobiology.
Journal ArticleDOI
Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry
Philipp Mertins,Philipp Mertins,Lauren C. Tang,Karsten Krug,David J. Clark,Marina A. Gritsenko,Lijun Chen,Karl R. Clauser,Therese R. W. Clauss,Punit Shah,Michael A. Gillette,Vladislav A. Petyuk,Stefani N. Thomas,D. R. Mani,Filip Mundt,Ronald J. Moore,Yingwei Hu,Rui Zhao,Michael Schnaubelt,Hasmik Keshishian,Matthew E. Monroe,Zhen Zhang,Namrata D. Udeshi,Deepak Mani,Sherri R. Davies,Raymond R. Townsend,Daniel W. Chan,Richard D. Smith,Hui Zhang,Tao Liu,Steven A. Carr +30 more
TL;DR: An optimized workflow for global proteome and phosphoproteome analysis of tissues or cell lines that uses isobaric tags (TMT (tandem mass tags)-10) for multiplexed analysis and relative quantification, and provides 3× higher throughput than iTRAQ-4-based methods with high intra- and inter-laboratory reproducibility is presented.
Journal ArticleDOI
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma
Michael A. Gillette,Michael A. Gillette,Shankha Satpathy,Song Cao,Saravana M. Dhanasekaran,Suhas Vasaikar,Karsten Krug,Francesca Petralia,Yize Li,Wen-Wei Liang,Boris Reva,Azra Krek,Jiayi Ji,Xiaoyu Song,Wenke Liu,Runyu Hong,Lijun Yao,Lili Blumenberg,Sara R. Savage,Michael C. Wendl,Bo Wen,Kai Li,Lauren C. Tang,Lauren C. Tang,Melanie A. MacMullan,Melanie A. MacMullan,Shayan C. Avanessian,M. Harry Kane,Chelsea J. Newton,MacIntosh Cornwell,Ramani B. Kothadia,Weiping Ma,Seungyeul Yoo,Rahul Mannan,Pankaj Vats,Chandan Kumar-Sinha,Emily Kawaler,Tatiana Omelchenko,Antonio Colaprico,Yifat Geffen,Yosef E. Maruvka,Felipe da Veiga Leprevost,Maciej Wiznerowicz,Maciej Wiznerowicz,Zeynep H. Gümüş,Rajwanth R. Veluswamy,Galen Hostetter,David I. Heiman,Matthew A. Wyczalkowski,Tara Hiltke,Mehdi Mesri,Christopher R. Kinsinger,Emily S. Boja,Gilbert S. Omenn,Arul M. Chinnaiyan,Henry Rodriguez,Qing Kay Li,Scott D. Jewell,Mathangi Thiagarajan,Gad Getz,Bing Zhang,David Fenyö,Kelly V. Ruggles,Marcin Cieslik,Ana I. Robles,Karl R. Clauser,Ramaswamy Govindan,Pei Wang,Alexey I. Nesvizhskii,Li Ding,D. R. Mani,Steven A. Carr,Alex Webster,Alicia Francis,Alyssa Charamut,Amanda G. Paulovich,Amy M. Perou,Andrew K. Godwin,Andrii Karnuta,Annette Marrero-Oliveras,Barbara Hindenach,Barbara Pruetz,Bartosz Kubisa,Brian J. Druker,Chet Birger,Corbin D. Jones,Dana R. Valley,Daniel C. Rohrer,Daniel Cui Zhou,Daniel W. Chan,David Chesla,David J. Clark,Dmitry Rykunov,Donghui Tan,Elena V. Ponomareva,Elizabeth R. Duffy,Eric J. Burks,Eric E. Schadt,Erik J. Bergstrom,Eugene S. Fedorov,Ewa P. Malc,George D. Wilson,Hai-Quan Chen,Halina M. Krzystek,Hongwei Liu,Houston Culpepper,Hua Sun,Hui Zhang,Jacob J. Day,James Suh,Jeffrey R. Whiteaker,Jennifer M. Eschbacher,John McGee,Karen A. Ketchum,Karin D. Rodland,Karna Robinson,Katherine A. Hoadley,Kei Suzuki,Ki Sung Um,Kim Elburn,Liang-Bo Wang,Lijun Chen,Linda Hannick,Liqun Qi,Lori J. Sokoll,Małgorzata Wojtyś,Marcin J. Domagalski,Marina A. Gritsenko,Mary Beth Beasley,Matthew E. Monroe,Matthew J. Ellis,Maureen Dyer,Meghan C. Burke,Melissa Borucki,Meng-Hong Sun,Michael H.A. Roehrl,Michael J. Birrer,Michael S. Noble,Michael Schnaubelt,Michael Vernon,Michelle Chaikin,Mikhail Krotevich,Munziba Khan,Myvizhi Esai Selvan,Nancy Roche,Nathan Edwards,Negin Vatanian,Olga Potapova,Pamela Grady,Peter B. McGarvey,Piotr A. Mieczkowski,Pushpa Hariharan,Rashna Madan,Ratna R. Thangudu,Richard D. Smith,Robert J. Welsh,Robert Zelt,Rohit Mehra,Ronald Matteotti,Sailaja Mareedu,Samuel H. Payne,Sandra Cottingham,Sanford P. Markey,Seema Chugh,Shaleigh Smith,Shirley Tsang,Shuang Cai,Simina M. Boca,Sonya Carter,Stacey Gabriel,Stephanie De Young,Stephen E. Stein,Sunita Shankar,Tanya Krubit,Tao Liu,Tara Skelly,Thomas L. Bauer,Uma Velvulou,Umut Ozbek,Vladislav A. Petyuk,Volodymyr Sovenko,William Bocik,William W. Maggio,Xi Chen,Yan Shi,Yige Wu,Yingwei Hu,Yuxing Liao,Zhen Zhang,Zhiao Shi +189 more
TL;DR: Comprehensive proteogenomic characterization of 110 tumors and 101 matched normal adjacent tissues (NATs) incorporating genomics, epigenomics, deep-scale proteomics, phosphoproteomics, and acetylproteomics identified therapeutic vulnerabilities associated with driver events involving KRAS, EGFR, and ALK.
Journal ArticleDOI
Proteogenomic Characterization of Endometrial Carcinoma.
Yongchao Dou,Emily Kawaler,Daniel Cui Zhou,Marina A. Gritsenko,Chen Huang,Lili Blumenberg,Alla Karpova,Vladislav A. Petyuk,Sara R. Savage,Shankha Satpathy,Wenke Liu,Yige Wu,Chia-Feng Tsai,Bo Wen,Zhi Li,Song Cao,Jamie Moon,Zhiao Shi,MacIntosh Cornwell,Matthew A. Wyczalkowski,Rosalie K. Chu,Suhas Vasaikar,Hua Zhou,Qingsong Gao,Ronald J. Moore,Kai Li,Sunantha Sethuraman,Matthew E. Monroe,Rui Zhao,David I. Heiman,Karsten Krug,Karl R. Clauser,Ramani Kothadia,Yosef E. Maruvka,Alexander R. Pico,Amanda E. Oliphant,Emily L. Hoskins,Samuel L. Pugh,Sean J.I. Beecroft,David W Adams,Jonathan C. Jarman,Andy T. Kong,Hui Yin Chang,Boris Reva,Yuxing Liao,Dmitry Rykunov,Antonio Colaprico,Xi Steven Chen,Andrzej Czekański,Marcin Jędryka,Rafal Matkowski,Maciej Wiznerowicz,Maciej Wiznerowicz,Tara Hiltke,Emily S. Boja,Christopher R. Kinsinger,Mehdi Mesri,Ana I. Robles,Henry Rodriguez,David G. Mutch,Katherine Fuh,Matthew J. Ellis,Deborah DeLair,Mathangi Thiagarajan,D. R. Mani,Gad Getz,Michael S. Noble,Alexey I. Nesvizhskii,Pei Wang,Matthew L. Anderson,Douglas A. Levine,Richard D. Smith,Samuel H. Payne,Kelly V. Ruggles,Karin D. Rodland,Karin D. Rodland,Li Ding,Bing Zhang,Tao Liu,David Fenyö,Anupriya Agarwal,Meenakshi Anurag,Dmitry M. Avtonomov,Chet Birger,Michael J. Birrer,Simina M. Boca,William Bocik,Uma Borate,Melissa Borucki,Meghan C. Burke,Shuang Cai,Anna Calinawan,Steven A. Carr,Sonya Carter,Patricia Castro,Sandra Cerda,Michelle Chaikin,Daniel W. Chan,Doug W. Chan,Alyssa Charamut,Feng Chen,Jin Chen,Lijun Chen,Lin Chen,David Chesla,Milan G. Chheda,Arul M. Chinnaiyan,Shrabanti Chowdhury,Marcin Cieslik,David J. Clark,Sandra Cottingham,Houston Culpepper,Jacob J. Day,Stephanie De Young,Emek Demir,Saravana M. Dhanasekaran,Rajiv Dhir,Marcin J. Domagalski,Peter Dottino,Brian J. Druker,Elizabeth R. Duffy,Maureen Dyer,Nathan Edwards,Robert Edwards,Kim Elburn,Jayson B. Field,Alicia Francis,Stacey Gabriel,Yifat Geffen,Daniel J. Geiszler,Michael A. Gillette,Andrew K. Godwin,Pamela Grady,Linda Hannick,Pushpa Hariharan,Sue Hilsenbeck,Barbara Hindenach,Katherine A. Hoadley,Runyu Hong,Galen Hostetter,James J. Hsieh,Yingwei Hu,Michael Ittmann,Eric J. Jaehnig,Scott D. Jewell,Jiayi Ji,Corbin D. Jones,Renee Karabon,Karen A. Ketchum,Munziba Khan,Beom-Jun Kim,Azra Krek,Tanya Krubit,Chandan Kumar-Sinha,Felipe D. Leprevost,Michael T. Lewis,Qing Kay Li,Yize Li,Hongwei Liu,Jan Lubinski,Weiping Ma,Rashna Madan,Ewa P. Malc,Anna Malovannaya,Sailaja Mareedu,Sanford P. Markey,Annette Marrero-Oliveras,John A. Martignetti,Jason E. McDermott,Peter B. McGarvey,John McGee,Piotr A. Mieczkowski,Francesmary Modugno,Rebecca I. Montgomery,Chelsea J. Newton,Gilbert S. Omenn,Amanda G. Paulovich,Amy M. Perou,Francesca Petralia,Paul D. Piehowski,Larisa Polonskaya,Liqun Qi,Shannon Richey,Karna Robinson,Nancy Roche,Daniel C. Rohrer,Eric E. Schadt,Michael Schnaubelt,Yan Shi,Tara Skelly,Lori J. Sokoll,Xiaoyu Song,Stephen E. Stein,James Suh,Donghui Tan,Darlene Tansil,Guo Ci Teo,Ratna R. Thangudu,Cristina E. Tognon,Elie Traer,Jeffrey W. Tyner,Ki Sung Um,Dana R. Valley,Negin Vatanian,Pankaj Vats,Uma Velvulou,Michael Vernon,Liang-Bo Wang,Ying Wang,Alex Webster,Thomas F. Westbrook,David C. Wheeler,Jeffrey R. Whiteaker,George D. Wilson,Yuriy Zakhartsev,Robert Zelt,Hui Zhang,Yuping Zhang,Zhen Zhang,Grace Zhao +219 more
TL;DR: A comprehensive proteogenomic characterization of endometrial carcinomas revealed possible new consequences of perturbations to the p53 and Wnt/β-catenin pathways, identified a potential role for circRNAs in the epithelial-mesenchymal transition, and provided new information about proteomic markers of clinical and genomic tumor subgroups, including relationships to known druggable pathways.