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Simina M. Boca
Researcher at Georgetown University Medical Center
Publications - 80
Citations - 5520
Simina M. Boca is an academic researcher from Georgetown University Medical Center. The author has contributed to research in topics: Cancer & Neuron. The author has an hindex of 23, co-authored 76 publications receiving 3816 citations. Previous affiliations of Simina M. Boca include National Institutes of Health & Silver Spring Networks.
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Journal ArticleDOI
Opportunities and obstacles for deep learning in biology and medicine.
Travers Ching,Daniel Himmelstein,Brett K. Beaulieu-Jones,Alexandr A. Kalinin,Brian T. Do,Gregory P. Way,Enrico Ferrero,Paul-Michael Agapow,Michael Zietz,Michael M. Hoffman,Michael M. Hoffman,Wei Xie,Gail L. Rosen,Benjamin J. Lengerich,Johnny Israeli,Jack Lanchantin,Stephen Woloszynek,Anne E. Carpenter,Avanti Shrikumar,Jinbo Xu,Evan M. Cofer,Evan M. Cofer,Christopher A. Lavender,Srinivas C. Turaga,Amr Alexandari,Zhiyong Lu,David J. Harris,Dave DeCaprio,Yanjun Qi,Anshul Kundaje,Yifan Peng,Laura K. Wiley,Marwin H. S. Segler,Simina M. Boca,S. Joshua Swamidass,Austin Huang,Anthony Gitter,Anthony Gitter,Casey S. Greene +38 more
TL;DR: It is found that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art.
Journal ArticleDOI
The Genetic Landscape of the Childhood Cancer Medulloblastoma
D. Williams Parsons,D. Williams Parsons,Meng Li,Xiaosong Zhang,Siân Jones,Rebecca J. Leary,Jimmy Lin,Simina M. Boca,Hannah Carter,Josue Samayoa,Chetan Bettegowda,Chetan Bettegowda,Gary L. Gallia,George I. Jallo,Zev A. Binder,Yuri Nikolsky,James Hartigan,Doug R. Smith,Daniela S. Gerhard,Daniel W. Fults,Scott R. VandenBerg,Mitchel S. Berger,Suely Kazue Nagahashi Marie,Sueli Mieko Oba Shinjo,Carlos Clara,Peter C. Phillips,Jane E. Minturn,Jaclyn A. Biegel,Alexander R. Judkins,Adam C. Resnick,Phillip B. Storm,Tom Curran,Yiping He,B.K. Ahmed Rasheed,Henry S. Friedman,Stephen T. Keir,Roger E. McLendon,Paul A. Northcott,Michael D. Taylor,Peter C. Burger,Gregory J. Riggins,Gregory J. Riggins,Rachel Karchin,Giovanni Parmigiani,Darell D. Bigner,Hai Yan,Nick Papadopoulos,Bert Vogelstein,Kenneth W. Kinzler,Victor E. Velculescu +49 more
TL;DR: Key differences between the genetic landscapes of adult and childhood cancers are demonstrated, dysregulation of developmental pathways as an important mechanism underlying MBs is highlighted, and a role for a specific type of histone methylation in human tumorigenesis is identified.
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
Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers
Rebecca J. Leary,Jimmy Lin,Jordan M. Cummins,Simina M. Boca,Laura D. Wood,D. Williams Parsons,Siân Jones,Tobias Sjöblom,Ben Ho Park,Ramon Parsons,Joseph Willis,Dawn M. Dawson,James K V Willson,Tatiana Nikolskaya,Yuri Nikolsky,Levy Kopelovich,Nick Papadopoulos,Len A. Pennacchio,Tian Li Wang,Sanford D. Markowitz,Giovanni Parmigiani,Kenneth W. Kinzler,Bert Vogelstein,Victor E. Velculescu +23 more
TL;DR: A genome-wide analysis of Copy number changes in breast and colorectal tumors using approaches that can reliably detect homozygous deletions and amplifications found that the number of genes altered by major copy number changes, deletion of all copies or amplification to at least 12 copies per cell, averaged 17 per tumor.
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.