84 research outputs found
A self-organized model for cell-differentiation based on variations of molecular decay rates
- Author
- A Bhattacharjya
- A Bossi
- A Ciechanover
- A Hoffmann
- A Visel
- AC Gavin
- AP Capaldi
- AU Viretta
- B de Chassey
- B SchwanhÀusser
- CC Guet
- CG Langton
- D Bratsun
- D Das
- D Ropers
- D StokiÄ
- EL Greer
- EM Ozbudak
- G Yagil
- GM Church
- H de Jong
- H Kitano
- I Shmulevich
- J Gertz
- J Gsponer
- J Paulsson
- JE Lee
- JH Park
- L Glass
- L Glass
- L Hood
- L Pirkkala
- M Mitchell
- M Ptashne
- M RewieĆski
- MA Beer
- Manfred Pöchacker
- Manuel Schölling
- MB Burg
- MJ Amorim
- N Kashtan
- NM Luscombe
- P Smolen
- Peter Csermely
- R Casey
- R Hanel
- R Jothi
- R MĂ©tivier
- R MĂ©tivier
- RP Zinzen
- Rudolf Hanel
- S Pigolotti
- S Semsey
- SA Kauffman
- SA Vokes
- Stefan Thurner
- TE Turner
- TI Lee
- TR Burkard
- X Qian
- Z Tothova
- Publication venue
- 'Public Library of Science (PLoS)'
- Publication date
- 01/01/2012
- Field of study
Systemic properties of living cells are the result of molecular dynamics
governed by so-called genetic regulatory networks (GRN). These networks capture
all possible features of cells and are responsible for the immense levels of
adaptation characteristic to living systems. At any point in time only small
subsets of these networks are active. Any active subset of the GRN leads to the
expression of particular sets of molecules (expression modes). The subsets of
active networks change over time, leading to the observed complex dynamics of
expression patterns. Understanding of this dynamics becomes increasingly
important in systems biology and medicine. While the importance of
transcription rates and catalytic interactions has been widely recognized in
modeling genetic regulatory systems, the understanding of the role of
degradation of biochemical agents (mRNA, protein) in regulatory dynamics
remains limited. Recent experimental data suggests that there exists a
functional relation between mRNA and protein decay rates and expression modes.
In this paper we propose a model for the dynamics of successions of sequences
of active subnetworks of the GRN. The model is able to reproduce key
characteristics of molecular dynamics, including homeostasis, multi-stability,
periodic dynamics, alternating activity, differentiability, and self-organized
critical dynamics. Moreover the model allows to naturally understand the
mechanism behind the relation between decay rates and expression modes. The
model explains recent experimental observations that decay-rates (or turnovers)
vary between differentiated tissue-classes at a general systemic level and
highlights the role of intracellular decay rate control mechanisms in cell
differentiation.Comment: 16 pages, 5 figure
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
- Author
- A. Abeshouse
- A. Ally
- A. Antenucci
- A. Arnaout
- A. Berchuck
- A. Bergeron
- A. Bossler
- A. Boussioutas
- A. Breggia
- A. Burnette
- A. Chen
- A. Clipca
- A. Davis
- A. De Rienzo
- A. De Rose
- A. Fehrenbach
- A. Gillis
- A. Gimenez-Roqueplo
- A. Gopalan
- A. Haddad
- A. Hartmann
- A. Jimeno
- A. Kastl
- A. Kendler
- A. Kibel
- A. Korkut
- A. Longatto-Filho
- A. Luna
- A. Malykh
- A. Mariamidze
- A. Mes-Masson
- A. Noss
- A. Ochoa
- A. Perin
- A. Piché
- A. Pickens
- A. Rao
- A. Sankarankuty
- A. Secord
- A. Sepulveda
- A. Shabunin
- A. Sharp
- A. Sood
- A. Spillane
- A. Tam
- A. Tischler
- A. Tsao
- A. Unterberg
- A. Vicha
- A. von Deimling
- A.C. Berger
- A.C. de Carvalho
- A.D. Cherniack
- A.D. Cherniack
- A.E. Sloan
- A.G. Robertson
- A.H. Bryce
- A.H. Perou
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- A.J. Mungall
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- A.V. Lee
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- T. Shelton
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- T. Smyrk
- T. Thompson
- T. Wang
- T. Wong
- T. Zelinka
- T.A. Chan
- T.M. Lichtenberg
- U. Veluvolu
- V. Cardinale
- V. Chandan
- V. Dhankani
- V. Jakrot
- V. Korchina
- V. Lyadov
- V. Reuter
- V. Thorsson
- V. Thorsson
- W. Barrett
- W. Eijckenboom
- W. Hale
- W. Kycler
- W. Liu
- W. Oosterhuis
- W. Urba
- W. Ye
- W. Zhang
- W. Zhou
- W.E. Grizzle
- W.G. Richards
- W.J. Edenfield
- W.K. Chatila
- W.K. Rathmell
- W.M. Linehan
- X. Liu
- X. Liu
- X. Sastre
- Y. Han
- Y. Liu
- Y. Shi
- Y. Sun
- Y. Tang
- Y. Wan
- Y. Wolinsky
- Z. Wang
- Z.J. Heins
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/01/2018
- Field of study
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
- Author
- Abdel-Rahman Mohamed H.
- Abeshouse Adam
- Adebamowo Clement
- Adebamowo Sally N.
- Agnew Kathy
- Ahn Keunsoo
- Ajani Jaffer A.
- Akbani Rehan
- Akbani Rehan
- Akeredolu Teniola
- Al-Ahmadie Hikmat
- Al-Ahmadie Hikmat
- Albert Monique
- Alexopoulou Iakovina
- Ally Adrian
- Alvaro Domenico
- Anderson Matthew L.
- Andry Chris
- Antenucci Anna
- Anur Pavana
- Anur Pavana
- Appelbaum Elizabeth L.
- Aredes NatĂĄlia D.
- Armenia Joshua
- Arnaout Angel
- Asa Sylvia L.
- Auman J. Todd
- Aymerich Marta
- Aziz Dina
- Bailey Matthew
- Balasundaram Miruna
- Balu Saianand
- Barnett Gene
- Barnholtz-Sloan Jill S.
- Barrett Wendi
- Bartlett John
- Bathe Oliver
- Baudin Eric
- Baylin Stephen
- Becker Karl-Friedrich
- Beer David
- Behera Madhusmita
- Behrens Carmen
- Bell Debra
- Bell Sue
- Bellair Michelle
- Bennett Joseph
- Benz Christopher
- Benz Christopher
- Berchuck Andrew
- Berger Ashton C.
- Bergeron Alain
- Berkowitz Ross
- Bernard Brady
- Beroukhim Rameen
- Beuschlein Felix
- Bifulco Carlo
- Bigner Darell
- Birrer Michael
- Birsoy Kivanc
- Bocklage Therese
- Bodenheimer Tom
- Bondaruk Jolanta
- Bootwalla Moiz S.
- Borad Mitesh
- Borgia Jeffrey A.
- Bossler Aaron
- Botnariuc Natalia
- Boussioutas Alex
- Bowen Jay
- Bowlby Reanne
- Bowlby Reanne
- Bowman Rayleen
- Bradford Carol
- Bragazzi Maria Consiglia
- Brat Daniel J.
- Breggia Anne
- Brennan Kevin
- Brewer Cathy
- Brimo Fadi
- Broaddus Russell
- Brooks Denise
- Broom Bradley M.
- Broudy Thomas
- Bryce Alan H.
- Bubley Glenn
- Bueno Raphael
- Bullman Susan
- Burnette Andrew
- Byers Lauren Averett
- Caesar-Johnson Samantha J.
- Calatozzolo Chiara
- Campbell Joshua D.
- Campo Elias
- Campos Benito
- Caraman Irina
- Cardinale Vincenzo
- Carey Francis
- Carey Thomas
- Carlotti Carlos Gilberto
- Carlsen Rebecca
- Carney Michael
- Carpino Guido
- Carroll Peter R.
- Carter Candace
- Carvalho Andre L.
- Castle Erik
- Castro Patricia D.
- Catto James
- Cebulla Colleen M.
- Cernat Mircea
- Chabot John
- Chakravarty Debyani
- Chambwe Nyasha
- Chan June M.
- Chan Timothy A.
- Chandan Vishal
- Chang Kyle
- Chatila Walid K.
- Chemencedji Inga
- Chen Amy
- Chen Chu
- Chen Jianhong
- Chen Ting-Wen
- Chen Zhong
- Cheng Feixiong
- Cheng Hui
- Cherniack Andrew D.
- Cherniack Andrew D.
- Chesla David
- Chevalier Simone
- Cheville John
- Chiu Hua-Sheng
- Cho Juok
- Chuah Eric
- Chudamani Sudha
- Chung Ki
- Cibulskis Carrie
- Clipca Adrian
- Coarfa Cristian
- Colman Howard
- Cope Leslie
- Copland John A.
- Corcoran Niall
- Cordes Matthew G.
- Costello Tony
- Cottingham Sandra
- Couce Marta
- Covington Kyle
- Crain Daniel
- Cramer Daniel
- Creaney Jenette
- Creighton Chad J.
- Creighton Chad J.
- Cuppini Lucia
- Curley Erin
- Cuzzubbo Stefania
- Czerniak Bogdan
- Danilova Ludmila
- Davis Amy
- de Bruijn Ino
- de Carvalho Ana C.
- de Krijger Ronald
- De Rienzo Assunta
- De Rose Agostino
- Defreitas Timothy
- Delman Keith
- Demchok John A.
- Desjardins Laurence
- Devine Karen
- Deyarmin Brenda
- Dhalla Noreen
- Dhanasekaran Renumathy
- Dhankani Varsha
- Dhir Rajiv
- Diao Lixia
- Dimeco Francesco
- Ding Li
- Dinh Huyen
- Dinkin Mikhail
- Dipersio John
- Disaia Philip
- Doddapaneni Harshavardhan
- Donehower Larry
- Donehower Lawrence A.
- Doruc Serghei
- Dos Santos Jose SebastiĂŁo
- Dottino Peter R.
- Drake Bettina
- Drill Esther
- Drummond Jennifer
- Drwiega Paul
- Dubina Michael
- Duell Rebecca
- Duffy Elizabeth R.
- Eckman John
- Edenfield W. Jeffrey
- Eijckenboom Wil
- Elder J. Bradley
- Engel Jay
- Eschbacher Jennifer
- Esmaeli Bita
- Evason Kimberley
- Facciolo Francesco
- Fan Cheng
- Fan Huihui
- Fan Huihui
- Fantacone-Campbell J. Leigh
- Farnell Michael
- Farver Carol
- Fassnacht Martin
- Fehrenbach Ashley
- Felau Ina
- Feldman Michael
- Feltmate Colleen
- Ferguson Martin L.
- Finocchiaro Gaetano
- Flores Elsa R.
- Flotte Thomas
- Fong Kwun M.
- Force Seth
- Forgie Ian
- Frazer Scott
- Fregnani José H.
- Fronick Catrina C.
- Fujimoto Junya
- Fulop Jordonna
- Fulton Lucinda A.
- Fulton Robert S.
- Gabra Hani
- Gabriel Stacey B.
- Galbraith Joseph
- Gao Galen F.
- Gao Jianjiong
- Gardner Johanna
- Gastier-Foster Julie M.
- Gaudio Eugenio
- Gay Carl M.
- Gehlenborg Nils
- Gerken Mark
- Gershenwald Jeffrey
- Getz Gad
- Gevaert Olivier
- Ghossein Ronald
- Giama Nasra
- Gibbs Richard A.
- Gilbert Sebastien
- Gillis Ad
- Gimenez-Roqueplo Anne-Paule
- Giné Eva
- Giordano Thomas
- Girard Nicolas
- Giuliante Felice
- Glenn Pat
- Glenn Robert
- Godwin Andrew K.
- Godwin Eryn M.
- Gonzalez Ana Maria Angulo
- Goodman Marc
- Gopalan Anuradha
- Goparaju Chandra
- Gorincioi Ghenadie
- Govindan Ramaswamy
- Graefen Markus
- Grazi Gianluca
- Grizzle William E.
- Gross Benjamin E.
- Guillermo Armando LĂłpez
- Gunaratne Preethi
- Guo Charles
- Ha Gavin
- Haddad Andrea
- Hagedorn Curt H.
- Hale Walker
- Han Yi
- Hanh Phan Thi
- Hansen Paul
- Harr Jodi
- Hartmann Arndt
- Haydu Lauren
- Hayes D. Neil
- Hayes D. Neil
- Hayward Nicholas
- Heath Sharon
- Hegde Apurva
- Hegde Apurva M.
- Heiman David I.
- Heins Zachary J.
- Henderson Joel
- Hermes Beth
- Hernandez Brenda
- Herold-Mende Christel
- Hersey Peter
- Hess Julian
- Hibshoosh Hanina
- Hilty Joe
- Hinoue Toshinori
- Ho Thai
- Hoadley Katherine A.
- Hoadley Katherine A.
- Holt Robert
- Hooke Jeffrey A.
- Hoon Dave
- Horowitz Neil
- Houck John
- Hovens Christopher
- Hoyle Alan P.
- Hu Hai
- Hu Jianhong
- Huland Hartwig
- Hung Nguyen Phi
- Huntsman David
- Hutter Carolyn M.
- Iacocca Mary
- Ittmann Michael
- Jacobus Laura
- Jakrot Valerie
- Janssen Klaus-Peter
- Jefferys Stuart R.
- Jimeno Antonio
- Jones Corbin D.
- Jones Steven J. M.
- Ju Zhenlin
- Juhl Hartmut
- Jungk Christin
- Junker Kerstin
- Kakavand Hojabr
- Kalkanis Steven
- Kanchi Rupa S.
- Kanchi Rupa S.
- Kandoth Cyriac
- Kang Koo Jeong
- Karlan Beth Y.
- Kasaian Katayoon
- Kasapi Melpomeni
- Kastl Alison
- Kebebew Electron
- Kefford Richard
- Kelley Robin K.
- Kemp Rafael
- Kendall Sara
- Kendler Ady
- Kendrick Michael
- Khuri Fadlo
- Kibel Adam
- Kim Jaegil
- Knijnenburg Theo
- Knudson Michael
- Knutson Tina
- Kocher Jean-Pierre
- Kohl Bernard
- Kopp Karla
- Korchina Viktoriya
- Korkut Anil
- Korpershoek Esther
- Korst Robert
- Kovatich Albert J.
- Kramer Roger
- Kucherlapati Melanie H.
- Kucherlapati Raju S.
- Kumar Bahavna
- Kundra Ritika
- Kvecher Leonid
- Kycler Witold
- La Konnor
- Lacombe Louis
- Ladanyi Marc
- Lai Phillip H.
- Laird Peter W.
- Laird Peter W.
- Landen Charles N.
- Landrum Lisa
- Lang James
- Larson Caroline
- Latour Mathieu
- Lau Kevin
- Lawrence Michael S.
- Lazar Alexander J.
- Lazar Alexander J.
- Le Xuan
- Lechan Ronald
- Lee Darlene
- Lee Jung Il
- Lee Kenneth
- Lee Sandra
- Lehman Norman L.
- Leinonen Kalle
- Leraas Kristen M.
- Levine Douglas A.
- Lewis Lora
- Ley Timothy
- Li Jun
- Li Wei
- Liang Han
- Lichtenberg Tara M.
- Lin Pei
- Linehan W. Marston
- Ling Shiyun
- Lipp Eric
- Liptay Michael J.
- Liu Jia
- Liu Wenbin
- Liu Xiuping
- Liu Yuexin
- Liu Yuexin
- Logothetis Christopher
- Lohavanichbutr Pawadee
- Lolla Laxmi
- Long Georgina
- Longatto-Filho Adhemar
- Looijenga Leendert
- Lu Yiling
- Luketich James
- Luna Augustin
- Lyadov Vladimir
- Ma Deqin
- Ma Wencai
- Ma Yussanne
- Madan Rashna
- Maglinte Dennis T.
- Magliocca Kelly
- Maithel Shishir
- Mallery David
- Malykh Andrei
- Mandt Randy
- Manikhas George
- Mann Graham
- Mannel Robert
- Mannelli Massimo
- Mardis Elaine R.
- Mariamidze Armaz
- Mariani Odette
- Marino Mirella
- Marks Jeffrey
- Marra Marco A.
- Martignetti John A.
- Martin Julie
- Mattei Luca
- Mayo Michael
- Mccall Shannon
- Mcgraw Mary
- Mckercher Ginette
- Mclellan Michael D.
- Mclendon Roger
- Mcpherson Christopher
- Meier Sam
- Melamed Jonathan
- Meng Shaowu
- Meric-Bernstam Funda
- Merola Roberta
- Mes-Masson Anne-Marie
- Metwalli Adam R.
- Meyerson Matthew
- Mieczkowski Piotr A.
- Mikkelsen Tom
- Milhem Mohammed
- Miller Christopher A.
- Miller Judy
- Miller Michael
- Mills Gordon B.
- Mirsaidi Cyrus
- Moiseenko Fedor
- Moncrieff Marc
- Moore Kathleen
- Moore Richard A.
- Moran Cesar
- Morgan Margaret
- Morris Scott
- Morrison Carl
- Morton Donna
- Mose Lisle E.
- Moser Catherine
- Moxley Katherine
- Moyer Jeffey
- Mungall Andrew J.
- Mungall Karen
- Mungall Karen L.
- Mura Sergiu
- Mural Richard J.
- Murawa Dawid
- Muto Michael
- Muzny Donna
- Myers Jerome
- Nagorney David
- Nair Praveen
- Naresh Rashi
- Naska Theresa
- Nelson Mark
- Ng Kwok-Shing
- Nguyen Phuong
- Nissan Moriah G.
- Noble Michael S.
- Noss Ardene
- Noushmehr Houtan
- O'Brien Daniel
- O'Neill Brian Patrick
- Ochoa Angelica
- Ojesina Akinyemi I.
- Olabode Oluwole
- Olson Jeffrey J.
- Omberg Larsson
- Oosterhuis Wolter
- Ostrom Quinn T.
- Owonikoko Taofeek
- Pacak Karel
- Paklina Oxana
- Parfitt Jeremy
- Park Joong-Won
- Parker Joel S.
- Pass Harvey
- Patel Tushar
- Paulauskis Joseph
- Pedamallu Chandra Sekhar
- Pennell Nathan A.
- Penny Robert
- Perin Alessandro
- Perou Amy H.
- Perou Charles M.
- Petersen Gloria
- Peterson Lisa
- Peto Myron
- Peto Myron
- Phillips Joanna
- Phillips Sarah M.
- Phu Bui Duc
- Piché Alain
- Pickens Alan
- Pickering Curtis R.
- Pihl Todd
- Pilarski Robert
- Pinero Edna M. Mora
- Pinto Peter A.
- Pirtac Maria
- Pollo Bianca
- Pool Mark
- Porten Sima
- Postier Russel
- Potapova Olga
- Powers James
- Prados Michael
- Prince Mark
- Prunello Marcos
- Que Florencia
- Quinn Michael
- Quintero-Aguilo Mario
- Rabeno Brenda
- Rader Janet S.
- Rai Karan
- Ramalingam Suresh
- Ramirez Nilsa C.
- Ramondetta Lois
- Rao Arvind
- Rassl Doris M.
- Rathmell W. Kimryn
- Raut Chandrajit P.
- Raymond Daniel
- Reis Rui M.
- Reuter Victor
- Reynolds Sheila
- Reznik Ed
- Rice David
- Richards William G.
- Rintoul Robert C.
- Rivera Michael
- Roach Jeffrey
- Roberts Lewis
- Robertson A. Gordon
- Robertson A. Gordon
- Robinson Bruce
- Roggin Kevin
- Roman-Roman Sergio
- Rosenthal Howard G.
- Rozek Laura
- Rubin Mark A.
- Rustgi Anil K.
- Ryan Michael
- Saad Fred
- Sadeghi Sara
- Sadeghi Sara
- Saksena Gordon
- Sanchez-Vega Francisco
- Sander Chris
- Sankarankuty Ajith
- Santibanez Jireh
- Sastre Xavier
- Sauter Guido
- Saw Robyn
- Scapulatempo-Neto Cristovam
- Scarpace Lisa
- Schadendorf Dirk
- Schein Jacqueline E.
- Schiffman Mark
- Schilero Cathy
- Schlomm Thorsten
- Schmidt Heather K.
- Schmidt Laura S.
- Schoenfield Lynn
- Schultz Andre
- Schultz Nikolaus
- Schumacher Steven E.
- Scolyer Richard
- Secord Angeles
- Seder Christopher W.
- Sekhon Harman
- Senecal Kelly
- Sepulveda Antonia
- Setdikova Galiya
- Sexton Katherine C.
- Shabunin Alexey
- Shannon Kerwin
- Sharp Alexis
- Shelley Carl Simon
- Shelton Candace
- Shelton Troy
- Shen Hui
- Shen Hui
- Shen Ronglei
- Sheridan Robert
- Sherman Mark
- Sheth Margi
- Shi Yan
- Shih Juliann
- Shih Juliann
- Shimmel Kristen
- Shin Dong M.
- Shinbrot Eve
- Shipman Cassaundra
- Shmulevich Ilya
- Shriver Craig D.
- Sica Gabriel
- Sifri Suzanne
- Sigmund Rita
- Signoretti Sabina
- Silveira Henrique C. S.
- Simko Jeffry
- Simon Ronald
- Simons Janae V.
- Singer Samuel
- Singh Bhuvanesh
- Singh Rosy
- Sipahimalani Payal
- Skelly Tara
- Sloan Andrew E.
- Slotta-Huspenina Julia
- Smallridge Robert
- Smith Jennifer
- Smith-McCune Karen
- Smolenski Kathy
- Smyrk Thomas
- Sofia Heidi J.
- Soloway Matthew G.
- Somiari Stella
- Sood Anil
- Spellman Paul
- Spillane Andrew
- Stancul Irina
- Stanton Melissa
- Staugaitis Susan M.
- Steele Ruth
- Stepa Serghei
- Stern Marc-Henri
- Stoehr Christine
- Stoehr Robert
- Stoop Hans
- Stretch Onathan
- Stuart Joshua M.
- Stuart Joshua M.
- Su Tao
- Sumazin Pavel
- Sumer S. Onur
- Sun Qiang
- Sun Yichao
- Swanson Patricia
- Swisher Elizabeth
- Synott Maria
- Tam Angela
- Tamakawa Raina
- Tamboli Pheroze
- Tan Donghui
- Tang Yufang
- Tarnuzzer Roy
- Taubert Helge
- Tavobilov Mikhail
- Taylor Alison M.
- Taylor Barry S.
- Tcaciuc Diana
- Tennstedt Pierre
- Thiessen Nina
- Thomas George
- Thompson Eric
- Thompson John
- Thompson R. Houston
- Thompson Timothy
- Thorp Richard
- Thorsson Vesteinn
- Tien Nguyen Viet
- Timmers Henri
- Tirapelli Daniela
- Tischler Arthur
- Torbenson Michael
- Troncoso Patricia
- Tsai Kenneth Y.
- Tsao Anne
- Tse Kane
- Tucker Kelinda
- TĂȘtu Bernard
- Unterberg Andreas
- Urba Walter
- Valdivieso Federico
- Van Bang Nguyen
- Van Den Berg David J.
- van Kessel Kim E.
- Van Meir Erwin G.
- Van Tine Brian
- Van Waes Carter
- Vandenberg Scott
- Veluvolu Umadevi
- Vicha Ales
- Vidal Daniel O.
- Vocke Cathy D.
- Voet Doug
- von Deimling Andreas
- Voronina Olga
- Wach Sven
- Wakely Paul
- Waldmann Jens
- Walker Joan
- Walter Vonn
- Wan Yunhu
- Wang Chen
- Wang Jing
- Wang Jing
- Wang Jioajiao
- Wang Linghua
- Wang Min
- Wang Timothy
- Wang Zhining
- Warnick Ronald
- Weinstein John N.
- Weinstein John N.
- Weisenberger Daniel J.
- Wentzensen Nicolas
- Westervelt Peter
- Wheeler David A.
- Wilkerson Matthew D.
- Williams Felicia
- Wilmott James
- Wilson Richard K.
- Wise Lisa
- Wistuba Ignacio
- Wiznerowicz Maciej
- Wolf Gregory
- Wolinsky Yingli
- Wong Christopher K.
- Wong Christopher K.
- Wong Tina
- Worrell Robert
- Wu Ye
- Wullich Bernd
- Xi Liu
- Yang Hannah
- Yang Ian
- Yang Ju Dong
- Yang Liming
- Yau Christina
- Yau Christina
- Yena Peggy
- Zach Leigh Anne
- Zaren Howard
- Zelinka Tomas
- Zenklusen Jean C.
- Zhang Hailei
- Zhang Hongxin
- Zhang Hongzheng
- Zhang Jiashan (Julia)
- Zhang Jiexin
- Zhang Lizhi
- Zhang Wei
- Zhao Fengmei
- Zhou Jane H.
- Zhou Wanding
- Zmuda Erik
- Zuna Rosemary
- Zuna Rosemary
- Zwarthoff Ellen C.
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/01/2018
- Field of study
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing
molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin
Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context
- Author
- Abdel-Rahman Mohamed H.
- Abeshouse Adam
- Adebamowo Clement
- Adebamowo Sally N.
- Agnew Kathy
- Ahn Keunsoo
- Ajani Jaffer A.
- Akbani Rehan
- Akeredolu Teniola
- Al-Ahmadie Hikmat
- Albert Monique
- Alexopoulou Iakovina
- Ally Adrian
- Alvaro Domenico
- Anderson Matthew L.
- Andry Chris
- Antenucci Anna
- Anur Pavana
- Appelbaum Elizabeth L.
- Aredes NatĂĄlia D.
- Armenia Joshua
- Arnaout Angel
- Asa Sylvia L.
- Auman J. Todd
- Aymerich Marta
- Aziz Dina
- Bailey Matthew
- Balasundaram Miruna
- Balu Saianand
- Barnett Gene
- Barnholtz-Sloan Jill S.
- Barrett Wendi
- Bartlett John
- Bathe Oliver
- Baudin Eric
- Baylin Stephen
- Becker Karl-Friedrich
- Beer David
- Behera Madhusmita
- Behrens Carmen
- Bell Debra
- Bell Sue
- Bellair Michelle
- Bennett Joseph
- Benz Christopher
- Berchuck Andrew
- Berger Ashton C.
- Bergeron Alain
- Berkowitz Ross
- Bernard Brady
- Beroukhim Rameen
- Beuschlein Felix
- Bifulco Carlo
- Bigner Darell
- Birrer Michael
- Birsoy Kivanc
- Bocklage Therese
- Bodenheimer Tom
- Bondaruk Jolanta
- Bootwalla Moiz S.
- Borad Mitesh
- Borgia Jeffrey A.
- Bossler Aaron
- Botnariuc Natalia
- Boussioutas Alex
- Bowen Jay
- Bowlby Reanne
- Bowman Rayleen
- Bradford Carol
- Bragazzi Maria Consiglia
- Brat Daniel J.
- Breggia Anne
- Brewer Cathy
- Brimo Fadi
- Broaddus Russell
- Brooks Denise
- Broom Bradley M.
- Broudy Thomas
- Bryce Alan H.
- Bubley Glenn
- Bueno Raphael
- Burnette Andrew
- Caesar-Johnson Samantha J.
- Calatozzolo Chiara
- Campo Elias
- Campos Benito
- Caraman Irina
- Cardinale Vincenzo
- Carey Francis
- Carey Thomas
- Carlotti Carlos Gilberto
- Carlsen Rebecca
- Carney Michael
- Carpino Guido
- Carroll Peter R.
- Carter Candace
- Carvalho Andre L.
- Castle Erik
- Castro Patricia D.
- Catto James
- Cebulla Colleen M.
- Cernat Mircea
- Chabot John
- Chakravarty Debyani
- Chambwe Nyasha
- Chan June M.
- Chan Timothy A.
- Chandan Vishal
- Chang Kyle
- Chatila Walid K.
- Chatterjee Sujash S.
- Chemencedji Inga
- Chen Amy
- Chen Chu
- Chen Ting-Wen
- Cheng Feixiong
- Cherniack Andrew D.
- Chesla David
- Chevalier Simone
- Cheville John
- Chiu Hua-Sheng
- Cho Juok
- Chuah Eric
- Chudamani Sudha
- Chung Ki
- Cibulskis Carrie
- Clipca Adrian
- Colman Howard
- Cope Leslie
- Copland John A.
- Corcoran Niall
- Cordes Matthew G.
- Costello Tony
- Cottingham Sandra
- Couce Marta
- Covington Kyle
- Crain Daniel
- Cramer Daniel
- Creaney Jenette
- Creighton Chad J.
- Cuppini Lucia
- Curley Erin
- Cuzzubbo Stefania
- Czerniak Bogdan
- Danilova Ludmila
- Davis Amy
- de Bruijn Ino
- de Carvalho Ana C.
- de Krijger Ronald
- De Rienzo Assunta
- De Rose Agostino
- Defreitas Timothy
- Delman Keith
- Demchok John A.
- Desjardins Laurence
- Devine Karen
- Deyarmin Brenda
- Dhalla Noreen
- Dhanasekaran Renumathy
- Dhankani Varsha
- Dhir Rajiv
- Dimeco Francesco
- Ding Li
- Dinh Huyen
- Dinkin Mikhail
- Dipersio John
- Disaia Philip
- Doddapaneni Harshavardhan
- Donehower Lawrence A.
- Doruc Serghei
- Dos Santos Jose SebastiĂŁo
- Dottino Peter R.
- Drake Bettina
- Drummond Jennifer
- Drwiega Paul
- Dubina Michael
- Duell Rebecca
- Duffy Elizabeth R.
- Eckman John
- Edenfield W. Jeffrey
- Eijckenboom Wil
- Elder J. Bradley
- Engel Jay
- Eschbacher Jennifer
- Esmaeli Bita
- Evason Kimberley
- Facciolo Francesco
- Fan Cheng
- Fan Huihui
- Fantacone-Campbell J. Leigh
- Farnell Michael
- Farver Carol
- Fassnacht Martin
- Fehrenbach Ashley
- Felau Ina
- Feldman Michael
- Feltmate Colleen
- Ferguson Martin L.
- Finocchiaro Gaetano
- Flotte Thomas
- Fong Kwun M.
- Force Seth
- Forgie Ian
- Frazer Scott
- Fregnani José H.
- Fronick Catrina C.
- Fujimoto Junya
- Fulop Jordonna
- Fulton Lucinda A.
- Fulton Robert S.
- Gabra Hani
- Gabriel Stacey B.
- Galbraith Joseph
- Gao Galen F.
- Gao Jianjiong
- Gardner Johanna
- Gastier-Foster Julie M.
- Gaudio Eugenio
- Gehlenborg Nils
- Gerken Mark
- Gershenwald Jeffrey
- Getz Gad
- Ghossein Ronald
- Giama Nasra
- Gibbs Richard A.
- Gilbert Sebastien
- Gillis Ad
- Gimenez-Roqueplo Anne-Paule
- Giné Eva
- Giordano Thomas
- Girard Nicolas
- Giuliante Felice
- Glenn Pat
- Glenn Robert
- Godwin Andrew K.
- Godwin Eryn M.
- Gonzalez Ana Maria Angulo
- Goodman Marc
- Gopalan Anuradha
- Goparaju Chandra
- Gorincioi Ghenadie
- Govindan Ramaswamy
- Graefen Markus
- Grazi Gianluca
- Grizzle William E.
- Gross Benjamin E.
- Guillermo Armando LĂłpez
- Gunaratne Preethi H.
- Guo Charles
- Ha Gavin
- Haddad Andrea
- Hagedorn Curt H.
- Hale Walker
- Han Yi
- Hanh Phan Thi
- Hansen Paul
- Harr Jodi
- Hartmann Arndt
- Haydu Lauren
- Hayes D. Neil
- Hayward Nicholas
- Heath Sharon
- Hegde Apurva M.
- Heiman David I.
- Heins Zachary J.
- Henderson Joel
- Hermes Beth
- Hernandez Brenda
- Herold-Mende Christel
- Hersey Peter
- Hess Julian
- Hibshoosh Hanina
- Hilty Joe
- Hinoue Toshinori
- Ho Thai
- Hoadley Katherine A.
- Holt Robert
- Hooke Jeffrey A.
- Hoon Dave
- Horowitz Neil
- Houck John
- Hovens Christopher
- Hoyle Alan P.
- Hu Hai
- Hu Jianhong
- Huland Hartwig
- Hung Nguyen Phi
- Huntsman David
- Hutter Carolyn M.
- Iacocca Mary
- Ittmann Michael
- Jacobus Laura
- Jakrot Valerie
- Janssen Klaus-Peter
- Jefferys Stuart R.
- Jimeno Antonio
- Jones Corbin D.
- Jones Steven J. M.
- Ju Zhenlin
- Juhl Hartmut
- Jungk Christin
- Junker Kerstin
- Kakavand Hojabr
- Kalkanis Steven
- Kanchi Rupa S.
- Kandoth Cyriac
- Kang Koo Jeong
- Karlan Beth Y.
- Kasaian Katayoon
- Kasapi Melpomeni
- Kastl Alison
- Kebebew Electron
- Kefford Richard
- Kelley Robin K.
- Kemp Rafael
- Kendall Sara
- Kendler Ady
- Kendrick Michael
- Khuri Fadlo
- Kibel Adam
- Kim Jaegil
- Knijnenburg Theo
- Knudson Michael
- Knutson Tina
- Kocher Jean-Pierre
- Kohl Bernard
- Kopp Karla
- Korchina Viktoriya
- Korkut Anil
- Korpershoek Esther
- Korst Robert
- Kovatich Albert J.
- Kramer Roger
- Kucherlapati Melanie H.
- Kucherlapati Raju S.
- Kumar Bahavna
- Kundra Ritika
- Kvecher Leonid
- Kycler Witold
- La Konnor
- Lacombe Louis
- Ladanyi Marc
- Lai Phillip H.
- Laird Peter W.
- Landen Charles N.
- Landrum Lisa
- Lang James
- Larson Caroline
- Latour Mathieu
- Lau Kevin
- Lawrence Michael S.
- Lazar Alexander J.
- Le Xuan
- Lechan Ronald
- Lee Darlene
- Lee Jung Il
- Lee Kenneth
- Lee Sandra
- Lehman Norman L.
- Leinonen Kalle
- Leraas Kristen M.
- Levine Douglas A.
- Lewis Lora
- Ley Timothy
- Li Jun
- Li Wei
- Liang Han
- Lichtenberg Tara M.
- Lin Pei
- Linehan W. Marston
- Ling Shiyun
- Lipp Eric
- Liptay Michael J.
- Liu Jia
- Liu Wenbin
- Liu Xiuping
- Liu Yuexin
- Logothetis Christopher
- Lohavanichbutr Pawadee
- Lolla Laxmi
- Long Georgina
- Longatto-Filho Adhemar
- Looijenga Leendert
- Lu Yiling
- Luketich James
- Luna Augustin
- Lyadov Vladimir
- Ma Deqin
- Ma Yussanne
- Madan Rashna
- Maglinte Dennis T.
- Magliocca Kelly
- Maithel Shishir
- Mallery David
- Malykh Andrei
- Mandt Randy
- Manikhas George
- Mann Graham
- Mannel Robert
- Mannelli Massimo
- Mardis Elaine R.
- Mariamidze Armaz
- Mariani Odette
- Marino Mirella
- Marks Jeffrey
- Marra Marco A.
- Martignetti John A.
- Martin Julie
- Mattei Luca
- Mayo Michael
- Mccall Shannon
- Mcgraw Mary
- Mckercher Ginette
- Mclellan Michael D.
- Mclendon Roger
- Mcpherson Christopher
- Meier Sam
- Melamed Jonathan
- Meng Shaowu
- Meric-Bernstam Funda
- Merola Roberta
- Mes-Masson Anne-Marie
- Metwalli Adam R.
- Meyerson Matthew
- Mieczkowski Piotr A.
- Mikkelsen Tom
- Milhem Mohammed
- Miller Christopher A.
- Miller Judy
- Miller Michael
- Mills Gordon B.
- Mirsaidi Cyrus
- Moiseenko Fedor
- Moncrieff Marc
- Moore Kathleen
- Moore Richard A.
- Moran Cesar
- Morgan Margaret
- Morris Scott
- Morrison Carl
- Morton Donna
- Mose Lisle E.
- Moser Catherine
- Moxley Katherine
- Moyer Jeffey
- Mungall Andrew J.
- Mungall Karen
- Mura Sergiu
- Mural Richard J.
- Murawa Dawid
- Muto Michael
- Muzny Donna
- Myers Jerome
- Nagorney David
- Nair Praveen
- Naresh Rashi
- Naska Theresa
- Nelson Mark
- Ng Kwok-Shing
- Nguyen Phuong
- Nissan Moriah G.
- Noble Michael S.
- Noss Ardene
- Noushmehr Houtan
- O'Brien Daniel
- O'Neill Brian Patrick
- Ochoa Angelica
- Olabode Oluwole
- Olson Jeffrey J.
- Omberg Larsson
- Oosterhuis Wolter
- Ostrom Quinn T.
- Owonikoko Taofeek
- Pacak Karel
- Paklina Oxana
- Pan Yinghong
- Parfitt Jeremy
- Park Joong-Won
- Parker Joel S.
- Pass Harvey
- Patel Ektaben
- Patel Tushar
- Patil Sagar L.
- Paulauskis Joseph
- Pennell Nathan A.
- Penny Robert
- Perin Alessandro
- Perou Amy H.
- Perou Charles M.
- Petersen Gloria
- Peterson Lisa
- Peto Myron
- Phillips Joanna
- Phillips Sarah M.
- Phu Bui Duc
- Piché Alain
- Pickens Alan
- Pihl Todd
- Pilarski Robert
- Pinero Edna M. Mora
- Pinto Peter A.
- Pirtac Maria
- Pollo Bianca
- Pool Mark
- Porten Sima
- Postier Russel
- Potapova Olga
- Powers James
- Prados Michael
- Prince Mark
- Que Florencia
- Quinn Michael
- Quintero-Aguilo Mario
- Rabeno Brenda
- Rai Karan
- Ramalingam Suresh
- Ramirez Nilsa C.
- Ramondetta Lois
- Rao Arvind
- Rassl Doris M.
- Rathmell W. Kimryn
- Raut Chandrajit P.
- Raymond Daniel
- Reis Rui M.
- Reuter Victor
- Reynolds Sheila
- Reznik Ed
- Rice David
- Richards William G.
- Rintoul Robert C.
- Rivera Michael
- Roach Jeffrey
- Roberts Lewis
- Robertson A. Gordon
- Robinson Bruce
- Roggin Kevin
- Roman-Roman Sergio
- Rosenthal Howard G.
- Rozek Laura
- Rubin Mark A.
- Ryan Michael
- Saad Fred
- Sadeghi Sara
- Saksena Gordon
- Sanchez-Vega Francisco
- Sander Chris
- Sankarankuty Ajith
- Santibanez Jireh
- Sastre Xavier
- Sauter Guido
- Saw Robyn
- Scapulatempo-Neto Cristovam
- Scarpace Lisa
- Schadendorf Dirk
- Schein Jacqueline E.
- Schiffman Mark
- Schilero Cathy
- Schlomm Thorsten
- Schmidt Heather K.
- Schmidt Laura S.
- Schoenfield Lynn
- Schultz Nikolaus
- Schumacher Steven E.
- Scolyer Richard
- Secord Angeles
- Seder Christopher W.
- Sekhon Harman
- Senecal Kelly
- Sepulveda Antonia
- Setdikova Galiya
- Sexton Katherine C.
- Shabunin Alexey
- Shannon Kerwin
- Sharp Alexis
- Shelley Carl Simon
- Shelton Candace
- Shelton Troy
- Shen Hui
- Sheridan Robert
- Sherman Mark
- Sheth Margi
- Shi Yan
- Shih Juliann
- Shimmel Kristen
- Shin Dong M.
- Shinbrot Eve
- Shipman Cassaundra
- Shmulevich Ilya
- Shriver Craig D.
- Sica Gabriel
- Sifri Suzanne
- Sigmund Rita
- Signoretti Sabina
- Silveira Henrique C. S.
- Simko Jeffry
- Simon Ronald
- Simons Janae V.
- Singer Samuel
- Singh Bhuvanesh
- Singh Rosy
- Singh Vivek P.
- Sipahimalani Payal
- Skelly Tara
- Sloan Andrew E.
- Slotta-Huspenina Julia
- Smallridge Robert
- Smith Jennifer
- Smith-McCune Karen
- Smolenski Kathy
- Smyrk Thomas
- Sofia Heidi J.
- Soloway Matthew G.
- Somiari Stella
- Somvanshi Sonal
- Sood Anil
- Sood Anil K.
- Spellman Paul
- Spillane Andrew
- Stancul Irina
- Stanton Melissa
- Staugaitis Susan M.
- Steele Ruth
- Stepa Serghei
- Stern Marc-Henri
- Stoehr Christine
- Stoehr Robert
- Stoop Hans
- Stretch Jonathan
- Stuart Joshua M.
- Su Tao
- Sumazin Pavel
- Sumer S. Onur
- Sun Qiang
- Sun Yichao
- Swanson Patricia
- Swisher Elizabeth
- Synott Maria
- Tam Angela
- Tamakawa Raina
- Tamboli Pheroze
- Tan Donghui
- Tang Yufang
- Tarnuzzer Roy
- Taubert Helge
- Tavobilov Mikhail
- Taylor Barry S.
- Tcaciuc Diana
- Tennstedt Pierre
- Thiessen Nina
- Thomas George
- Thompson Eric
- Thompson John
- Thompson R. Houston
- Thompson Timothy
- Thorp Richard
- Thorsson Vesteinn
- Tien Nguyen Viet
- Timmers Henri
- Tirapelli Daniela
- Tischler Arthur
- Torbenson Michael
- Troncoso Patricia
- Tsao Anne
- Tse Kane
- Tucker Kelinda
- TĂȘtu Bernard
- Unterberg Andreas
- Urba Walter
- Valdivieso Federico
- Van Bang Nguyen
- Van Den Berg David J.
- van Kessel Kim E.
- Van Meir Erwin G.
- Van Tine Brian
- Vandenberg Scott
- Veluvolu Umadevi
- Vicha Ales
- Vidal Daniel O.
- Vocke Cathy D.
- Voet Doug
- von Deimling Andreas
- Voronina Olga
- Wach Sven
- Wakely Paul
- Waldmann Jens
- Walker Joan
- Wan Yunhu
- Wang Jing
- Wang Jioajiao
- Wang Linghua
- Wang Min
- Wang Timothy
- Wang Zhining
- Warnick Ronald
- Weinstein John N.
- Weisenberger Daniel J.
- Wentzensen Nicolas
- Westervelt Peter
- Wheeler David A.
- Wilkerson Matthew D.
- Williams Felicia
- Wilmott James
- Wilson Richard K.
- Wise Lisa
- Wistuba Ignacio
- Wiznerowicz Maciej
- Wolf Gregory
- Wolinsky Yingli
- Wong Christopher K.
- Wong Tina
- Worrell Robert
- Wu Ye
- Wullich Bernd
- Xi Liu
- Yang Hannah
- Yang Ian
- Yang Ju Dong
- Yang Liming
- Yau Christina
- Yena Peggy
- Zach Leigh Anne
- Zaren Howard
- Zelinka Tomas
- Zenklusen Jean C.
- Zhang Hailei
- Zhang Hongxin
- Zhang Hongzheng
- Zhang Jiashan (Julia)
- Zhang Jiexin
- Zhang Lizhi
- Zhang Wei
- Zhao Fengmei
- Zhou Wanding
- Zmuda Erik
- Zorman Barry
- Zuna Rosemary
- Zwarthoff Ellen C.
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/01/2018
- Field of study
Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts
Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images
- Author
- Abdel-Rahman Mohamed H.
- Abeshouse Adam
- Adebamowo Clement
- Adebamowo Sally N.
- Agnew Kathy
- Ahn Keunsoo
- Ajani Jaffer A.
- Akbani Rehan
- Akeredolu Teniola
- Al-Ahmadie Hikmat
- Albert Monique
- Alexopoulou Iakovina
- Ally Adrian
- Alvaro Domenico
- Anderson Matthew L.
- Andry Chris
- Antenucci Anna
- Anur Pavana
- Appelbaum Elizabeth L.
- Aredes NatĂĄlia D.
- Armenia Joshua
- Arnaout Angel
- Asa Sylvia L.
- Auman J. Todd
- Aymerich Marta
- Aziz Dina
- Bailey Matthew
- Balasundaram Miruna
- Balu Saianand
- Barnett Gene
- Barnholtz-Sloan Jill S.
- Barrett Wendi
- Bartlett John
- Bathe Oliver
- Batiste Rebecca
- Baudin Eric
- Baylin Stephen
- Becker Karl-Friedrich
- Beer David
- Behera Madhusmita
- Behrens Carmen
- Bell Debra
- Bell Sue
- Bellair Michelle
- Bennett Joseph
- Benz Christopher
- Berchuck Andrew
- Berger Ashton C.
- Bergeron Alain
- Berkowitz Ross
- Bernard Brady
- Beroukhim Rameen
- Beuschlein Felix
- Bifulco Carlo
- Bigner Darell
- Birrer Michael
- Birsoy Kivanc
- Bocklage Therese
- Bodenheimer Tom
- Bondaruk Jolanta
- Bootwalla Moiz S.
- Borad Mitesh
- Borgia Jeffrey A.
- Bossler Aaron
- Botnariuc Natalia
- Boussioutas Alex
- Bowen Jay
- Bowlby Reanne
- Bowman Rayleen
- Bradford Carol
- Bragazzi Maria Consiglia
- Brat Daniel J.
- Breggia Anne
- Brewer Cathy
- Brimo Fadi
- Broaddus Russell
- Brooks Denise
- Broom Bradley M.
- Broudy Thomas
- Bryce Alan H.
- Bubley Glenn
- Bueno Raphael
- Burnette Andrew
- Caesar-Johnson Samantha J.
- Calatozzolo Chiara
- Campo Elias
- Campos Benito
- Caraman Irina
- Cardinale Vincenzo
- Carey Francis
- Carey Thomas
- Carlotti Carlos Gilberto
- Carlsen Rebecca
- Carney Michael
- Carpino Guido
- Carroll Peter R.
- Carter Candace
- Carvalho Andre L.
- Castle Erik
- Castro Patricia D.
- Catto James
- Cebulla Colleen M.
- Cernat Mircea
- Chabot John
- Chakravarty Debyani
- Chambwe Nyasha
- Chan June M.
- Chan Timothy A.
- Chandan Vishal
- Chang Kyle
- Chatila Walid K.
- Chemencedji Inga
- Chen Amy
- Chen Chu
- Cheng Feixiong
- Cherniack Andrew D.
- Chesla David
- Chevalier Simone
- Cheville John
- Cho Juok
- Chuah Eric
- Chudamani Sudha
- Chung Ki
- Cibulskis Carrie
- Clipca Adrian
- Colman Howard
- Cope Leslie
- Copland John A.
- Corcoran Niall
- Cordes Matthew G.
- Costello Tony
- Cottingham Sandra
- Couce Marta
- Covington Kyle
- Crain Daniel
- Cramer Daniel
- Creaney Jenette
- Creighton Chad J.
- Cuppini Lucia
- Curley Erin
- Cuzzubbo Stefania
- Czerniak Bogdan
- Danilova Ludmila
- Davis Amy
- de Bruijn Ino
- de Carvalho Ana C.
- de Krijger Ronald
- De Rienzo Assunta
- De Rose Agostino
- Defreitas Timothy
- Delman Keith
- Demchok John A.
- Desjardins Laurence
- Devine Karen
- Deyarmin Brenda
- Dhalla Noreen
- Dhanasekaran Renumathy
- Dhankani Varsha
- Dhir Rajiv
- Dimeco Francesco
- Ding Li
- Dinh Huyen
- Dinkin Mikhail
- Dipersio John
- Disaia Philip
- Doddapaneni Harshavardhan
- Donehower Lawrence A.
- Doruc Serghei
- Dos Santos Jose SebastiĂŁo
- Dottino Peter R.
- Drake Bettina
- Drummond Jennifer
- Drwiega Paul
- Dubina Michael
- Duell Rebecca
- Duffy Elizabeth R.
- Eckman John
- Edenfield W. Jeffrey
- Eijckenboom Wil
- Elder J. Bradley
- Engel Jay
- Eschbacher Jennifer
- Esmaeli Bita
- Evason Kimberley
- Facciolo Francesco
- Fan Cheng
- Fan Huihui
- Fantacone-Campbell J. Leigh
- Farnell Michael
- Farver Carol
- Fassnacht Martin
- Fehrenbach Ashley
- Felau Ina
- Feldman Michael
- Feltmate Colleen
- Ferguson Martin L.
- Finocchiaro Gaetano
- Flotte Thomas
- Fong Kwun M.
- Force Seth
- Forgie Ian
- Frazer Scott
- Fregnani José H.
- Fronick Catrina C.
- Fujimoto Junya
- Fulop Jordonna
- Fulton Lucinda A.
- Fulton Robert S.
- Gabra Hani
- Gabriel Stacey B.
- Galbraith Joseph
- Gao Galen F.
- Gao Jianjiong
- Gardner Johanna
- Gastier-Foster Julie M.
- Gaudio Eugenio
- Gehlenborg Nils
- Gerken Mark
- Gershenwald Jeffrey
- Getz Gad
- Ghossein Ronald
- Giama Nasra
- Gibbs Richard A.
- Gilbert Sebastien
- Gillis Ad
- Gimenez-Roqueplo Anne-Paule
- Giné Eva
- Giordano Thomas
- Girard Nicolas
- Giuliante Felice
- Glenn Pat
- Glenn Robert
- Godwin Andrew K.
- Godwin Eryn M.
- Gonzalez Ana Maria Angulo
- Goodman Marc
- Gopalan Anuradha
- Goparaju Chandra
- Gorincioi Ghenadie
- Govindan Ramaswamy
- Graefen Markus
- Grazi Gianluca
- Grizzle William E.
- Gross Benjamin E.
- Guillermo Armando LĂłpez
- Guo Charles
- Gupta Rajarsi
- Ha Gavin
- Haddad Andrea
- Hagedorn Curt H.
- Hale Walker
- Han Yi
- Hanh Phan Thi
- Hansen Paul
- Harr Jodi
- Hartmann Arndt
- Haydu Lauren
- Hayes D. Neil
- Hayward Nicholas
- Heath Sharon
- Hegde Apurva M.
- Heiman David I.
- Heins Zachary J.
- Henderson Joel
- Hermes Beth
- Hernandez Brenda
- Herold-Mende Christel
- Hersey Peter
- Hess Julian
- Hibshoosh Hanina
- Hilty Joe
- Hinoue Toshinori
- Ho Thai
- Hoadley Katherine A.
- Holt Robert
- Hooke Jeffrey A.
- Hoon Dave
- Horowitz Neil
- Hou Le
- Houck John
- Hovens Christopher
- Hoyle Alan P.
- Hu Hai
- Hu Jianhong
- Huland Hartwig
- Hung Nguyen Phi
- Huntsman David
- Hutter Carolyn M.
- Iacocca Mary
- Ittmann Michael
- Jacobus Laura
- Jakrot Valerie
- Janssen Klaus-Peter
- Jefferys Stuart R.
- Jimeno Antonio
- Jones Corbin D.
- Jones Steven J. M.
- Ju Zhenlin
- Juhl Hartmut
- Jungk Christin
- Junker Kerstin
- Kakavand Hojabr
- Kalkanis Steven
- Kanchi Rupa S.
- Kandoth Cyriac
- Kang Koo Jeong
- Karlan Beth Y.
- Kasaian Katayoon
- Kasapi Melpomeni
- Kastl Alison
- Kebebew Electron
- Kefford Richard
- Kelley Robin K.
- Kemp Rafael
- Kendall Sara
- Kendler Ady
- Kendrick Michael
- Khuri Fadlo
- Kibel Adam
- Kim Jaegil
- Knijnenburg Theo
- Knudson Michael
- Knutson Tina
- Kocher Jean-Pierre
- Kohl Bernard
- Kopp Karla
- Korchina Viktoriya
- Korkut Anil
- Korpershoek Esther
- Korst Robert
- Kovatich Albert J.
- Kramer Roger
- Kucherlapati Melanie H.
- Kucherlapati Raju S.
- Kumar Bahavna
- Kundra Ritika
- Kurc Tahsin
- Kvecher Leonid
- Kycler Witold
- La Konnor
- Lacombe Louis
- Ladanyi Marc
- Lai Phillip H.
- Laird Peter W.
- Landen Charles N.
- Landrum Lisa
- Lang James
- Larson Caroline
- Latour Mathieu
- Lau Kevin
- Lawrence Michael S.
- Lazar Alexander J.
- Lazar Alexander J.
- Le Xuan
- Lechan Ronald
- Lee Darlene
- Lee Jung Il
- Lee Kenneth
- Lee Sandra
- Lehman Norman L.
- Leinonen Kalle
- Leraas Kristen M.
- Levine Douglas A.
- Lewis Lora
- Ley Timothy
- Li Jun
- Li Wei
- Liang Han
- Lichtenberg Tara M.
- Lin Pei
- Linehan W. Marston
- Ling Shiyun
- Lipp Eric
- Liptay Michael J.
- Liu Jia
- Liu Wenbin
- Liu Xiuping
- Liu Yuexin
- Logothetis Christopher
- Lohavanichbutr Pawadee
- Lolla Laxmi
- Long Georgina
- Longatto-Filho Adhemar
- Looijenga Leendert
- Lu Yiling
- Luketich James
- Luna Augustin
- Lyadov Vladimir
- Ma Deqin
- Ma Yussanne
- Madan Rashna
- Maglinte Dennis T.
- Magliocca Kelly
- Maithel Shishir
- Mallery David
- Malykh Andrei
- Mandt Randy
- Manikhas George
- Mann Graham
- Mannel Robert
- Mannelli Massimo
- Mardis Elaine R.
- Mariamidze Armaz
- Mariani Odette
- Marino Mirella
- Marks Jeffrey
- Marra Marco A.
- Martignetti John A.
- Martin Julie
- Mattei Luca
- Mayo Michael
- Mccall Shannon
- Mcgraw Mary
- Mckercher Ginette
- Mclellan Michael D.
- Mclendon Roger
- Mcpherson Christopher
- Meier Sam
- Melamed Jonathan
- Meng Shaowu
- Meric-Bernstam Funda
- Merola Roberta
- Mes-Masson Anne-Marie
- Metwalli Adam R.
- Meyerson Matthew
- Mieczkowski Piotr A.
- Mikkelsen Tom
- Milhem Mohammed
- Miller Christopher A.
- Miller Judy
- Miller Michael
- Mills Gordon B.
- Mirsaidi Cyrus
- Moiseenko Fedor
- Moncrieff Marc
- Moore Kathleen
- Moore Richard A.
- Moran Cesar
- Morgan Margaret
- Morris Scott
- Morrison Carl
- Morton Donna
- Mose Lisle E.
- Moser Catherine
- Moxley Katherine
- Moyer Jeffey
- Mungall Andrew J.
- Mungall Karen
- Mura Sergiu
- Mural Richard J.
- Murawa Dawid
- Muto Michael
- Muzny Donna
- Myers Jerome
- Nagorney David
- Nair Praveen
- Naresh Rashi
- Naska Theresa
- Nelson Mark
- Ng Kwok-Shing
- Nguyen Phuong
- Nguyen Vu
- Nissan Moriah G.
- Noble Michael S.
- Noss Ardene
- Noushmehr Houtan
- O'Brien Daniel
- O'Neill Brian Patrick
- Ochoa Angelica
- Olabode Oluwole
- Olson Jeffrey J.
- Omberg Larsson
- Oosterhuis Wolter
- Ostrom Quinn T.
- Owonikoko Taofeek
- Pacak Karel
- Paklina Oxana
- Parfitt Jeremy
- Park Joong-Won
- Parker Joel S.
- Pass Harvey
- Patel Tushar
- Paulauskis Joseph
- Pennell Nathan A.
- Penny Robert
- Perin Alessandro
- Perou Amy H.
- Perou Charles M.
- Petersen Gloria
- Peterson Lisa
- Peto Myron
- Phillips Joanna
- Phillips Sarah M.
- Phu Bui Duc
- Piché Alain
- Pickens Alan
- Pihl Todd
- Pilarski Robert
- Pinero Edna M. Mora
- Pinto Peter A.
- Pirtac Maria
- Pollo Bianca
- Pool Mark
- Porten Sima
- Postier Russel
- Potapova Olga
- Powers James
- Prados Michael
- Prince Mark
- Que Florencia
- Quinn Michael
- Quintero-Aguilo Mario
- Rabeno Brenda
- Rai Karan
- Ramalingam Suresh
- Ramirez Nilsa C.
- Ramondetta Lois
- Rao Arvind
- Rao Arvind U. K.
- Rassl Doris M.
- Rathmell W. Kimryn
- Raut Chandrajit P.
- Raymond Daniel
- Reis Rui M.
- Reuter Victor
- Reynolds Sheila
- Reznik Ed
- Rice David
- Richards William G.
- Rintoul Robert C.
- Rivera Michael
- Roach Jeffrey
- Roberts Lewis
- Robertson A. Gordon
- Robinson Bruce
- Roggin Kevin
- Roman-Roman Sergio
- Rosenthal Howard G.
- Rozek Laura
- Rubin Mark A.
- Ryan Michael
- Saad Fred
- Sadeghi Sara
- Saksena Gordon
- Saltz Joel
- Samaras Dimitris
- Sanchez-Vega Francisco
- Sander Chris
- Sankarankuty Ajith
- Santibanez Jireh
- Sastre Xavier
- Sauter Guido
- Saw Robyn
- Scapulatempo-Neto Cristovam
- Scarpace Lisa
- Schadendorf Dirk
- Schein Jacqueline E.
- Schiffman Mark
- Schilero Cathy
- Schlomm Thorsten
- Schmidt Heather K.
- Schmidt Laura S.
- Schoenfield Lynn
- Schultz Nikolaus
- Schumacher Steven E.
- Scolyer Richard
- Secord Angeles
- Seder Christopher W.
- Sekhon Harman
- Senecal Kelly
- Sepulveda Antonia
- Setdikova Galiya
- Sexton Katherine C.
- Shabunin Alexey
- Shannon Kerwin
- Sharma Ashish
- Sharp Alexis
- Shelley Carl Simon
- Shelton Candace
- Shelton Troy
- Shen Hui
- Sheridan Robert
- Sherman Mark
- Sheth Margi
- Shi Yan
- Shih Juliann
- Shimmel Kristen
- Shin Dong M.
- Shinbrot Eve
- Shipman Cassaundra
- Shmulevich Ilya
- Shmulevich Ilya
- Shriver Craig D.
- Shroyer Kenneth R.
- Sica Gabriel
- Sifri Suzanne
- Sigmund Rita
- Signoretti Sabina
- Silveira Henrique C. S.
- Simko Jeffry
- Simon Ronald
- Simons Janae V.
- Singer Samuel
- Singh Bhuvanesh
- Singh Pankaj
- Singh Rosy
- Sipahimalani Payal
- Skelly Tara
- Sloan Andrew E.
- Slotta-Huspenina Julia
- Smallridge Robert
- Smith Jennifer
- Smith-McCune Karen
- Smolenski Kathy
- Smyrk Thomas
- Sofia Heidi J.
- Soloway Matthew G.
- Somiari Stella
- Sood Anil
- Spellman Paul
- Spillane Andrew
- Stancul Irina
- Stanton Melissa
- Staugaitis Susan M.
- Steele Ruth
- Stepa Serghei
- Stern Marc-Henri
- Stoehr Christine
- Stoehr Robert
- Stoop Hans
- Stretch Onathan
- Stuart Joshua M.
- Su Tao
- Sumer S. Onur
- Sun Qiang
- Sun Yichao
- Swanson Patricia
- Swisher Elizabeth
- Synott Maria
- Tam Angela
- Tamakawa Raina
- Tamboli Pheroze
- Tan Donghui
- Tang Yufang
- Tarnuzzer Roy
- Taubert Helge
- Tavobilov Mikhail
- Taylor Barry S.
- Tcaciuc Diana
- Tennstedt Pierre
- Thiessen Nina
- Thomas George
- Thompson Eric
- Thompson John
- Thompson R. Houston
- Thompson Timothy
- Thorp Richard
- Thorsson Vesteinn
- Thorsson VĂ©steinn
- Tien Nguyen Viet
- Timmers Henri
- Tirapelli Daniela
- Tischler Arthur
- Torbenson Michael
- Troncoso Patricia
- Tsao Anne
- Tse Kane
- Tucker Kelinda
- TĂȘtu Bernard
- Unterberg Andreas
- Urba Walter
- Valdivieso Federico
- Van Arnam John
- Van Bang Nguyen
- Van Den Berg David J.
- van Kessel Kim E.
- Van Meir Erwin G.
- Van Tine Brian
- Vandenberg Scott
- Veluvolu Umadevi
- Vicha Ales
- Vidal Daniel O.
- Vocke Cathy D.
- Voet Doug
- von Deimling Andreas
- Voronina Olga
- Wach Sven
- Wakely Paul
- Waldmann Jens
- Walker Joan
- Wan Yunhu
- Wang Jing
- Wang Jioajiao
- Wang Linghua
- Wang Min
- Wang Timothy
- Wang Zhining
- Warnick Ronald
- Weinstein John N.
- Weisenberger Daniel J.
- Wentzensen Nicolas
- Westervelt Peter
- Wheeler David A.
- Wilkerson Matthew D.
- Williams Felicia
- Wilmott James
- Wilson Richard K.
- Wise Lisa
- Wistuba Ignacio
- Wiznerowicz Maciej
- Wolf Gregory
- Wolinsky Yingli
- Wong Christopher K.
- Wong Tina
- Worrell Robert
- Wu Ye
- Wullich Bernd
- Xi Liu
- Yang Hannah
- Yang Ian
- Yang Ju Dong
- Yang Liming
- Yau Christina
- Yena Peggy
- Zach Leigh Anne
- Zaren Howard
- Zelinka Tomas
- Zenklusen Jean C.
- Zhang Hailei
- Zhang Hongxin
- Zhang Hongzheng
- Zhang Jiashan (Julia)
- Zhang Jiexin
- Zhang Lizhi
- Zhang Wei
- Zhao Fengmei
- Zhao Tianhao
- Zhou Wanding
- Zmuda Erik
- Zuna Rosemary
- Zwarthoff Ellen C.
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/01/2018
- Field of study
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images
of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL
maps are derived through computational staining using a convolutional neural network trained to
classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and
correlation with overall survival. TIL map structural patterns were grouped using standard
histopathological parameters. These patterns are enriched in particular T cell subpopulations
derived from molecular measures. TIL densities and spatial structure were differentially enriched
among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial
infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic
patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for
the TCGA image archives with insights into the tumor-immune microenvironment
Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas
- Author
- Abdel-Rahman Mohamed H.
- Abeshouse Adam
- Adebamowo Clement
- Adebamowo Sally N.
- Agnew Kathy
- Ahn Keunsoo
- Ajani Jaffer A.
- Akbani Rehan
- Akeredolu Teniola
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- Longatto-Filho Adhemar
- Looijenga Leendert
- Lu Yiling
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- Sun Qiang
- Sun Yichao
- Swanson Patricia
- Swisher Elizabeth
- Synott Maria
- Tam Angela
- Tamakawa Raina
- Tamboli Pheroze
- Tan Donghui
- Tang Yufang
- Tarnuzzer Roy
- Taubert Helge
- Tavobilov Mikhail
- Taylor Barry S.
- Tcaciuc Diana
- Tennstedt Pierre
- Thiessen Nina
- Thomas George
- Thompson Eric
- Thompson John
- Thompson R. Houston
- Thompson Timothy
- Thorp Richard
- Thorsson Vesteinn
- Tien Nguyen Viet
- Timmers Henri
- Tirapelli Daniela
- Tischler Arthur
- Torbenson Michael
- Trivedi Mihir
- Troncoso Patricia
- Tsao Anne
- Tse Kane
- Tucker Kelinda
- TĂȘtu Bernard
- Unterberg Andreas
- Urba Walter
- Valdivieso Federico
- Van Bang Nguyen
- Van Den Berg David J.
- van Kessel Kim E.
- Van Meir Erwin G.
- Van Tine Brian
- Vandenberg Scott
- Veluvolu Umadevi
- Ventura Andrea
- Vicha Ales
- Vidal Daniel O.
- Vocke Cathy D.
- Voet Doug
- von Deimling Andreas
- Voronina Olga
- Wach Sven
- Wakely Paul
- Waldmann Jens
- Walker Joan
- Wan Yunhu
- Wang Jing
- Wang Jioajiao
- Wang Linghua
- Wang Min
- Wang Timothy
- Wang Zhining
- Warnick Ronald
- Weinstein John N.
- Weisenberger Daniel J.
- Wentzensen Nicolas
- Westervelt Peter
- Wheeler David A.
- Wilkerson Matthew D.
- Williams Felicia
- Wilmott James
- Wilson Richard K.
- Wise Lisa
- Wistuba Ignacio
- Wiznerowicz Maciej
- Wolf Gregory
- Wolinsky Yingli
- Wong Christopher K.
- Wong Tina
- Worrell Robert
- Wu Ye
- Wullich Bernd
- Xi Liu
- Yang Hannah
- Yang Ian
- Yang Ju Dong
- Yang Liming
- Yau Christina
- Yena Peggy
- Zach Leigh Anne
- Zaren Howard
- Zelinka Tomas
- Zenklusen Jean C.
- Zhang Hailei
- Zhang Hongxin
- Zhang Hongzheng
- Zhang Jiashan (Julia)
- Zhang Jiexin
- Zhang Lizhi
- Zhang Wei
- Zhang Xiaoyang
- Zhao Fengmei
- Zhao Wei
- Zhou Wanding
- Zmuda Erik
- Zuna Rosemary
- Zwarthoff Ellen C.
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/01/2018
- Field of study
Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN
Microarray Profiling of Phage-Display Selections for Rapid Mapping of Transcription FactorâDNA Interactions
- Author
- A Rosenberg
- AC Gavin
- B Dreier
- C Butteroni
- C Cicchini
- CT Harbison
- D Liko
- D Shore
- DJ Rodi
- EK De Silva
- G Ammerer
- Gordon Freckleton
- H Gadgil
- I Fingerman
- IR Graham
- James R. Broach
- JD Lieb
- JT Kadonaga
- JY Sze
- K Hertveldt
- L Bruhn
- M Dequard-Chablat
- M Isalan
- M Kellis
- M Moore
- M Pritsker
- M Thompson
- MA Beer
- MH Kuo
- Michael Snyder
- MK Alexander
- ML Bulyk
- ML Vignais
- MM Kasten
- MR Parthun
- MS Singer
- NN Iscove
- Novagen
- O Elemento
- O Elemento
- P Hegde
- P Jorgensen
- P Konig
- PF Cliften
- S Danner
- S Fields
- S Mukherjee
- S Tan
- S Tan
- S Tavazoie
- SA Wolfe
- Saeed Tavazoie
- SK Kurdistani
- Soyeon I. Lippman
- T Ito
- X Cheng
- Y Zhang
- Publication venue
- Public Library of Science
- Publication date
- 01/04/2009
- Field of study
Modern computational methods are revealing putative transcription-factor (TF) binding sites at an extraordinary rate. However, the major challenge in studying transcriptional networks is to map these regulatory element predictions to the protein transcription factors that bind them. We have developed a microarray-based profiling of phage-display selection (MaPS) strategy that allows rapid and global survey of an organism's proteome for sequence-specific interactions with such putative DNA regulatory elements. Application to a variety of known yeast TF binding sites successfully identified the cognate TF from the background of a complex whole-proteome library. These factors contain DNA-binding domains from diverse families, including Myb, TEA, MADS box, and C2H2 zinc-finger. Using MaPS, we identified Dot6 as a trans-active partner of the long-predicted orphan yeast element Polymerase A & C (PAC). MaPS technology should enable rapid and proteome-scale study of bi-molecular interactions within transcriptional networks
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.
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- A. Abeshouse
- A. Ally
- A. Antenucci
- A. Arnaout
- A. Berchuck
- A. Bergeron
- A. Bossler
- A. Boussioutas
- A. Breggia
- A. Burnette
- A. Chen
- A. Clipca
- A. Davis
- A. De Rienzo
- A. De Rose
- A. Fehrenbach
- A. Gillis
- A. Gimenez-Roqueplo
- A. Gopalan
- A. Haddad
- A. Hartmann
- A. Jimeno
- A. Kastl
- A. Kendler
- A. Kibel
- A. Korkut
- A. Longatto-Filho
- A. Luna
- A. Malykh
- A. Mariamidze
- A. Mes-Masson
- A. Noss
- A. Ochoa
- A. Perin
- A. Piché
- A. Pickens
- A. Rao
- A. Sankarankuty
- A. Secord
- A. Sepulveda
- A. Shabunin
- A. Sharp
- A. Sood
- A. Spillane
- A. Tam
- A. Tischler
- A. Tsao
- A. Unterberg
- A. Vicha
- A. von Deimling
- A.C. Berger
- A.C. de Carvalho
- A.D. Cherniack
- A.E. Sloan
- A.G. Robertson
- A.H. Bryce
- A.H. Perou
- A.J. Kovatich
- A.J. Lazar
- A.J. Lazar
- A.J. Lazar
- A.J. Mungall
- A.K. Godwin
- A.L. Carvalho
- A.L. Guillermo
- A.M. Hegde
- A.M.A. Gonzalez
- A.P. Hoyle
- A.R. Metwalli
- B. Bernard
- B. Campos
- B. Czerniak
- B. Deyarmin
- B. Drake
- B. Esmaeli
- B. Hermes
- B. Hernandez
- B. Kohl
- B. Kumar
- B. Pollo
- B. Rabeno
- B. Robinson
- B. Singh
- B. Tê
- B. Van Tine
- B. Wullich
- B.A. Van Tine
- B.A. Van Tine
- B.D. Phu
- B.E. Gross
- B.M. Broom
- B.P. O’
- B.S. Taylor
- B.Y. Karlan
- C. Adebamowo
- C. Andry
- C. Behrens
- C. Benz
- C. Bifulco
- C. Bradford
- C. Brewer
- C. Calatozzolo
- C. Carter
- C. Chen
- C. Cibulskis
- C. Fan
- C. Farver
- C. Feltmate
- C. Goparaju
- C. Guo
- C. Herold-Mende
- C. Hovens
- C. Jungk
- C. Kandoth
- C. Larson
- C. Logothetis
- C. Mcpherson
- C. Mirsaidi
- C. Moran
- C. Morrison
- C. Moser
- C. Sander
- C. Scapulatempo-Neto
- C. Schilero
- C. Shelton
- C. Shipman
- C. Stoehr
- C. Yau
- C.A. Miller
- C.C. Fronick
- C.D. Jones
- C.D. Shriver
- C.D. Vocke
- C.G. Carlotti
- C.H. Hagedorn
- C.J. Creighton
- C.K. Wong
- C.M. Cebulla
- C.M. Hutter
- C.M. Perou
- C.N. Landen
- C.P. Raut
- C.S. Shelley
- C.W. Seder
- D. Alvaro
- D. Aziz
- D. Beer
- D. Bell
- D. Bigner
- D. Brooks
- D. Chakravarty
- D. Chesla
- D. Crain
- D. Cramer
- D. Hoon
- D. Huntsman
- D. Lee
- D. Mallery
- D. Morton
- D. Murawa
- D. Muzny
- D. Nagorney
- D. O’
- D. Raymond
- D. Rice
- D. Schadendorf
- D. Tan
- D. Tcaciuc
- D. Tirapelli
- D. Voet
- D.A. Levine
- D.A. Wheeler
- D.I. Heiman
- D.J. Brat
- D.J. Van Den Berg
- D.J. Weisenberger
- D.M. Rassl
- D.M. Shin
- D.N. Hayes
- D.O. Vidal
- D.T. Maglinte
- E. Baudin
- E. Campo
- E. Castle
- E. Chuah
- E. Curley
- E. Gaudio
- E. Giné
- E. Kebebew
- E. Korpershoek
- E. Lipp
- E. Reznik
- E. Shinbrot
- E. Swisher
- E. Thompson
- E. Zmuda
- E.C. Zwarthoff
- E.G. Van Meir
- E.L. Appelbaum
- E.M. Godwin
- E.M.M. Pinero
- E.R. Duffy
- E.R. Mardis
- F. Beuschlein
- F. Brimo
- F. Carey
- F. Chen
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- F. Cheng
- F. Dimeco
- F. Facciolo
- F. Giuliante
- F. Khuri
- F. Meric-Bernstam
- F. Moiseenko
- F. Que
- F. Saad
- F. Sanchez-Vega
- F. Valdivieso
- F. Williams
- F. Zhao
- G. Barnett
- G. Bubley
- G. Carpino
- G. Finocchiaro
- G. Getz
- G. Gorincioi
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- Z. Wang
- Z.J. Heins
- Publication venue
- Cell Rep
- Publication date
- 01/01/2018
- Field of study
Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy
Accelerated surgery versus standard care in hip fracture (HIP ATTACK): an international, randomised, controlled trial
- Author
- Abarca Javiera
- Abarca Luis
- Abdlaziz Ihab
- Abraham Valsamma
- Accetta Riccardo
- Adhye Bharati Anil
- Adili Anthony
- Adinarayanan S
- Aframian Arash
- Aguado Hector J
- Aguilar Marc
- Ahmed Tashfeen
- Ahn Henry
- Ali Arif
- Almas Ayesha
- Alvarado Kim A
- AmbroĆŒy Wojciech
- Anaya Rafael
- Andres-Peiro Jose-Vicente
- Anjum Anila
- Arnuntasupakul Vanlapa
- Arroyo Marta
- Ashraf Mohammed
- Ashraf Muhammad
- Atrey Amit
- Avram Victoria RA
- Balaguer-Castro Mariano
- Balasubramanian Kumar
- Balonov Konstantin
- Bangdiwala Shrikant I
- Bardana Davide D
- Barnawal Satish Prasad
- Bartley Debra
- Baños Victoria
- Beaupre Lauren
- Begum Dilshad
- Belley-Cote Emilie P
- Bentoumi Souad
- Beretta Luigi
- Bergese Sergio D
- Bernaus MartĂ
- Beroud Sebastien
- Bhandari Mohit
- Bhutia Jigme Tshering
- Biccard Bruce M
- Bicknell Ryan T
- Bidkar Prasanna Udupi
- Bilchod Prashanth Nabhirajappa
- Binda Mirko
- Biscardi Anna
- Bisland Stuart
- Bogallo Jose Manuel
- Bohm Eric R
- Bokhari Syedah Saira
- Bonadies Marika
- Boon Huck Wee
- Borate Madhav Pandurang
- Borges Flavia K
- Brokelman Roy B.G.
- Campbell Aaron R
- Campbell Ryan Jonathan
- Cano Juan Ramon
- Carey Timothy
- Carreras-Castañer Anna
- Cassidy Charles
- CastillĂłn Pablo
- Cecconi Maurizio
- Chalacheewa Theerawat
- Chandran Nitheesh
- Chaudier Philippe
- Chaw Sook Hui
- Chee KH
- Chen Brian P-J
- Chetty Sean
- Chin Im Im
- Choi Stephen
- Chouhan Devendra K
- Clark Molly E
- Clinckaert Carol
- Cobben Jan-Hein MG
- Coles Chad P
- Colnaghi Eleonora
- Colombo Chiara
- Colomina Maria J
- Comstock Curt
- Conen David
- Cornu Olivier
- Correia Patricia
- Coughlin Ryan
- Coupal Stephanie A
- Cowan David D
- Crawford Gordon A
- Cruz Encarnacion
- Cullinan Claude
- CĂĄmara-Cabrera Jaume
- Daniels Timothy R
- Dashputra Ravi Prabhakar
- David Jean Stephane
- de Beer Justin
- De Blasio Giuseppe
- De Caso Julio
- De Clippeleir Dirk
- Dealbert Alfred
- Deheshi Benjamin
- Dehghan Niloofar
- Denaro Giuseppe
- Devereaux PJ
- Dhillon Mandeep S
- Dillane Derek
- Dillingham Sally
- Ding Anthony
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- Duncan Andrew W
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- Grzelak Adrian
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- Yuste Antoni
- Yusuf Salim
- Zabalza Ana
- Zaki Amna
- Zhao Yanrui
- Zhou Junlin
- ĆlÄczka PaweĆ
- ĆwiÄch Mariusz
- Publication venue
- 'Elsevier BV'
- Publication date
- 29/02/2020
- Field of study
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.
- Author
- Aanensen David M
- Abudahab Khalil
- Acheson Erwan
- Adams Alexander
- Adams Helen
- Adriaenssens Evelien M
- Afifi Safiah
- Aggarwal Dinesh
- Ahmad Shazaad SY
- Alam Mohammad T
- Alcolea-Medina Adela
- Alderton Alex
- Alikhan Nabil-Fareed
- Allan John
- Allara Elias
- Amato Roberto
- Andersson Monique
- Angyal Adrienn
- Aranday-Cortes Elihu
- Ariani Cristina
- Asad Hibo
- Asamaphan Patawee
- Ashworth Jordan
- Atkinson Laura
- Attwood Stephen
- Auckland Cressida
- Awan Ali R
- Aydin Alp
- Baker David J
- Baker Paul
- Balcazar Carlos E
- Ball Jonathan
- Barton Edward
- Bashton Matthew
- Batra Rahul
- Baxter Laura
- Beale Mathew A
- Beaver Charlotte
- Beckett Angela
- Beer Robert
- Beggs Andrew
- Bell Andrew
- Bellis Katherine L
- Berger Duncan J
- Berriman Matt
- Berry Lisa
- Berry Louise
- Betancor Gilberto
- Betteridge Emma
- Bewshea Claire M
- Bibby David
- Bicknell Kelly
- Birchley Alec
- Bird Paul
- Bishop Chloe
- Blane Beth
- Bolt Frances
- Bonsall David
- Boswell Tim
- Bosworth Andrew
- Bourgeois Yann
- Boyd Olivia
- Boyes John
- Bradley Declan T
- Bradshaw Daniel
- Breen Cassie
- Bresner Catherine
- Breuer Judith
- Bridgewater Hannah E
- Brooks Tony T
- Broos Alice
- Brown Julianne Rose
- Brown Paul E
- Brown Rebecca
- Brunker Kirstyn
- Bucca Giselda
- Buck David
- Buddenborg Sarah K
- Bull Matthew
- Bull Matthew
- Burton-Fanning Shirelle
- Butcher Ethan
- Caddy Sarah L
- Caller Laura G
- Campbell Sharon
- Carlile Matthew
- Carmichael Stephen N
- Casey Anna
- Castellano Sergi
- Chalker Vicki
- Chand Meera
- Chapman Michael R
- Chappell Joseph G
- Charalampous Themoula
- Charles Ian G
- Chaudhry Yasmin
- Chauhan Anoop J
- Cheng Jeffrey KJ
- Churcher Carol M
- Clark Gemma
- Coll Francesc
- Collins Jennifer
- Colquhoun Rachel
- Colquhoun Rachel M
- Connor Thomas R
- Connor Thomas R
- Constantinidou Chrystala
- Coombes Jason
- Corden Sally
- Cormie Claire
- Cortes Nicholas
- Cortes Nick
- Cottrell Simon
- Coupland Lindsay J
- Cowell Angela
- Cox Alison
- Craine Noel
- Cronin Michelle
- Crooke Derrick
- Curran Martin D
- Curran Tanya
- da Silva Filipe Ana
- da Silva Filipe Ana
- Dabrera Gavin
- Danesh John
- Darby Alistair C
- Davidson Rose K
- Davies Alisha
- Davis Thomas
- de Cesare Mariateresa
- De Lacy Elen
- de Oliveira Martins Leonardo
- de Silva Thushan I
- Debebe Johnny
- Dervisevic Samir
- Dewar Rebecca
- Dias Joana
- Diaz Maria
- Dibling Thomas
- Dorman Matthew J
- Downing Fatima
- Drury Eleanor
- du Plessis Louis
- Duckworth Nichola
- Dyal Patricia L
- Eccles Richard
- Edgeworth Jonathan
- Edwards Sue
- Eldirdiri Sahar
- Ellaby Nicholas
- Ellard Sian
- Elliott Scott
- Eltringham Gary
- Elumogo Ngozi
- Essex Sarah
- Evans Cariad
- Evans Johnathan M
- Eyre David
- Fairley Derek J
- Fallon Karlie
- Farbos Audrey
- Farr Ben
- Feltwell Theresa
- Fina Laia
- Findlay Jacqueline
- Fisher Chloe L
- Fleming Vicki M
- Forrest Leysa M
- Forrest Sally
- Foulser Luke
- Francois Sarah
- Fraser Christophe
- Freeman Timothy M
- Frost Lucy R
- Fuller William
- Gallagher Eileen
- Gallagher Michael D
- Garcia-Casado Maria V
- Gaskin Amy
- Gatica-Wilcox Bree
- Gavriil Artemis
- Geidelberg Lily
- Geidelberg Lily
- Gemmell Matthew
- Georgana Iliana
- George Ryan P
- Gifford Laura
- Gilbert Lauren
- Gill Harmeet K
- Gilroy Rachel AJ
- Girgis Sophia T
- Glaysher Sharon
- Golubchik Tanya
- Goncalves Sonia
- Goodfellow Ian
- Goodfellow Ian G
- Goodwin Scott
- Graham Clive
- Graham Lee
- Grammatopoulos Dimitris
- Green Angie
- Green Luke R
- Greenaway Jane
- Gregory Richard
- Griffith Luke
- Groves Danielle C
- Groves Natalie
- Guest Martyn
- Gulliver Huw
- Gutierrez Ana Victoria
- Hadjirin Nazreen F
- Haldenby Sam T
- Hale Antony D
- Hall Grant
- Halstead Fenella
- Hamilton William L
- Haque Tanzina
- Harper Katherine L
- Harris Kathryn Ann
- Harrison Ewan M
- Harrison Ian
- Harrison James W
- Hartman Hassan
- Hattersley Andrew
- Heaney Judith
- Helmer Thomas
- Hesketh Andrew R
- Heyburn David
- Higginson Ellen E
- Hill Verity
- Hill Verity
- Hilvers Ember
- Hiscox Julian A
- Holden Matthew TG
- Holmes Alison
- Holmes Christopher
- Holmes Nadine
- Hoosdally Sarah
- Hopes Richard
- Hosmillo Myra
- Houldcroft Charlotte J
- Howe Robin
- Howson-Wells Hannah C
- Hubb Jonathan
- Hughes Joseph
- Hughes Margaret
- Hunter Adam D
- Hutchings Stephanie
- Impey Robert
- Irish-Tavares Dianne
- Iturriza-Gomara Miren
- Jackson Ben
- Jackson Ben
- Jackson David A
- Jackson David K
- Jackson Kathryn A
- Jahun Aminu S
- James Keith
- Jamrozy Dorota
- Jarrett Ruth
- Jeffries Aaron R
- Jesudason Natasha
- Jesudason Natasha G
- John Michaela
- Johnson Kate
- Johnson Natasha
- Johnson Rob
- Johnson Robert
- Johnston Ian
- Jones Hannah
- Jones Katie
- Jones Rachel
- Jones Sophie
- Jorgensen David
- Jorgensen David
- Joseph Amelia
- Justice Anita
- Kane Leanne
- Kay Gemma L
- Kay Sally
- Keatley Jon-Paul
- Keeley Alexander J
- Kenyon Anita
- Kermack Leanne M
- Khakh Manjinder
- Khokhar Fahad A
- Kidd Stephen
- Kingsley Robert A
- Kitchen Christine
- Knight Bridget A
- Kolyva Anastasia
- Koshy Cherian
- Kraemer Moritz
- Kristiansen Mark
- Kumziene-Summerhayes Sara
- Kwiatkowski Dominic
- Lackenby Angie
- Langford Cordelia
- Lawniczak Mara
- Le-Viet Thanh
- Lee David
- Lee Jack CD
- Letchford Laura
- Levene Nick
- Levett Lisa J
- Li Kathy
- Li Kathy K
- Liggett Steven
- Lindsey Benjamin B
- Lister Michelle M
- Livett Rich
- Lloyd Allyson
- Lo Stephanie
- Loh Joshua
- Loman Nicholas J
- Loman Nicholas J
- Loose Matthew W
- Loveson Katie F
- Lowe Hannah
- Lucaci Anita O
- Ludden Catherine
- Lynch Jessica
- Lyons Ronan A
- Macfarlane-Smith Louissa R
- Machin Nicholas W
- MacIntyre-Cockett George
- Madona Pinglawathee
- Maes Mailis
- Mahungu Tabitha W
- Mair Daniel
- Maksimovic Joshua
- Manesis Nikos
- Manley Robin
- Manso Carmen
- Marchbank Angela
- Martincorena Inigo
- Martinez-Nunez Rocio T
- Masoli Jane AH
- Mason Jenifer
- Mather Alison E
- Mbisa Tamyo
- McCluggage Kathryn
- McClure Patrick C
- McCrone John T
- McCrone JT
- McGuigan Samantha
- McHugh Martin P
- McKenna James P
- McKerr Caoimhe
- McMinn Liz
- McMurray Claire
- Meader Emma J
- Meadows Lizzie
- Menegazzo Mirko
- Meredith Luke W
- Merrick Ian
- Mestek-Boukhibar Lamia
- Miah Shahjahan
- Michell Stephen L
- Michelsen Michelle L
- Molnar Zoltan
- Monaghan Lynn
- Mookerjee Siddharth
- Moore Catherine
- Moore Catrin
- Moore Christopher
- Moore Nathan
- Morgan Mari
- Morgan Sian
- Mori Matilde
- Moses Samuel
- Muir Peter
- Munn Robert
- Myers Richard
- Nascimento Fabricia F
- Nascimento Fabricia F
- Naydenova Plamena
- Neaverson Alexandra S
- Nebbia Gaia
- Nelson Andrew
- Nelson Charlotte
- Nelson Rachel
- Nicholls Sam
- Nicholls Samuel M
- Nichols Jenna
- Niebel Marc O
- Niola Paola
- Nomikou Kyriaki
- O'Toole Elaine
- O'Toole Ăine
- Orton Richard J
- Osman Husam
- Ott Sascha
- OâGrady Justin
- OâToole Ăine
- Pacchiarini Nicole
- Pacchiarini Nicole
- Padgett Debra
- Page Andrew J
- Palmer Sophie
- Palmer Steve
- Panchbhaya Yasmin N
- Pandey Sarojini
- Park Naomi
- Parker Matthew D
- Parmar Surendra
- Parr Yasmin A
- Parsons Paul J
- Partridge David G
- Pascall David J
- Patel Gaurang
- Patel Minal
- Patel Vineet
- Paterson Steve
- Payne Brendan AI
- Peacock Sharon J
- Pearson Clare
- Perry Malorie
- Peto Timothy
- Pinckert Malte L
- Platt Steven
- Plimmer Amy
- Poplawski Radoslaw
- Potter Will
- Prakash Reenesh
- Prestwood Liam
- Price Anna
- Price Anna
- Price James
- Puethe Christoph
- Pybus Oliver
- Pybus Oliver G
- Pymont Hannah M
- Quail Mike
- Quick Joshua
- Raghwani Jayna
- Ragonnet-Cronin Manon
- Rainbow Lucille
- Rajatileka Shavanthi
- Rambaut Andrew
- Rambaut Andrew
- Ramsay Mary
- Randell Paul A
- Raviprakash Veena
- Raza Mohammad
- Resende Silva Paola C
- Rey Sara
- Rey Sara M
- Reynolds Nicola
- Richter Alex
- Robertson David L
- Robertson David L
- Robinson Esther
- Robinson Trevor I
- Robson Samuel C
- Rogers Hazel A
- Rooke Stefan
- Rowan Aileen
- Rowe Will
- Roy Sunando
- Rudder Steven
- Ruis Chris
- Ryan Felicity
- Sambles Christine M
- Sang Fei
- Scarlett Garry P
- Schaefer Ulf
- Scher Emily
- Scott Carol
- Scott Garren
- Sethi Dheeraj K
- Shaaban Sharif
- Shah Divya
- Shah Rajiv
- Shah Rajiv N
- Shankar Giri
- Shaw Robert
- Shepherd James
- Shepherd James G
- Sheriff Nicola
- Shirley Lesley
- Signell Adrian W
- Sillitoe John
- Simpson David A
- Singer Joshua B
- Sivaprakasam Venkat
- Siveroni Igor
- Siveroni Igor
- Sloan Tim J
- Sluga Graciela
- Smith Christen
- Smith Colin P
- Smith Darren L
- Smith Nikki
- Smith Wendy
- Smollett Katherine L
- Snell Luke B
- Souster Emily
- Southgate Joel
- Southgate Joel
- Spellman Karla
- Spencer-Chapman Michael
- Sridhar Sushmita
- Stanley Rachael
- Stanton Thomas D
- Starinskij Igor
- Stark Richard
- Stockton Joanne
- Stuart Claire
- Studholme David J
- Swindells Emma
- Swingler Tracey
- Taha Yusri
- Tang Julian
- Taylor Ben EW
- Taylor Graham P
- Taylor Sarah
- Taylor-Joyce Grace
- Tedim Ana P
- Temperton Ben
- Templeton Kate E
- Thompson Thomas
- Thomson Emma C
- Thomson Emma C
- Thomson Nicholas M
- Thornton Alicia
- Thurston Scott
- Todd John A
- Tong Lily
- Tonkin-Hill Gerry
- Torok M Estee
- Trebes Amy
- Trotter Alexander J
- Tsoleridis Theocharis
- Tucker Rachel M
- Turtle Lance
- Tutill Helena J
- Underwood Anthony P
- Unnikrishnan Meera
- Vamos Edith E
- Vasylyeva Tetyana
- Vattipally Sreenu
- Vipond Ian B
- Volz Erik
- Volz Erik M
- Wain John
- Walsh Sarah
- Wang Dennis
- Wantoch Michelle
- Warne Ben
- Warwick-Dugdale Joanna
- Wastenge Elizabeth
- Watkins Joanne
- Watts Joanne
- Waugh Sheila
- Webber Mark A
- Weeks Sam
- Weldon Danni
- Whitehead Mark
- Williams Charlotte A
- Williams Chris
- Williams David
- Williams Rachel J
- Williams Rebecca
- Williams Thomas
- Williamson Kathleen A
- Willingham Iona
- Wilson Harry D
- Wise Emma
- Workman Trudy
- Wright Victoria
- Wyles Matthew
- Wyllie Sarah
- Yakovleva Anna
- Yasir Muhammad
- Yeats Corin A
- Yew Wen C
- Young Gregory R
- Young Jamie
- Yu Xiaoyu
- Zarebski Alex
- Publication venue
- Cell
- Publication date
- 01/09/2020
- Field of study
Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant
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