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Wyświetlanie 1-10 z 12
Tytuł:
Augmenting precision medicine via targeted RNA-Seq detection of expressed mutations
Autorzy:
Pabón-Peña, Carlos
Scherer, Andreas
Łabaj, Paweł
Mason, Christopher E.
Lucas, Anne Bergstrom
Li, Jianying
Gong, Binsheng
Johann, Donald J.
Richmond, Todd A.
Mozsary, Christopher
Butler, Daniel
Ebrahim Sahraeian, Sayed Mohammad
Jones, Wendell
Maestro, Roberta
Xu, Joshua
Willey, James C.
Bushel, Pierre R.
Li, Dan
Pan, Bohu
Kusko, Rebecca
Novoradovskaya, Natalia
Kreil, David P.
Chen, Guangchun
Foox, Jonathan
Tilgner, Hagen U.
Opis:
In precision medicine, DNA-based assays are currently necessary but not always sufficient for predicting therapeutic efficacy of cancer drugs based on the mutational findings in a patient’s tumor specimen. Most drugs target proteins, but it is challenging and not yet cost-effective to perform high-throughput proteomics profiling, including mutational analysis, on cancer specimens. RNA may be an effective mediator for bridging the "DNA to protein divide" and provide more clarity and therapeutic predictability for precision oncology. While RNA sequencing (RNA-seq) has been increasingly used alongside DNA cancer mutation screening panels to assess the impact of variants on gene transcript expression and splicing, comprehensive evaluations of RNA panels and the integration of expressed mutation data analytics to supplement DNA panels are still limited. In this study, we conducted targeted RNA-seq on a reference sample set for expressed variant detection to explore its potential capability to complement DNA variant results or detect variants independently. The results indicated that, with a carefully controlled false positive rate ensuring high accuracy, RNA-seq uniquely identified variants with significant pathological relevance that were missed by DNA-seq, demonstrating its potential to uncover clinically actionable mutations. On the other hand, while some variants were detected by both approaches, others were missed by one or the other, reflecting either the nature of these variants or limitations of the bioinformatics tools used. Variants missed by RNA-seq are often not expressed or expressed at very low levels, suggesting they may be of lower clinical relevance. Incorporating RNA-seq into clinical biomarker panels will ultimately advance precision medicine and improve patient outcomes by improving the strength and reliability of somatic mutation findings for clinical diagnosis, prognosis and prediction of therapeutic efficacy.
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Tytuł:
Long-term nitrogen deposition reduces the diversity of nitrogen-fixing plants
Autorzy:
Lenoir, Jonathan
Reyes-Mendez, Evelin Y.
Orczewska, Anna
Heinken, Thilo
Reczyńska, Kamila
Jha, Rohit Raj
Van Calster, Hans
Schmidt, Wolfgang
Verheyen, Kris
Guralnick, Robert P.
Decocq, Guillaume
Świerkosz, Krzysztof
Folk, Ryan
Berki, Imre
Schei, Fride Høistad
Brunet, Jörg
Moreno-García, Pablo
Petřík, Petr
Máliš, František
Liu, Yu
Bernhardt-Römermann, Markus
De Frenne, Pieter
Naaf, Tobias
Standovár, Tibor
Kopecký, Martin
Chudomelová, Markéta
Hédl, Radim
Baeten, Lander
Waller, Donald M.
Becker-Scarpitta, Antoine
Teleki, Balázs
Macek, Martin
Grytnes, John-Arvid
Closset, Deborah
Montaño-Centellas, Flavia
Li, Daijiang
Stachurska-Swakoń, Alina
Vild, Ondřej
Gilliam, Frank S.
Jaroszewicz, Bogdan
Opis:
Biological nitrogen fixation is a fundamental part of ecosystem functioning. Anthropogenic nitrogen deposition and climate change may, however, limit the competitive advantage of nitrogen-fixing plants, leading to reduced relative diversity of nitrogen-fixing plants. Yet, assessments of changes of nitrogen-fixing plant long-term community diversity are rare. Here, we examine temporal trends in the diversity of nitrogen-fixing plants and their relationships with anthropogenic nitrogen deposition while accounting for changes in temperature and aridity. We used forest-floor vegetation resurveys of temperate forests in Europe and the United States spanning multiple decades. Nitrogen-fixer richness declined as nitrogen deposition increased over time but did not respond to changes in climate. Phylogenetic diversity also declined, as distinct lineages of N-fixers were lost between surveys, but the “winners” and “losers” among nitrogen-fixing lineages varied among study sites, suggesting that losses are context dependent. Anthropogenic nitrogen deposition reduces nitrogen-fixing plant diversity in ways that may strongly affect natural nitrogen fixation.
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Tytuł:
Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions
Autorzy:
Ma, Charles
Supplee, Julianna
Zhang, Sa
Kreil, David Philip
Blomquist, Thomas M.
Tom, Nikola
Xiao, Chunlin
Li, Weihua
LoCoco, Jennifer S.
Jones, Wendell
Megherbi, Dalila B.
Hipp, Jennifer
Horvath, Kyle
Strahl, Maya
Marella, Narasimha
Silla-Castro, Juan Carlos
López, Mario Solís
Qu, Wubin
Liang, Yu
Verma, Suman
Eterovic, Agda Karina
Pirooznia, Mehdi
Pabón-Peña, Carlos
Ghosal, Abhisek
Craig, Daniel J.
Chen, Tao
Hennigan, Brittany
Deveson, Ira W.
Qiu, Fujun
Chang, Chia-Jung
del Pozo, Angela
Tang, Lin-ya
Yip, Shun H.
Duncan, Daniel
Hu, Jianhong
Stetson, Daniel
Shi, Tieliu
Li, Quan-Zhen
Shaknovich, Rita
Chin, Christopher R.
Richmond, Todd A.
Willey, James C.
Bhandari, Ambica
Sebra, Robert
Zhang, Guangliang
Burgess, Daniel
Tichý, Boris
Jarosz, Mirna
Liu, Liang-Chun
Fan, Xiaohui
Szankasi, Philippe
Bushel, Pierre R.
Haseley, Nathan
Gong, Binsheng
Scherer, Andreas
Glenn, Sean
Crawford, Erin
Hong, Huixiao
Martín-Arenas, Rubén
Hung, Li-Yuan
Wirta, Valtteri
Chaubey, Alka
Bao, Wenjun
Li, Zhiguang
Shi, Leming
Zhou, Xiaoyan
Kerkhof, Jennifer
Lader, Eric
Garcia, Elena Vallespin
Chierici, Marco
Xu, Shibei
Li, Dan
Xu, Joshua
Liu, Zhichao
Morrison, Tom
Walker, Kimbley
Tan, Haowen
Mason, Christopher E.
Johann, Donald J.
Łabaj, Paweł
Butler, Daniel J.
Wang, Junwen
Best, Hunter
Ning, Baitang
Parsons, Barbara L.
Arib, Hanane
Thierry-Mieg, Danielle
Lapunzina, Pablo
Blackburn, James
Tao, Yonghui
Wang, Charles
Thomas, David
Zhao, Meiru
Happe, Scott
Cai, Wanshi
Zheng, Yuanting
Stuart, Alan
Shi, Qiang
Sadikovic, Bekim
Giorda, Kristina
Boardman, Lisa
Wen, Zhining
Kusko, Rebecca
Xu, Chang
Raymond, Amelia
Chen, Guangchun
Mittal, Vinay K.
Hang, Xinyi
Meng, Qingchang
Zhang, Yifan
Li, Peng
Wang, Yexun
Thakkar, Shraddha
Thodima, Venkat J.
Wilkins, Katherine
Tong, Weida
Mieczkowski, Piotr A.
Lucas, Anne Bergstrom
Cooley Coleman, Jessica
Liu, Shaoqing
Ringler, Rebecca
Lai, Kevin
Schulze, Egbert
Yu, Ying
Mercer, Timothy
Muzny, Donna
Guan, Meijian
Yang, Mary
Rindler, Paul
Song, Ping
Paweletz, Cloud P.
Wu, Leihong
Bao, Longlong
Kipp, Benjamin
Attwooll, Claire
Wang, Shangzi
Haag, Christine
Smith, Melissa
Thierry-Mieg, Jean
Furlanello, Cesare
Bisgin, Halil
Ying, Jianming
Novoradovskaya, Natalia
Zhang, Zhihong
Babson, Kevin
Close, Devin
Conroy, Jeffrey
Burgher, Blake
Xiao, Wenzhong
Cawley, Simon
Foox, Jonathan
Opis:
Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Tytuł:
sPlot : a new tool for global vegetation analyses
Autorzy:
Ejrnæs, Rasmus
Kącki, Zygmunt
Curran, Michael
Landucci, Flavia
Zizka, Georg
Macanović, Armin
Stančić, Zvjezdana
Uogintas, Domas
Lenoir, Jonathan
Jiménez-Alfaro, Borja
Moeslund, Jesper Erenskjold
Vanselow, Kim André
Noroozi, Jalil
Sop, Tenekwetche
Peyre, Gwendolyn
Schaminée, Joop H. J.
Winter, Marten
Küzmič, Filip
Brisse, Henry
Dimopoulos, Panayotis
Mencuccini, Maurizio
Sandel, Brody
Revermann, Rasmus
Walker, Donald A.
Rodwell, John
Wohlgemuth, Thomas
Holubová, Dana
Šilc, Urban
Berg, Christian
Fotiadis, Georgios
El-Sheikh, Mohamed Abd El-Rouf Mousa
Weiher, Evan
Smyth, Anita
Li, Ching‐Feng
Kolomiychuk, Vitaliy
Jansen, Florian
Purschke, Oliver
Alvarez, Miguel
de Ruffray, Patrice
Violle, Cyrille
Casella, Laura
Wagner, Viktoria
Lopez-Gonzalez, Gabriela
Kavgacı, Ali
Cayuela, Luis
Apostolova, Iva
Rūsiņa, Solvita
Arnst, Elise
He, Tianhua
Jandt, Ute
Işık Gürsoy, Deniz
De Bie, Els
Agrillo, Emiliano
Jiroušek, Martin
Schmiedel, Ute
Wana, Desalegn
Sabatini, Francesco Maria
Swacha, Grzegorz
Hölzel, Norbert
Fagúndez, Jaime
Bergeron, Yves
Rašomavičius, Valerijus
Svenning, Jens-Christian
Samimi, Cyrus
Overbeck, Gerhard E.
Schrodt, Franziska
Sparrow, Ben
Kuzemko, Anna
Pedashenko, Hristo
Škvorc, Željko
Virtanen, Risto
Kozhevnikov, Maria
Munzinger, Jérôme
Niinemets, Ülo
García-Mijangos, Itziar
Nobis, Marcin
Bjorkman, Anne D.
Beckmann, Michael
Tsiripidis, Ioannis
Uğurlu, Emin
de Gasper, André Luis
Field, Richard
Tang, Zhiyao
Angelini, Pierangela
Boyle, Brad
Bruelheide, Helge
Finckh, Manfred
Jürgens, Norbert
Yamalov, Sergey
Lee, Michael T.
Borchardt, Peter
Turtureanu, Pavel Dan
Dengler, Jürgen
Černý, Tomáš
Kearsley, Elizabeth
Hennekens, Stephan M.
Manning, Peter
Valachovič, Milan
Kattge, Jens
von Wehrden, Henrik
Nowak, Arkadiusz
Peterka, Tomáš
Bergmeier, Erwin
Korolyuk, Andrey
Whitfeld, Timothy
Minden, Vanessa
Csiky, János
Wesche, Karsten
Byun, Chaeho
Mahdavi, Parastoo
Peñuelas, Josep
Krstonošić, Daniel
Chepinoga, Victor
Liu, Hongyan
Martynenko, Vassiliy
Peet, Robert K.
Pauchard, Anibal
Vélez-Martin, Eduardo
Chytrý, Milan
Venanzoni, Roberto
Gutierrez, Alvaro G.
Attorre, Fabio
Indreica, Adrian
Higuchi, Pedro
Aćić, Svetlana
Ćušterevska, Renata
Hatim, Mohamed Z.
Bondareva, Viktoria
Vibrans, Alexander Christian
Vashenyak, Yulia
Willner, Wolfgang
Homeier, Jürgen
Petřík, Petr
Onyshchenko, Viktor
Phillips, Oliver L.
Arfin Khan, Mohammed A. S.
Müller, Jonas V.
Kühl, Hjalmar
Prokhorov, Vadim
Wiser, Susan
Ambarlı, Didem
Baraloto, Christopher
Kühn, Ingolf
Enquist, Brian
Forey, Estelle
Pillar, Valério D.
Golub, Valentin
Schmidt, Marco
Breen, Amy
De Sanctis, Michele
Sopotlieva, Desislava
Font, Xavier
Botta-Dukát, Zoltán
Ewald, Jörg
Janssen, John
Jedrzejek, Birgit
Marcenò, Corrado
Moretti, Marco
Aubin, Isabelle
Haider, Sylvia
Vassilev, Kiril
Knollová, Ilona
Zverev, Andrei
Biurrun, Idoia
Dressler, Stefan
Levesley, Aurora
Pérez-Haase, Aaron
Ruprecht, Eszter
Dajić Stevanović, Zora
Kessler, Michael
Lysenko, Tatiana
Ozinga, Wim A.
Cabido, Marcelo R.
Šibík, Jozef
Jansen, Steven
Kozub, Łukasz
Dostawca treści:
Repozytorium Uniwersytetu Jagiellońskiego
Artykuł
Wyświetlanie 1-10 z 12

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