Academic Unit: Systems Biology / Type: Articles | Search Results | Academic Commons

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1. Generation of pralatrexate resistant T-cell lymphoma lines reveals two patterns of acquired drug resistance that is overcome with epigenetic modifiers

: Scotto, Luigi; Kinahan, Cristina; Casadei, Beatrice; Mangone, Michael; Douglass Jr, Eugene F.; Vundavalli, Murty V.; Marchi, Enrica; Ma, Helen; Chauncey, George; Montanari, Francesca; Califano, Andrea; O’Connor, Owen Anthony
: 2020
: Articles
: LymphomasDrug resistance

2. A sequential Monte Carlo algorithm for inference of subclonal structure in cancer

: Ogundijo, Oyetunji Enoch; Zhu, Kaiyi; Wang, Xiaodong; Anastassiou, Dimitris
: 2019
: Articles
: Tumors--Growth--Mathematical modelsMonte Carlo methodOncology

3. Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis

: Bansal, Mukesh; He, Jing; Peyton, Michael; Kustagi, Manjunath; Iyer, Archana; Comb, Michael; White, Michael; Minna, John D.; Califano, Andrea
: 2019
: Articles
: AdenocarcinomaMolecular biologyLungs--Cancer--Molecular aspectsProteomics

4. Meta-analysis of expression and methylation signatures indicates a stress-related epigenetic mechanism in multiple neuropsychiatric disorders

: Zhu, Kaiyi; Ou Yang, Tai-Hsien; Dorie, Vincent Joseph; Zheng, Tian; Anastassiou, Dimitris
: 2019
: Articles
: Neurobehavioral disordersPathologyEpigeneticsMethylationStress (Psychology)--Physiological aspectsSystems biology

5. Accurate and sensitive quantification of protein-DNA binding affinity

: Rastogi, Chaitanya; Rube, Hans Tomas; Kribelbauer, Judith Franziska; Crocker, Justin; Loker, Ryan Edmund; Martini, Gabriella D.; Laptenko, Oleg; Freed-Pastor, William Allen; Prives, Carol L.; Stern, David L.; Mann, Richard S.; Bussemaker, Harmen J.
: 2018
: Articles
: Transcription factorsDNA-protein interactionsProtein bindingProbabilities--Mathematical models

6. A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigenomes

: Youn, Ahrim; Kim, Kyung In; Rabadan, Raul; Tycko, Benjamin; Shen, Yufeng; Wang, Shuang
: 2018
: Articles
: DNA--MethylationGene expressionCancer--Genetic aspectsTumorsEpigenetics

7. A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers

: Šuštić, Tonći; van Wageningen, Sake; Bosdriesz, Evert; Reid, Robert J. D.; Dittmar, John; Lieftink, Cor; Beijersbergen, Roderick L.; Wessels, Lodewyk F. A.; Rothstein, Rodney; Bernards, René
: 2018
: Articles
: Mutation (Biology)Colon (Anatomy)--CancerGenomicsMolecular biology

8. Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

: Yuan, Yuan; Xie, Shirley; Darnell, Jennifer C.; Darnell, Andrew J.; Saito, Yuhki; Phatnani, Hemali P.; Murphy, Elisabeth A.; Zhang, Chaolin; Maniatis, Tom; Darnell, Robert B.
: 2018
: Articles
: Motor neuronsCytoskeletonSeptinsRNA splicingBiology

9. Characterization of kinase gene expression and splicing profile in prostate cancer with RNA-Seq data

: Feng, Huijuan; Li, Tingting; Zhang, Xuegong
: 2018
: Articles
: Prostate--CancerGene expressionRNA splicingProtein kinasesGenomicsBioinformatics

10. cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg

: Newcomb, Susan Elizabeth; Voutev, Roumen; Jory, Aurelie E.; Delker, Rebecca; Slattery, Matthew; Mann, Richard S.
: 2018
: Articles
: Drosophila melanogaster--GeneticsGrowth factors--ReceptorsCloningBiologyGene expression

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