SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions
Zhou, Wanding, Triche, Timothy J, Laird, Peter W, Shen, Hui
Published in Nucleic acids research (16.11.2018)
Published in Nucleic acids research (16.11.2018)
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Journal Article
Low-level processing of Illumina Infinium DNA Methylation BeadArrays
Triche, Jr, Timothy J, Weisenberger, Daniel J, Van Den Berg, David, Laird, Peter W, Siegmund, Kimberly D
Published in Nucleic acids research (01.04.2013)
Published in Nucleic acids research (01.04.2013)
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BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies
Zhou, Wanding, Johnson, Benjamin K, Morrison, Jacob, Beddows, Ian, Eapen, James, Katsman, Efrat, Semwal, Ayush, Habib, Walid Abi, Heo, Lyong, Laird, Peter W, Berman, Benjamin P, Triche, Timothy J, Shen, Hui
Published in Nucleic acids research (12.04.2024)
Published in Nucleic acids research (12.04.2024)
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Journal Article
Author Correction: CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes
Unterman, Irene, Avrahami, Dana, Katsman, Efrat, Triche, Jr, Timothy J, Glaser, Benjamin, Berman, Benjamin P
Published in Genome Biology (08.07.2024)
Published in Genome Biology (08.07.2024)
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Persistence of SARS CoV-2 S1 Protein in CD16+ Monocytes in Post-Acute Sequelae of COVID-19 (PASC) up to 15 Months Post-Infection
Patterson, Bruce K, Francisco, Edgar B, Yogendra, Ram, Long, Emily, Pise, Amruta, Rodrigues, Hallison, Hall, Eric, Herrera, Monica, Parikh, Purvi, Guevara-Coto, Jose, Triche, Timothy J, Scott, Paul, Hekmati, Saboor, Maglinte, Dennis, Chang, Xaiolan, Mora-Rodríguez, Rodrigo A, Mora, Javier
Published in Frontiers in immunology (10.01.2022)
Published in Frontiers in immunology (10.01.2022)
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Discovery and validation of a prostate cancer genomic classifier that predicts early metastasis following radical prostatectomy
Erho, Nicholas, Crisan, Anamaria, Vergara, Ismael A, Mitra, Anirban P, Ghadessi, Mercedeh, Buerki, Christine, Bergstralh, Eric J, Kollmeyer, Thomas, Fink, Stephanie, Haddad, Zaid, Zimmermann, Benedikt, Sierocinski, Thomas, Ballman, Karla V, Triche, Timothy J, Black, Peter C, Karnes, R Jeffrey, Klee, George, Davicioni, Elai, Jenkins, Robert B
Published in PloS one (24.06.2013)
Published in PloS one (24.06.2013)
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Dysregulated heparan sulfate proteoglycan metabolism promotes Ewing sarcoma tumor growth
Vasileva, Elena, Warren, Mikako, Triche, Timothy J, Amatruda, James F
Published in eLife (14.03.2022)
Published in eLife (14.03.2022)
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Journal Article
The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex
Prensner, John R, Iyer, Matthew K, Sahu, Anirban, Asangani, Irfan A, Cao, Qi, Patel, Lalit, Vergara, Ismael A, Davicioni, Elai, Erho, Nicholas, Ghadessi, Mercedeh, Jenkins, Robert B, Triche, Timothy J, Malik, Rohit, Bedenis, Rachel, McGregor, Natalie, Ma, Teng, Chen, Wei, Han, Sumin, Jing, Xiaojun, Cao, Xuhong, Wang, Xiaoju, Chandler, Benjamin, Yan, Wei, Siddiqui, Javed, Kunju, Lakshmi P, Dhanasekaran, Saravana M, Pienta, Kenneth J, Feng, Felix Y, Chinnaiyan, Arul M
Published in Nature genetics (01.11.2013)
Published in Nature genetics (01.11.2013)
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Long Noncoding RNA Expression Independently Predicts Outcome in Pediatric Acute Myeloid Leukemia
Farrar, Jason E, Smith, Jenny L, Othus, Megan, Huang, Benjamin J, Wang, Yi-Cheng, Ries, Rhonda, Hylkema, Tiffany, Pogosova-Agadjanyan, Era L, Challa, Sneha, Leonti, Amanda, Shaw, Timothy I, Triche, Jr, Timothy J, Gamis, Alan S, Aplenc, Richard, Kolb, E Anders, Ma, Xiaotu, Stirewalt, Derek L, Alonzo, Todd A, Meshinchi, Soheil
Published in Journal of clinical oncology (01.06.2023)
Published in Journal of clinical oncology (01.06.2023)
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EGFR-dependent endocytosis of Wnt9a and Fzd9b promotes β-catenin signaling during hematopoietic stem cell development in zebrafish
Nguyen, Nicole, Carpenter, Kelsey A, Ensing, Jessica, Gilliland, Carla, Rudisel, Emma J, Mu, Emily M, Thurlow, Kate E, Triche, Jr, Timothy J, Grainger, Stephanie
Published in Science signaling (16.04.2024)
Published in Science signaling (16.04.2024)
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Journal Article
Comprehensive Transcriptome Profiling of Cryptic CBFA2T3-GLIS2 Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study
Smith, Jenny L, Ries, Rhonda E, Hylkema, Tiffany, Alonzo, Todd A, Gerbing, Robert B, Santaguida, Marianne T, Eidenschink Brodersen, Lisa, Pardo, Laura, Cummings, Carrie L, Loeb, Keith R, Le, Quy, Imren, Suzan, Leonti, Amanda R, Gamis, Alan S, Aplenc, Richard, Kolb, E Anders, Farrar, Jason E, Triche, Jr, Timothy J, Nguyen, Cu, Meerzaman, Daoud, Loken, Michael R, Oehler, Vivian G, Bolouri, Hamid, Meshinchi, Soheil
Published in Clinical cancer research (01.02.2020)
Published in Clinical cancer research (01.02.2020)
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Journal Article
A B-cell developmental gene regulatory network is activated in infant AML
Bolouri, Hamid, Ries, Rhonda, Pardo, Laura, Hylkema, Tiffany, Zhou, Wanding, Smith, Jenny L, Leonti, Amanda, Loken, Michael, Farrar, Jason E, Triche, Jr, Timothy J, Meshinchi, Soheil
Published in PloS one (18.11.2021)
Published in PloS one (18.11.2021)
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Journal Article
Ten quick tips for deep learning in biology
Lee, Benjamin D, Gitter, Anthony, Greene, Casey S, Raschka, Sebastian, Maguire, Finlay, Titus, Alexander J, Kessler, Michael D, Lee, Alexandra J, Chevrette, Marc G, Stewart, Paul Allen, Britto-Borges, Thiago, Cofer, Evan M, Yu, Kun-Hsing, Carmona, Juan Jose, Fertig, Elana J, Kalinin, Alexandr A, Signal, Brandon, Lengerich, Benjamin J, Triche, Jr, Timothy J, Boca, Simina M
Published in PLoS computational biology (01.03.2022)
Published in PLoS computational biology (01.03.2022)
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Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications
Shen, Lishuang, Bard, Jennifer Dien, Triche, Timothy J., Judkins, Alexander R., Biegel, Jaclyn A., Gai, Xiaowu
Published in Emerging microbes & infections (01.01.2021)
Published in Emerging microbes & infections (01.01.2021)
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Translational Activation of Snail1 and Other Developmentally Regulated Transcription Factors by YB-1 Promotes an Epithelial-Mesenchymal Transition
Evdokimova, Valentina, Tognon, Cristina, Ng, Tony, Ruzanov, Peter, Melnyk, Natalya, Fink, Dieter, Sorokin, Alexey, Ovchinnikov, Lev P., Davicioni, Elai, Triche, Timothy J., Sorensen, Poul H.B.
Published in Cancer cell (05.05.2009)
Published in Cancer cell (05.05.2009)
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Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma
Negri, Gian Luca, Grande, Bruno M, Delaidelli, Alberto, El‐Naggar, Amal, Cochrane, Dawn, Lau, Ching C, Triche, Timothy J, Moore, Richard A, Jones, Steven JM, Montpetit, Alexandre, Marra, Marco A, Malkin, David, Morin, Ryan D, Sorensen, Poul H
Published in The Journal of pathology (01.11.2019)
Published in The Journal of pathology (01.11.2019)
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