Search Results - "Chenchik, Alex"

p53 cooperates with DNA methylation and a suicidal interferon response to maintain epigenetic silencing of repeats and noncoding RNAs by Leonova, Katerina I, Brodsky, Leonid, Lipchick, Brittany, Pal, Mahadeb, Novototskaya, Liliya, Chenchik, Alex A, Sen, Ganes C, Komarova, Elena A, Gudkov, Andrei V

“…Large parts of mammalian genomes are transcriptionally inactive and enriched with various classes of interspersed and tandem repeats. Here we show that the…”
Get full text

165 Microsampling for RNA biomarker profiling in blood by Kobzik, Lester, Makhanov, Mikhail, Chenchik, Alex

“…BackgroundMulti-omic analysis of microsamples of lancet-induced blood drops allows frequent capture and quantitation of numerous metabolites, lipids,…”
Get full text

154 Universal synthetic spike-in controls for accurate adaptive immune receptor profiling by Chenchik, Alex, Liu, Tianbing, Makhanov, Mikhail, Hu, Dongfang, Diehl, Paul

“…BackgroundThe results of adaptive immune receptor (AIR) repertoire diversity assays can be affected by various biases from differences in conditions in the…”
Get full text

Oncogenic context shapes the fitness landscape of tumor suppression by Blair, Lily M., Juan, Joseph M., Sebastian, Lafia, Tran, Vy B., Nie, Wensheng, Wall, Gregory D., Gerceker, Mehmet, Lai, Ian K., Apilado, Edwin A., Grenot, Gabriel, Amar, David, Foggetti, Giorgia, Do Carmo, Mariana, Ugur, Zeynep, Deng, Debbie, Chenchik, Alex, Paz Zafra, Maria, Dow, Lukas E., Politi, Katerina, MacQuitty, Jonathan J., Petrov, Dmitri A., Winslow, Monte M., Rosen, Michael J., Winters, Ian P.

“…Tumors acquire alterations in oncogenes and tumor suppressor genes in an adaptive walk through the fitness landscape of tumorigenesis. However, the…”
Get full text

Peptides genetically selected for NF-κB activation cooperate with oncogene Ras and model carcinogenic role of inflammation by Natarajan, Venkatesh, Komarov, Andrei P., Ippolito, Thomas, Bonneau, Kyle, Chenchik, Alex A., Gudkov, Andrei V.

“…Chronic inflammation is associated with increased cancer risk. Furthermore, the transcription factor NF-κB, a central regulator of inflammatory responses, is…”
Get full text

shRNA library screening identifies nucleocytoplasmic transport as a mediator of BCR-ABL1 kinase-independent resistance by Khorashad, Jamshid S., Eiring, Anna M., Mason, Clinton C., Gantz, Kevin C., Bowler, Amber D., Redwine, Hannah M., Yu, Fan, Kraft, Ira L., Pomicter, Anthony D., Reynolds, Kimberly R., Iovino, Anthony J., Zabriskie, Matthew S., Heaton, William L., Tantravahi, Srinivas K., Kauffman, Michael, Shacham, Sharon, Chenchik, Alex, Bonneau, Kyle, Ullman, Katharine S., O'Hare, Thomas, Deininger, Michael W.

“…The mechanisms underlying tyrosine kinase inhibitor (TKI) resistance in chronic myeloid leukemia (CML) patients lacking explanatory BCR-ABL1 kinase domain…”
Get full text

Long-distance effects of insertional mutagenesis by Singhal, Ruchi, Deng, Xiaotao, Chenchik, Alex A, Kandel, Eugene S

“…Most common systems of genetic engineering of mammalian cells are associated with insertional mutagenesis of the modified cells. Insertional mutagenesis is…”
Get full text

Measurement of Cancer Cell Growth Heterogeneity through Lentiviral Barcoding Identifies Clonal Dominance as a Characteristic of In Vivo Tumor Engraftment by Nolan-Stevaux, Olivier, Tedesco, Donato, Ragan, Seamus, Makhanov, Mikhail, Chenchik, Alex, Ruefli-Brasse, Astrid, Quon, Kim, Kassner, Paul D

“…Advances in the fields of cancer initiating cells and high-throughput in vivo shRNA screens have highlighted a need to observe the growth of tumor cells in…”
Get full text

The 10th Santorini conference: Systems medicine, personalised health and therapy. "The odyssey from hope to practice: Patient first. Keep Ithaca always in your mind ", Santorini, Greece, 23-26 May 2022 by Visvikis-Siest, Sophie, Stathopoulou, Maria G, Sunder-Plassmann, Raute, Alizadeh, Behrooz Z, Barouki, Robert, Chatzaki, Ekaterina, Dagher, Georges, Dedoussis, George, Deloukas, Panagiotis, Haliassos, Alexander, Hiegel, Brigitte Boisson, Manolopoulos, Vangelis, Masson, Christine, Paré, Guillaume, Paulmichl, Markus, Petrelis, Alexandros M, Sipeky, Csilla, Süsleyici, Belgin, Weryha, Georges, Chenchik, Alex, Diehl, Paul, Everts, Robin E, Haushofer, Alexander, Lamont, John, Mercado, Ruth, Meyer, Heiko, Munoz-Galeano, Herna, Murray, Helena, Nhat, Ferrier, Nofziger, Charity, Schnitzel, Wolfgang, Kanoni, Stavroula

Get full text

Use of RNAi screens to uncover resistance mechanisms in cancer cells and identify synthetic lethal interactions by Diehl, Paul, Tedesco, Donato, Chenchik, Alex

“…RNAi loss-of-function screens, which have proven effective to identify genes functionally responsible for cellular phenotypes, can be designed to use different…”
Get full text

Gene Expression Profiling in Postmortem Rett Syndrome Brain: Differential Gene Expression and Patient Classification by Colantuoni, Carlo, Jeon, Ok-Hee, Hyder, Karim, Chenchik, Alex, Khimani, Anis H., Narayanan, Vinodh, Hoffman, Eric P., Kaufmann, Walter E., Naidu, SakkuBai, Pevsner, Jonathan

“…The identification of mutations in the transcriptional repressor methyl-CpG-binding protein 2 (MECP2) gene in Rett Syndrome (RTT) suggests that an…”
Get full text

Screening of cell death genes with a mammalian genome-wide RNAi library by Tsujii, Hisayo, Eguchi, Yutaka, Chenchik, Alex, Mizutani, Takayuki, Yamada, Kayoko, Tsujimoto, Yoshihide

“…We report the construction and application of a mammalian genome-wide RNAi library. The oligodeoxynucleotides encoding ~200,000 shRNA sequences that targeted…”
Get full text

Specific pattern of p53 phosphorylation during nitric oxide-induced cell cycle arrest by NAKAYA, Naoki, LOWE, Scott W, TAYA, Yoichi, CHENCHIK, Alex, ENIKOLOPOV, Grigori

“…Nitric oxide (NO) is an efficient inhibitor of cell proliferation. Here we show that part of the antiproliferative activity of NO in fibroblasts is mediated…”
Get full text

Equalizing cDNA Subtraction Based on Selective Suppression of Polymerase Chain Reaction: Cloning of Jurkat Cell Transcripts Induced by Phytohemaglutinin and Phorbol 12-Myristate 13-Acetate by Gurskaya, Nadya G., Diatchenko, Luda, Chenchik, Alex, Siebert, Paul D., Khaspekov, George L., Lukyanov, Konstantin A., Vagner, Laura L., Ermolaeva, Olga D., Lukyanov, Sergey A., Sverdlov, Eugene D.

“…The major drawback of subtractive cDNA libraries is that the original disproportion in concentrations of different types of transcripts is preserved. This…”
Get full text

Abstract 3426: Combining cell barcoding and CRISPR sgRNA libraries with targeted gene expression for single-cell genetic analysis of tumor metastasis by Chenchik, Alex, Diehl, Paul, Makhanov, Mikhail

“…Abstract Pooled lentiviral libraries of CRISPR sgRNAs to mediate genome-wide gene knockout have become an invaluable tool for uncovering the functional genetic…”
Get full text

Use of SMART-generated cDNA for gene expression studies in multiple human tumors by Zhumabayeva, B, Diatchenko, L, Chenchik, A, Siebert, P D

“…We demonstrate here that SMART PCR-amplified cDNAs arrayed on a nylon membrane are suitable for high-throughput tissue expression profiling when starting…”
Get full text

Synthetic TCR/BCR RNA spike-in controls for assessing immune receptor profiling assay accuracy by Chenchik, Alex, Liu, Tianbing, Makhanov, Mikhail, Hu, Dongfang, Ghias, Khadija, Diehl, Paul

“…Abstract Synthetic TCR and BCR RNA spike-in controls can be used as universal standards to account for biases caused by PCR and NGS steps of adaptive immune…”
Get full text

Streamlined 96-well plate method for simultaneous single-cell TCR immune receptor repertoire analysis and immunophenotyping by Chenchik, Alex, Liu, Tianbing, Makhanov, Mikhail, Hu, Dongfang, Kobzik, Lester, Ghias, Khadija, Diehl, Paul

“…Abstract This study describes an efficient immune profiling method by FACS-sorting single cells in a 96-well plate to assess clonotype repertoire diversity,…”
Get full text

Longitudinal analysis of immunological response to vaccination by Chenchik, Alex, Kobzik, Lester, Liu, Tianbing, Hu, Dongfang, Makhanov, Mikhail, Paraiso, Kitt, Ghias, Khadija, Diehl, Paul

“…Abstract This study explores the dynamic nature of the immune responses to vaccination with Td (Tetanus-diphtheria), PPSV23 (pneumococcal), and Shingrix…”
Get full text

T-cell and B-cell receptor repertoire profiling for biomarker discovery by Chenchik, Alex, Makhanov, Mikhail, Liu, Tianbing, Hu, Dongfang, Diehl, Paul, Kobzik, Lester

“…Abstract T-cell receptor (TCR) and B-cell receptor (BCR) repertoire profiling, also referred to as adaptive immune receptor repertoire (AIRR) profiling, holds…”
Get full text