Publications by authors named "Alexander Shishkin"

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Consortium of Indigenous Fecal Bacteria in the Treatment of Metabolic Syndrome.
Elena Ermolenko, Marina Kotyleva, Anna Kotrova, Sergey Tichonov, Nadezhda Lavrenova, Alexander Shishkin

Microorganisms· August 2022

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Partners in crime: Tbf1 and Vid22 promote expansions of long human telomeric repeats at an interstitial chromosome position in yeast.
Elina A Radchenko, Anna Y Aksenova, Kirill V Volkov, Alexander A Shishkin, Youri I Pavlov

PNAS Nexus· July 2022

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Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.
Steven M Blue, Brian A Yee, Gabriel A Pratt, Jasmine R Mueller, Samuel S Park, Alexander A Shishkin

Nat Protoc· May 2022

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Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML.
Gabriela Krivdova, Veronique Voisin, Erwin M Schoof, Sajid A Marhon, Alex Murison, Alexander A Shishkin

Cell Rep· March 2022

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Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors.
Emily C Wheeler, Anthony Q Vu, Jaclyn M Einstein, Matthew DiSalvo, Noorsher Ahmed, Alexander A Shishkin

Nat Methods· June 2020

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Microfluidic SlipChip device for multistep multiplexed biochemistry on a nanoliter scale.
Dmitriy V Zhukov, Eugenia M Khorosheva, Tahmineh Khazaei, Wenbin Du, David A Selck, Alexander A Shishkin

Lab Chip· October 2019

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Methane adsorption and methanol desorption of copper modified boron silicate.
Xueting Wang, Alexander Shishkin, Felix Hemmingsson, Magnus Skoglundh, Francisco Javier Martinez-Casado

RSC Adv· October 2018

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Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.
Sofia A Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt, Alexander A Shishkin

Cell· July 2018

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A Defective mRNA Cleavage and Polyadenylation Complex Facilitates Expansions of Transcribed (GAA) Repeats Associated with Friedreich's Ataxia.
Ryan J McGinty, Franco Puleo, Anna Y Aksenova, Julia A Hisey, Alexander A Shishkin

Cell Rep· September 2017

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The Genome-Wide Analysis of Carcinoembryonic Antigen Signaling by Colorectal Cancer Cells Using RNA Sequencing.
Olga Bajenova, Anna Gorbunova, Igor Evsyukov, Michael Rayko, Svetlana Gapon, Alexander Shishkin

PLoS One· August 2017

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Variation in single-nucleotide sensitivity of eCLIP derived from reverse transcription conditions.
Eric L Van Nostrand, Alexander A Shishkin, Gabriel A Pratt, Thai B Nguyen, Gene W Yeo

Methods· August 2017

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Defining the 5΄ and 3΄ landscape of the Drosophila transcriptome with Exo-seq and RNaseH-seq.
Shaked Afik, Osnat Bartok, Maxim N Artyomov, Alexander A Shishkin, Sabah Kadri

Nucleic Acids Res· June 2017

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Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP).
Eric L Van Nostrand, Gabriel A Pratt, Alexander A Shishkin, Chelsea Gelboin-Burkhart, Mark Y Fang

Nat Methods· June 2016

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Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs.
Jenny Chen, Alexander A Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza

Genome Biol· February 2016

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Expansion of Interstitial Telomeric Sequences in Yeast.
Anna Y Aksenova, Gil Han, Alexander A Shishkin, Kirill V Volkov, Sergei M Mirkin

Cell Rep· November 2015

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The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3.
Colleen A McHugh, Chun-Kan Chen, Amy Chow, Christine F Surka, Christina Tran, Alexander A Shishkin

Nature· May 2015

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Simultaneous generation of many RNA-seq libraries in a single reaction.
Alexander A Shishkin, Georgia Giannoukos, Alper Kucukural, Dawn Ciulla, Michele Busby

Nat Methods· April 2015

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Genetic and epigenetic fine mapping of causal autoimmune disease variants.
Kyle Kai-How Farh, Alexander Marson, Jiang Zhu, Markus Kleinewietfeld, William J Housley, Alexander A Shishkin

Nature· February 2015

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RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites.
Jesse M Engreitz, Klara Sirokman, Patrick McDonel, Alexander A Shishkin, Christine Surka

Cell· September 2014

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Genome rearrangements caused by interstitial telomeric sequences in yeast.
Anna Y Aksenova, Patricia W Greenwell, Margaret Dominska, Alexander A Shishkin, Jane C Kim

Proc Natl Acad Sci U S A· December 2013

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High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.
Schraga Schwartz, Sudeep D Agarwala, Maxwell R Mumbach, Marko Jovanovic, Philipp Mertins, Alexander Shishkin

Cell· December 2013

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The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome.
Jesse M Engreitz, Amy Pandya-Jones, Patrick McDonel, Alexander Shishkin, Klara Sirokman

Science· August 2013

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Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.
Casey A Gifford, Michael J Ziller, Hongcang Gu, Cole Trapnell, Julie Donaghey, Alexander A Shishkin

Cell· May 2013

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Role of DNA polymerases in repeat-mediated genome instability.
Kartik A Shah, Alexander A Shishkin, Irina Voineagu, Youri I Pavlov, Polina V Shcherbakova

Cell Rep· November 2012

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Genome-wide screen identifies pathways that govern GAA/TTC repeat fragility and expansions in dividing and nondividing yeast cells.
Yu Zhang, Alexander A Shishkin, Yuri Nishida, Dana Marcinkowski-Desmond, Natalie Saini

Mol Cell· October 2012

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