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A. Gnirke · SciRah

Researcher profile · Semantic Scholar

A. Gnirke

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A. Gnirke — researcher profile on SciRah

h-index: 72
Works: 149
Citations: 63K

Most-cited papers

Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
M. Grabherr, B. Haas, M. Yassour, J. Levin +17 more
2011Nature Biotechnology18K citations Open access
Semantic Scholar
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Adrian L. Sanborn, Suhas S. P. Rao, Su-Chen Huang, Neva C. Durand +13 more
2015Proceedings of the National Academy of Sciences of the United States of America1,636 citations Open access
Semantic Scholar
High-quality draft assemblies of mammalian genomes from massively parallel sequence data
S. Gnerre, I. Maccallum, D. Przybylski, Filipe J. Ribeiro +16 more
2010Proceedings of the National Academy of Sciences of the United States of America1,625 citations Open access
Semantic Scholar
Charting a dynamic DNA methylation landscape of the human genome
Michael J. Ziller, H. Gu, F. Müller, Julie Donaghey +8 more
2013Nature1,328 citations Open access
Semantic Scholar
Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs
M. Guttman, M. Garber, J. Levin, Julie Donaghey +9 more
2010Nature Biotechnology1,265 citations Open access
Semantic Scholar
Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak
Stephen Gire, A. Goba, K. Andersen, Rachel S. G. Sealfon +54 more
2014Science1,233 citations Open access
Semantic Scholar
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
A. Shalek, R. Satija, X. Adiconis, Rona S. Gertner +14 more
2013Nature1,201 citations Open access
Semantic Scholar
Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
D. Aird, M. Ross, Weikai Chen, M. Danielsson +5 more
2011Genome Biology1,198 citations Open access
Semantic Scholar
Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines
C. Bock, E. Kiskinis, Griet Verstappen, H. Gu +9 more
2011Cell1,007 citations Open access
Semantic Scholar
A unique regulatory phase of DNA methylation in the early mammalian embryo
Zachary D. Smith, Michelle M. Chan, T. Mikkelsen, H. Gu +3 more
2012Nature994 citations Open access
Semantic Scholar
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications
R. A. Harris, Ting Wang, C. Coarfa, R. Nagarajan +35 more
2010Nature Biotechnology718 citations Open access
Semantic Scholar
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
H. Gu, Zachary D. Smith, C. Bock, Patrick J. Boyle +2 more
2011Nature Protocols702 citations
Semantic Scholar
Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
M. Rabani, J. Levin, Lin Fan, X. Adiconis +8 more
2011Nature Biotechnology598 citations Open access
Semantic Scholar
Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.
M. Soumillon, A. Necsulea, M. Weier, D. Brawand +10 more
2013Cell Reports573 citations Open access
Semantic Scholar
Analysis of the African coelacanth genome sheds light on tetrapod evolution
Chris T. Amemiya, J. Alföldi, Alison P. Lee, Shao-Hua Fan +87 more
2013Nature570 citations Open access
Semantic Scholar
Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples
X. Adiconis, Diego Borges-Rivera, R. Satija, D. DeLuca +10 more
2013Nature Methods488 citations Open access
Semantic Scholar
Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells
Jing Liao, R. Karnik, H. Gu, Michael J. Ziller +14 more
2015Nature Genetics459 citations Open access
Semantic Scholar
Transcriptional and Epigenetic Dynamics During Specification of Human Embryonic Stem Cells
C. Gifford, Michael J. Ziller, H. Gu, C. Trapnell +20 more
2013Cell442 citations Open access
Semantic Scholar
Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
A. Brinkman, H. Gu, Stefanie J. J. Bartels, Yingying Zhang +7 more
2012Genome Research411 citations Open access
Semantic Scholar
Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types
Michael J. Ziller, F. Müller, Jing Liao, Yingying Zhang +8 more
2011PLoS Genetics408 citations Open access
Semantic Scholar
A high throughput Chromatin ImmunoPrecipitation approach reveals principles of dynamic gene regulation in mammals
M. Garber, N. Yosef, Alon Goren, R. Raychowdhury +23 more
2012Molecules and Cells399 citations Open access
Semantic Scholar
Virus genomes reveal factors that spread and sustained the Ebola epidemic
G. Dudas, L. Carvalho, T. Bedford, A. Tatem +92 more
2017Nature398 citations Open access
Semantic Scholar
Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay
A. Melnikov, A. Murugan, Xiao-Lan Zhang, T. Teşileanu +9 more
2012Nature Biotechnology384 citations
Semantic Scholar
Locally disordered methylation forms the basis of intra-tumor methylome variation in chronic lymphocytic leukemia
D. Landau, Kendell Clement, Michael J. Ziller, Patrick J. Boyle +22 more
2014Cancer Cell371 citations Open access
Semantic Scholar
DNA methylation dynamics during in vivo differentiation of blood and skin stem cells
C. Bock, Isabel Beerman, Wen-Hui Lien, Zachary D. Smith +6 more
2012Molecules and Cells371 citations Open access
Semantic Scholar
Reprogramming factor expression induces rapid and widespread targeted chromatin remodeling
Richard P. Koche, Zachary D. Smith, Mazhar Adli, H. Gu +4 more
2011Cell Stem Cell365 citations Open access
Semantic Scholar
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
H. Gu, C. Bock, T. Mikkelsen, N. Jäger +5 more
2010Nature Methods337 citations Open access
Semantic Scholar
Genome sequencing reveals Zika virus diversity and spread in the Americas
H. C. Metsky, C. B. Matranga, S. Wohl, S. Schaner +57 more
2017bioRxiv328 citations Open access
Semantic Scholar
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
N. Grubaugh, J. Ladner, M. Kraemer, G. Dudas +65 more
2017Nature321 citations Open access
Semantic Scholar
Simultaneous generation of many RNA-seq libraries in a single reaction
Alexander A. Shishkin, G. Giannoukos, Alper Kucukural, Dawn M. Ciulla +12 more
2015Nature Methods302 citations Open access
Semantic Scholar
Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone
Daniel J. Park, G. Dudas, Shirlee Wohl, A. Goba +82 more
2015Cell290 citations Open access
Semantic Scholar
Mutations causing medullary cystic kidney disease type 1 (MCKD1) lie in a large VNTR in MUC1 missed by massively parallel sequencing
Andrew W. Kirby, A. Gnirke, D. Jaffe, V. Barešová +39 more
2013Nature Genetics281 citations Open access
Semantic Scholar
Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
J. Lemieux, K. Siddle, B. Shaw, Christine Loreth +49 more
2020Science277 citations Open access
Semantic Scholar
Clinical sequencing uncovers origins and evolution of Lassa virus
K. Andersen, B. Shapiro, C. B. Matranga, Rachel S. G. Sealfon +67 more
2015Cell272 citations Open access
Semantic Scholar
Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling
Patrick J. Boyle, Kendell Clement, H. Gu, Zachary D. Smith +7 more
2012Genome Biology254 citations Open access
Semantic Scholar
Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells
Jiho Choi, A. Huebner, Kendell Clement, Ryan M. Walsh +19 more
2017Nature250 citations Open access
Semantic Scholar
Transcription factor binding dynamics during human ESC differentiation
Alexander M. Tsankov, H. Gu, V. Akopian, Michael J. Ziller +4 more
2015Nature247 citations Open access
Semantic Scholar
Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
G. Giannoukos, Dawn M. Ciulla, Katherine H. Huang, B. Haas +9 more
2012Genome Biology240 citations Open access
Semantic Scholar
Epigenetic evolution and lineage histories of chronic lymphocytic leukemia
Federico Gaiti, R. Chaligné, H. Gu, Ryan Brand +22 more
2019Nature235 citations Open access
Semantic Scholar
Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes
A. Melnikov, P. Rogov, Li Wang, A. Gnirke +1 more
2014bioRxiv188 citations Open access
Semantic Scholar
Dissecting neural differentiation regulatory networks through epigenetic footprinting
Michael J. Ziller, Reuven Edri, Yakey Yaffe, Julie Donaghey +17 more
2014Nature188 citations Open access
Semantic Scholar
Small Molecule Targets TMED9 and Promotes Lysosomal Degradation to Reverse Proteinopathy.
Moran Dvela-Levitt, M. Kost-Alimova, M. Emani, Eva Kohnert +34 more
2019Cell183 citations Open access
Semantic Scholar
Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer
Zachary D. Smith, Jian-Tao Shi, H. Gu, Julie Donaghey +5 more
2017Nature162 citations Open access
Semantic Scholar
Genetic determinants and epigenetic effects of pioneer factor occupancy
Julie Donaghey, S. Thakurela, J. Charlton, Jenny Chen +13 more
2018Nature Genetics157 citations Open access
Semantic Scholar
Cancer-germline antigen expression discriminates clinical outcome to CTLA-4 blockade
S. Shukla, Pavan Bachireddy, B. Schilling, Christina Galonska +28 more
2018Cell153 citations Open access
Semantic Scholar
Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples
C. B. Matranga, K. Andersen, S. Winnicki, Michele Busby +23 more
2014Genome Biology153 citations Open access
Semantic Scholar
Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
M. Yassour, Jenna Pfiffner, J. Levin, X. Adiconis +5 more
2010Genome Biology149 citations Open access
Semantic Scholar
Capturing sequence diversity in metagenomes with comprehensive and scalable probe design
Hayden C. Metsky, K. Siddle, A. Gladden-Young, J. Qu +43 more
2019Nature Biotechnology139 citations Open access
Semantic Scholar
Genome-wide tracking of dCas9-methyltransferase footprints
Christina Galonska, J. Charlton, Alexandra L. Mattei, Julie Donaghey +12 more
2018Nature Communications139 citations Open access
Semantic Scholar
Hybrid selection for sequencing pathogen genomes from clinical samples
A. Melnikov, K. Galinsky, P. Rogov, T. Fennell +13 more
2011Genome Biology122 citations Open access
Semantic Scholar

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