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Nicolas Robine on Muck Rack

Nicolas Robine

New York
As seen in: Nature, Science Magazine, Cell Press
Director, Computational Biology. [nrobine]@nygenome[.org] RNA-Seq / Cancer Genomics / anything NYC / mostly in English, sometimes in French.
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Articles

Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic - Nature Biotechnology

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By Pi-Chuan Chang, Ayse G. Keskus, Asher Bryant, Yongmei Zhao, Giuseppe Narzisi, Irina Pushel, Tomi Pastinen, T. Rhyker Ranallo-Benavidez, Christine Brown, Nicolas Robine, Floris P. Barthel, Midhat S. Farooqi, Karen H Miga, Andrew Carroll, Mikhail Kolmogorov, Benedict Paten, Lisa A. Lansdon
| Nature Verified
Abstract Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies offer potential advantages in repeat mapping and variant phasing. We present DeepSomatic, a deep-learning method for detecting somatic small nucleotide variations and insertions and deletions from both short-read and long-read data.
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Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics - Nature Genetics

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By Kevin Johnson, Masashi Nomura, Luciano Garofano, Djamel Nehar-Belaid, Noam Galili Darnell, Lillian Bussema, Frederick S. Varn, Fulvio D’Angelo, Kevin Anderson, Nicolas Robine, Catherine Reeves, Anuja Lipsa, Anna Golebiewska, Simone P Niclou, Sun Ha Paek, Franck Bielle, Alice Laurenge, Bertrand Mathon, David Ashley, Keith L. Ligon, Jason T. Huse, Anna Lasorella, Antonio Iavarone, Itay Tirosh
| Nature Verified
Abstract The evolution of isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) after standard-of-care therapy remains poorly understood. Here we analyzed matched primary and recurrent GBMs from 59 patients using single-nucleus RNA sequencing and bulk DNA sequencing, assessing the longitudinal evolution of the GBM ecosystem across layers of cellular and molecular heterogeneity.
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Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing - Nature Biotechnology

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By Ayse G. Keskus, Asher Bryant, Yongmei Zhao, Giuseppe Narzisi, Pi-Chuan Chang, Andrew Carroll, Tomi Pastinen, Kishwar Shafin, Karen H Miga, Salem Malikic, Chi-Ping Day, Nicolas Robine, Cenk Sahinalp, Benedict Paten, Anton Goretsky, Irina Pushel
| Nature Verified
Abstract For the detection of somatic structural variation (SV) in cancer genomes, long-read sequencing is advantageous over short-read sequencing with respect to mappability and variant phasing. However, most current long-read SV detection methods are not developed for the analysis of tumor genomes characterized by complex rearrangements and heterogeneity. Here, we present Severus, a breakpoint graph-based algorithm for somatic SV calling from long-read cancer sequencing.
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