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Xian Adiconis
Researcher at Broad Institute
Publications - 59
Citations - 26444
Xian Adiconis is an academic researcher from Broad Institute. The author has contributed to research in topics: Gene & Population. The author has an hindex of 30, co-authored 49 publications receiving 21074 citations. Previous affiliations of Xian Adiconis include Massachusetts Institute of Technology.
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Journal ArticleDOI
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Manfred Grabherr,Brian J. Haas,Moran Yassour,Moran Yassour,Joshua Z. Levin,Dawn Thompson,Ido Amit,Xian Adiconis,Lin Fan,Raktima Raychowdhury,Qiandong Zeng,Zehua Chen,Evan Mauceli,Nir Hacohen,Andreas Gnirke,Nicholas Rhind,Federica Di Palma,Bruce W. Birren,Chad Nusbaum,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Nir Friedman,Aviv Regev +22 more
TL;DR: The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
Journal ArticleDOI
Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
Mitchell Guttman,Manuel Garber,Joshua Z. Levin,Julie Donaghey,James T. Robinson,Xian Adiconis,Lin Fan,Magdalena J. Koziol,Magdalena J. Koziol,Andreas Gnirke,Chad Nusbaum,John L. Rinn,John L. Rinn,Eric S. Lander,Eric S. Lander,Eric S. Lander,Aviv Regev,Aviv Regev +17 more
TL;DR: Scripture, a method to reconstruct the transcriptome of a mammalian cell using only RNA-Seq reads and the genome sequence, is presented and the power of ab initio reconstruction is demonstrated to render a comprehensive picture of mammalian transcriptomes.
Journal ArticleDOI
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
Alex K. Shalek,Rahul Satija,Xian Adiconis,Rona S. Gertner,Jellert T. Gaublomme,Raktima Raychowdhury,Schraga Schwartz,Nir Yosef,Christine M. Malboeuf,Diana Lu,John J. Trombetta,David Gennert,Andreas Gnirke,Alon Goren,Alon Goren,Nir Hacohen,Nir Hacohen,Joshua Z. Levin,Hongkun Park,Hongkun Park,Aviv Regev,Aviv Regev +21 more
TL;DR: The authors used single-cell RNA-Seq to investigate heterogeneity in the response of bone marrow derived dendritic cells (BMDCs) to lipopolysaccharide (LPS) and found extensive, and previously unobserved, bimodal variation in mRNA abundance and splicing patterns.
Journal ArticleDOI
Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
Karthik Shekhar,Sylvain W. Lapan,Sylvain W. Lapan,Irene E. Whitney,Nicholas M. Tran,Evan Z. Macosko,Evan Z. Macosko,Monika S. Kowalczyk,Xian Adiconis,Joshua Z. Levin,James Nemesh,James Nemesh,Melissa Goldman,Melissa Goldman,Steven A. McCarroll,Steven A. McCarroll,Constance L. Cepko,Constance L. Cepko,Aviv Regev,Aviv Regev,Aviv Regev,Joshua R. Sanes +21 more
TL;DR: This work provides a systematic methodology for achieving comprehensive molecular classification of neurons, identifies novel neuronal types, and uncovers transcriptional differences that distinguish types within a class.
Journal ArticleDOI
Comprehensive comparative analysis of strand-specific RNA sequencing methods
Joshua Z. Levin,Moran Yassour,Moran Yassour,Xian Adiconis,Chad Nusbaum,Dawn Thompson,Nir Friedman,Andreas Gnirke,Aviv Regev +8 more
TL;DR: In this paper, the authors developed a comprehensive computational pipeline to compare library quality metrics from any RNA-seq method, using the well-annotated Saccharomyces cerevisiae transcriptome as a benchmark.