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1

Individual brain organoids reproducibly form cell diversity of the human cerebral cortex

Velasco, Silvia, Kedaigle, Amanda J., Simmons, Sean K., Nash, Allison, Rocha, Marina, Quadrato, Giorgia, Paulsen, Bruna, Nguyen, Lan, Adiconis, Xian, Regev, Aviv, Levin, Joshua Z., Arlotta, Paola

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 33.38 MB

english, 2019

2

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Grabherr, Manfred G, Haas, Brian J, Yassour, Moran, Levin, Joshua Z, Thompson, Dawn A, Amit, Ido, Adiconis, Xian, Fan, Lin, Raychowdhury, Raktima, Zeng, Qiandong

Journal:

Nature Biotechnology

Année:

2011

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2011

3

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics

Shekhar, Karthik, Lapan, Sylvain W., Whitney, Irene E., Tran, Nicholas M., Macosko, Evan Z., Kowalczyk, Monika, Adiconis, Xian, Levin, Joshua Z., Nemesh, James, Goldman, Melissa, McCarroll, Steven A.,

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 21.90 MB

english, 2016

4

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Shalek, Alex K., Satija, Rahul, Adiconis, Xian, Gertner, Rona S., Gaublomme, Jellert T., Raychowdhury, Raktima, Schwartz, Schraga, Yosef, Nir, Malboeuf, Christine, Lu, Diana, Trombetta, John J., Genne

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 5.34 MB

english, 2013

5

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Ding, Jiarui, Adiconis, Xian, Simmons, Sean K., Kowalczyk, Monika S., Hession, Cynthia C., Marjanovic, Nemanja D., Hughes, Travis K., Wadsworth, Marc H., Burks, Tyler, Nguyen, Lan T., Kwon, John Y. H.

Journal:

Nature Biotechnology

Année:

2020

Fichier:

PDF, 14.35 MB

2020

6

Distinct subnetworks of the thalamic reticular nucleus

Li, Yinqing, Lopez-Huerta, Violeta G., Adiconis, Xian, Levandowski, Kirsten, Choi, Soonwook, Simmons, Sean K., Arias-Garcia, Mario A., Guo, Baolin, Yao, Annie Y., Blosser, Timothy R., Wimmer, Ralf D.,

Journal:

Année:

2020

Fichier:

PDF, 13.50 MB

2020

7

The TaqIB and −629C>A polymorphisms at the cholesteryl ester transfer protein locus: associations with lipid levels in a multiethnic population. The 1998 Singapore National Health Survey

ES Tai, JM Ordovas, D Corella, M Deurenberg-Yap, E Chan, X Adiconis, SK Chew, LM Loh, CE Tan

Journal:

Clinical Genetics

Année:

2003

Langue:

english

Fichier:

PDF, 135 KB

english, 2003

8

Polymorphisms at the SRBI locus are associated with lipoprotein levels in subjects with heterozygous familial hypercholesterolemia

ES Tai, X Adiconis, JM Ordovas, R Carmena-Ramon, J Real, D Corella, J Ascaso, R Carmena

Journal:

Clinical Genetics

Année:

2003

Langue:

english

Fichier:

PDF, 80 KB

english, 2003

9

Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites

Josiemer Mattei, Laurence D Parnell, Chao-Qiang Lai, Bibiana Garcia-Bailo, Xian Adiconis, Jian Shen, Donna Arnett, Serkalem Demissie, Katherine L Tucker, Jose M Ordovas

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2009

10

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

Donaghey, Julie, Robinson, James, Adiconis, Xian, Fan, Lin, Koziol, Magdalena J, Gnirke, Andreas, Nusbaum, Chad, Guttman, Mitchell, Garber, Manuel, Levin, Joshua Z

Journal:

Nature Biotechnology

Année:

2010

Langue:

english

Fichier:

PDF, 952 KB

english, 2010

11

Corrigendum: Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

Guttman, Mitchell, Garber, Manuel, Levin, Joshua Z, Donaghey, Julie, Robinson, James, Adiconis, Xian, Fan, Lin, Koziol, Magdalena J, Gnirke, Andreas, Nusbaum, Chad

Journal:

Nature Biotechnology

Année:

2010

Langue:

english

Fichier:

PDF, 62 KB

english, 2010

12

Comprehensive comparative analysis of strand-specific RNA sequencing methods

Levin, Joshua Z, Yassour, Moran, Adiconis, Xian, Nusbaum, Chad, Thompson, Dawn Anne, Friedman, Nir, Gnirke, Andreas, Regev, Aviv

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 1.48 MB

english, 2010

13

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

Rabani, Michal, Levin, Joshua Z, Fan, Lin, Adiconis, Xian, Raychowdhury, Raktima, Garber, Manuel, Gnirke, Andreas, Nusbaum, Chad, Hacohen, Nir, Friedman, Nir

Journal:

Nature Biotechnology

Année:

2011

Langue:

english

Fichier:

PDF, 963 KB

english, 2011

14

Associations between plasma lipid parameters and APOC3 and APOA4 genotypes in a healthy population are independent of dietary cholesterol intake

Kristin L. Herron, Ingrid E. Lofgren, Xian Adiconis, Jose M. Ordovas, Maria Luz Fernandez

Journal:

Atherosclerosis

Année:

2006

Langue:

english

Fichier:

PDF, 141 KB

english, 2006

15

Comparative analysis of RNA sequencing methods for degraded or low-input samples

Adiconis, Xian, Borges-Rivera, Diego, Satija, Rahul, DeLuca, David S, Busby, Michele A, Berlin, Aaron M, Sivachenko, Andrey, Thompson, Dawn Anne, Wysoker, Alec, Fennell, Timothy, Gnirke, Andreas, Poch

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 717 KB

english, 2013

16

RNA-Seq methods for imperfect samples: development, evaluation and applications

Xian Adiconis, Lin Fan, David DeLuca, Andrey Sivachenko, Nathalie Pochet…

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 333 KB

english, 2011

17

RNA-Seq methods for imperfect samples: development, evaluation and applications

Xian Adiconis, Lin Fan, David DeLuca, Andrey Sivachenko, Nathalie Pochet…

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 373 KB

english, 2011

18

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

Moran Yassour, Jenna Pfiffner, Joshua Z Levin, Xian Adiconis…

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 931 KB

english, 2010

19

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

Joshua Z Levin, Michael F Berger, Xian Adiconis, Peter Rogov…

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 221 KB

english, 2009

20

Development and evaluation of RNA-seq methods

Joshua Levin, Xian Adiconis, Moran Yassour, Dawn Thompson…

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 168 KB

english, 2010

21

Integrative analysis of the melanoma transcriptome

Berger, M. F., Levin, J. Z., Vijayendran, K., Sivachenko, A., Adiconis, X., Maguire, J., Johnson, L. A., Robinson, J., Verhaak, R. G., Sougnez, C., Onofrio, R. C., Ziaugra, L., Cibulskis, K., Laine, E

Journal:

Genome Research

Année:

2010

Langue:

english

Fichier:

PDF, 1.14 MB

english, 2010

22

Corrigendum: Comparative analysis of RNA sequencing methods for degraded or low-input samples

Adiconis, Xian, Borges-Rivera, Diego, Satija, Rahul, DeLuca, David S, Busby, Michele A, Berlin, Aaron M, Sivachenko, Andrey, Thompson, Dawn Anne, Wysoker, Alec, Fennell, Timothy, Gnirke, Andreas, Poch

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 96 KB

english, 2014

23

PPARGC1A Variation Associated With DNA Damage, Diabetes, and Cardiovascular Diseases: The Boston Puerto Rican Health Study

Lai, C.-Q., Tucker, K. L., Parnell, L. D., Adiconis, X., Garcia-Bailo, B., Griffith, J., Meydani, M., Ordovas, J. M.

Journal:

Année:

2008

Langue:

english

Fichier:

PDF, 211 KB

english, 2008

24

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

Yassour, M., Kaplan, T., Fraser, H. B., Levin, J. Z., Pfiffner, J., Adiconis, X., Schroth, G., Luo, S., Khrebtukova, I., Gnirke, A., Nusbaum, C., Thompson, D.-A., Friedman, N., Regev, A.

Journal:

Proceedings of the National Academy of Sciences

Année:

2009

Langue:

english

Fichier:

PDF, 776 KB

english, 2009

25

Fenofibrate Effect on Triglyceride and Postprandial Response of Apolipoprotein A5 Variants: The GOLDN Study

Lai, C.-Q., Arnett, D. K., Corella, D., Straka, R. J., Tsai, M. Y., Peacock, J. M., Adiconis, X., Parnell, L. D., Hixson, J. E., Province, M. A., Ordovas, J. M.

Journal:

Arteriosclerosis Thrombosis and Vascular Biology

Année:

2007

Langue:

english

Fichier:

PDF, 297 KB

english, 2007

26

genome from RNA-Seq data

Amit, Ido, Adiconis, Xian, Fan, Lin, Raychowdhury, Raktima, Chen, Zehua, Mauceli, Evan, Hacohen, Nir, Gnirke, Andreas, Rhind, Nicholas, Palma, Federica, Birren, Bruce W, Nusbaum, Chad, Lindblad-toh, K

Année:

2013

Langue:

english

Fichier:

PDF, 2.59 MB

english, 2013

27

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci

Cuomo, Christina A., Bakkeren, Guus, Khalil, Hala Badr, Panwar, Vinay, Joly, David, Linning, Rob, Sakthikumar, Sharadha, Song, Xiao, Adiconis, Xian, Fan, Lin, Goldberg, Jonathan M., Levin, Joshua Z.,

Journal:

G3 Genes|Genome|Genetics

Année:

2017

Langue:

english

Fichier:

PDF, 10.44 MB

english, 2017

28

RIPK1 mediates a disease-associated microglial response in Alzheimer’s disease

Ofengeim, Dimitry, Mazzitelli, Sonia, Ito, Yasushi, DeWitt, Judy Park, Mifflin, Lauren, Zou, Chengyu, Das, Sudeshna, Adiconis, Xian, Chen, Hongbo, Zhu, Hong, Kelliher, Michelle A., Levin, Joshua Z., Y

Journal:

Proceedings of the National Academy of Sciences

Année:

2017

Langue:

english

Fichier:

PDF, 1.41 MB

english, 2017

29

Comprehensive comparative analysis of 5′-end RNA-sequencing methods

Adiconis, Xian, Haber, Adam L., Simmons, Sean K., Levy Moonshine, Ami, Ji, Zhe, Busby, Michele A., Shi, Xi, Jacques, Justin, Lancaster, Madeline A., Pan, Jen Q., Regev, Aviv, Levin, Joshua Z.

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 1.92 MB

english, 2018

30

Massively Parallel Sequencing of Human Urinary Exosome/Microvesicle RNA Reveals a Predominance of Non-Coding RNA

Miranda, Kevin C., Bond, Daniel T., Levin, Joshua Z., Adiconis, Xian, Sivachenko, Andrey, Russ, Carsten, Brown, Dennis, Nusbaum, Chad, Russo, Leileata M., Sands, Jeff M.

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 1.81 MB

english, 2014

31

Author Correction: Comprehensive comparative analysis of 5′-end RNA-sequencing methods

Adiconis, Xian, Haber, Adam L., Simmons, Sean K., Moonshine, Ami Levy, Ji, Zhe, Busby, Michele A., Shi, Xi, Jacques, Justin, Lancaster, Madeline A., Pan, Jen Q., Regev, Aviv, Levin, Joshua Z.

Journal:

Année:

2018

Fichier:

PDF, 599 KB

2018

32

Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes

Tran, Nicholas M., Shekhar, Karthik, Whitney, Irene E., Jacobi, Anne, Benhar, Inbal, Hong, Guosong, Yan, Wenjun, Adiconis, Xian, Arnold, McKinzie E., Lee, Jung Min, Levin, Joshua Z., Lin, Dingchang, W

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 8.90 MB

english, 2019

33

Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes

Tran, Nicholas M., Shekhar, Karthik, Whitney, Irene E., Jacobi, Anne, Benhar, Inbal, Hong, Guosong, Yan, Wenjun, Adiconis, Xian, Arnold, McKinzie E., Lee, Jung Min, Levin, Joshua Z., Lin, Dingchang, W

Journal:

Année:

2019

Fichier:

PDF, 8.90 MB

2019

34

Single-cell transcriptomic profiling of the aging mouse brain

Ximerakis, Methodios, Lipnick, Scott L., Innes, Brendan T., Simmons, Sean K., Adiconis, Xian, Dionne, Danielle, Mayweather, Brittany A., Nguyen, Lan, Niziolek, Zachary, Ozek, Ceren, Butty, Vincent L.,

Journal:

Nature Neuroscience

Année:

2019

Fichier:

PDF, 5.05 MB

2019

35

Differential excitatory vs inhibitory SCN expression at single cell level regulate brain sodium channel function in neurodevelopmental disorders

Du, Juanjiangmeng, Simmons, Sean, Brunklaus, Andreas, Adiconis, Xian, Hession, Cynthia C., Fu, Zhanyan, Li, Yinqing, Shema, Reut, Møller, Rikke S., Barak, Boaz, Feng, Guoping, Meisler, Miriam, Sanders

Journal:

European Journal of Paediatric Neurology

Année:

2019

Fichier:

PDF, 1.71 MB

2019

36

Author Correction: Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

Ding, Jiarui, Adiconis, Xian, Simmons, Sean K., Kowalczyk, Monika S., Hession, Cynthia C., Marjanovic, Nemanja D., Hughes, Travis K., Wadsworth, Marc H., Burks, Tyler, Nguyen, Lan T., Kwon, John Y. H.

Journal:

Nature Biotechnology

Année:

2020

Fichier:

PDF, 496 KB

2020