Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Integrative single-cell analysis.

Literature DB >> 30696980

Integrative single-cell analysis.

Abstract

The recent maturation of single-cell RNA sequencing (scRNA-seq) technologies has coincided with transformative new methods to profile genetic, epigenetic, spatial, proteomic and lineage information in individual cells. This provides unique opportunities, alongside computational challenges, for integrative methods that can jointly learn across multiple types of data. Integrated analysis can discover relationships across cellular modalities, learn a holistic representation of the cell state, and enable the pooling of data sets produced across individuals and technologies. In this Review, we discuss the recent advances in the collection and integration of different data types at single-cell resolution with a focus on the integration of gene expression data with other types of single-cell measurement.

Entities: Chemical

Mesh：

Substances：
Proteins
RNA

Year: 2019 PMID： 30696980 DOI： 10.1038/s41576-019-0093-7

Source DB: PubMed Journal: Nat Rev Genet ISSN： 1471-0056 Impact factor: 53.242

94 in total

1. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.

Authors: Allon M Klein; Linas Mazutis; Ilke Akartuna; Naren Tallapragada; Adrian Veres; Victor Li; Leonid Peshkin; David A Weitz; Marc W Kirschner
Journal: Cell Date: 2015-05-21 Impact factor: 41.582

2. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Authors: Evan Z Macosko; Anindita Basu; Rahul Satija; James Nemesh; Karthik Shekhar; Melissa Goldman; Itay Tirosh; Allison R Bialas; Nolan Kamitaki; Emily M Martersteck; John J Trombetta; David A Weitz; Joshua R Sanes; Alex K Shalek; Aviv Regev; Steven A McCarroll
Journal: Cell Date: 2015-05-21 Impact factor: 41.582

3. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification.

Authors: Tamar Hashimshony; Florian Wagner; Noa Sher; Itai Yanai
Journal: Cell Rep Date: 2012-08-30 Impact factor: 9.423

4. Comprehensive single-cell transcriptional profiling of a multicellular organism.

Authors: Junyue Cao; Jonathan S Packer; Vijay Ramani; Darren A Cusanovich; Chau Huynh; Riza Daza; Xiaojie Qiu; Choli Lee; Scott N Furlan; Frank J Steemers; Andrew Adey; Robert H Waterston; Cole Trapnell; Jay Shendure
Journal: Science Date: 2017-08-18 Impact factor: 47.728

5. Sequencing thousands of single-cell genomes with combinatorial indexing.

Authors: Sarah A Vitak; Kristof A Torkenczy; Jimi L Rosenkrantz; Andrew J Fields; Lena Christiansen; Melissa H Wong; Lucia Carbone; Frank J Steemers; Andrew Adey
Journal: Nat Methods Date: 2017-01-30 Impact factor: 28.547

6. Tumour evolution inferred by single-cell sequencing.

Authors: Nicholas Navin; Jude Kendall; Jennifer Troge; Peter Andrews; Linda Rodgers; Jeanne McIndoo; Kerry Cook; Asya Stepansky; Dan Levy; Diane Esposito; Lakshmi Muthuswamy; Alex Krasnitz; W Richard McCombie; James Hicks; Michael Wigler
Journal: Nature Date: 2011-03-13 Impact factor: 49.962

7. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.

Authors: Diego Adhemar Jaitin; Ephraim Kenigsberg; Hadas Keren-Shaul; Naama Elefant; Franziska Paul; Irina Zaretsky; Alexander Mildner; Nadav Cohen; Steffen Jung; Amos Tanay; Ido Amit
Journal: Science Date: 2014-02-14 Impact factor: 47.728

8. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells.

Authors: Daniel Ramsköld; Shujun Luo; Yu-Chieh Wang; Robin Li; Qiaolin Deng; Omid R Faridani; Gregory A Daniels; Irina Khrebtukova; Jeanne F Loring; Louise C Laurent; Gary P Schroth; Rickard Sandberg
Journal: Nat Biotechnol Date: 2012-08 Impact factor: 54.908

9. Massively parallel digital transcriptional profiling of single cells.

Authors: Grace X Y Zheng; Jessica M Terry; Phillip Belgrader; Paul Ryvkin; Zachary W Bent; Ryan Wilson; Solongo B Ziraldo; Tobias D Wheeler; Geoff P McDermott; Junjie Zhu; Mark T Gregory; Joe Shuga; Luz Montesclaros; Jason G Underwood; Donald A Masquelier; Stefanie Y Nishimura; Michael Schnall-Levin; Paul W Wyatt; Christopher M Hindson; Rajiv Bharadwaj; Alexander Wong; Kevin D Ness; Lan W Beppu; H Joachim Deeg; Christopher McFarland; Keith R Loeb; William J Valente; Nolan G Ericson; Emily A Stevens; Jerald P Radich; Tarjei S Mikkelsen; Benjamin J Hindson; Jason H Bielas
Journal: Nat Commun Date: 2017-01-16 Impact factor: 14.919

10. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution.

Authors: M Ryan Corces; Jason D Buenrostro; Beijing Wu; Peyton G Greenside; Steven M Chan; Julie L Koenig; Michael P Snyder; Jonathan K Pritchard; Anshul Kundaje; William J Greenleaf; Ravindra Majeti; Howard Y Chang
Journal: Nat Genet Date: 2016-08-15 Impact factor: 38.330

300 in total

Review 1. The immunopathology of lung fibrosis: amphiregulin-producing pathogenic memory T helper-2 cells control the airway fibrotic responses by inducing eosinophils to secrete osteopontin.

Authors: Kiyoshi Hirahara; Ami Aoki; Yuki Morimoto; Masahiro Kiuchi; Mikiko Okano; Toshinori Nakayama
Journal: Semin Immunopathol Date: 2019-04-09 Impact factor: 9.623

2. SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery.

Authors: Siwen Hu-Lieskovan; Srabani Bhaumik; Kavita Dhodapkar; Jean-Charles J B Grivel; Sumati Gupta; Brent A Hanks; Sylvia Janetzki; Thomas O Kleen; Yoshinobu Koguchi; Amanda W Lund; Cristina Maccalli; Yolanda D Mahnke; Ruslan D Novosiadly; Senthamil R Selvan; Tasha Sims; Yingdong Zhao; Holden T Maecker
Journal: J Immunother Cancer Date: 2020-12 Impact factor: 13.751

Review 3. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.

Authors: Deanne M Taylor; Bruce J Aronow; Kai Tan; Kathrin Bernt; Nathan Salomonis; Casey S Greene; Alina Frolova; Sarah E Henrickson; Andrew Wells; Liming Pei; Jyoti K Jaiswal; Jeffrey Whitsett; Kathryn E Hamilton; Sonya A MacParland; Judith Kelsen; Robert O Heuckeroth; S Steven Potter; Laura A Vella; Natalie A Terry; Louis R Ghanem; Benjamin C Kennedy; Ingo Helbig; Kathleen E Sullivan; Leslie Castelo-Soccio; Arnold Kreigstein; Florian Herse; Martijn C Nawijn; Gerard H Koppelman; Melissa Haendel; Nomi L Harris; Jo Lynne Rokita; Yuanchao Zhang; Aviv Regev; Orit Rozenblatt-Rosen; Jennifer E Rood; Timothy L Tickle; Roser Vento-Tormo; Saif Alimohamed; Monkol Lek; Jessica C Mar; Kathleen M Loomes; David M Barrett; Prech Uapinyoying; Alan H Beggs; Pankaj B Agrawal; Yi-Wen Chen; Amanda B Muir; Lana X Garmire; Scott B Snapper; Javad Nazarian; Steven H Seeholzer; Hossein Fazelinia; Larry N Singh; Robert B Faryabi; Pichai Raman; Noor Dawany; Hongbo Michael Xie; Batsal Devkota; Sharon J Diskin; Stewart A Anderson; Eric F Rappaport; William Peranteau; Kathryn A Wikenheiser-Brokamp; Sarah Teichmann; Douglas Wallace; Tao Peng; Yang-Yang Ding; Man S Kim; Yi Xing; Sek Won Kong; Carsten G Bönnemann; Kenneth D Mandl; Peter S White
Journal: Dev Cell Date: 2019-03-28 Impact factor: 12.270

4. Chemical probes and methods for single-cell detection and quantification of epichaperomes in hematologic malignancies.

Authors: Swathi Merugu; Sahil Sharma; Justin Kaner; Chander Digwal; Mayumi Sugita; Suhasini Joshi; Tony Taldone; Monica L Guzman; Gabriela Chiosis
Journal: Methods Enzymol Date: 2020-05-10 Impact factor: 1.600

5. Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization.

Authors: Lihua Zhang; Shihua Zhang
Journal: Nucleic Acids Res Date: 2019-07-26 Impact factor: 16.971