Alex K. Shalek: search on Z-Library

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1

The Human Cell Atlas and equity: lessons learned

Majumder, Partha P., Mhlanga, Musa M., Shalek, Alex K.

Journal:

Nature Medicine

Year:

2020

File:

PDF, 744 KB

2020

2

Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion

Ranasinghe, Srinika, Lamothe, Pedro A., Soghoian, Damien Z., Kazer, Samuel W., Cole, Michael B., Shalek, Alex K., Yosef, Nir, Jones, R. Brad, Donaghey, Faith, Nwonu, Chioma, Jani, Priya, Clayton, Gina

Journal:

Year:

2016

Language:

english

File:

PDF, 2.75 MB

english, 2016

3

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:

Year:

2013

Language:

english

File:

PDF, 5.34 MB

english, 2013

4

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

Gifford, Casey A., Ziller, Michael J., Gu, Hongcang, Trapnell, Cole, Donaghey, Julie, Tsankov, Alexander, Shalek, Alex K., Kelley, David R., Shishkin, Alexander A., Issner, Robbyn, Zhang, Xiaolan, Coy

Journal:

Year:

2013

Language:

english

File:

PDF, 2.76 MB

english, 2013

5

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

Avraham, Roi, Haseley, Nathan, Brown, Douglas, Penaranda, Cristina, Jijon, Humberto B., Trombetta, John J., Satija, Rahul, Shalek, Alex K., Xavier, Ramnik J., Regev, Aviv, Hung, Deborah T.

Journal:

Year:

2015

File:

PDF, 53 KB

2015

6

Computational Methods for Single-Cell RNA Sequencing

Hie, Brian, Peters, Joshua, Nyquist, Sarah K., Shalek, Alex K., Berger, Bonnie, Bryson, Bryan D.

Journal:

Annual Review of Biomedical Data Science

Year:

2020

File:

PDF, 928 KB

2020

7

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

Gierahn, Todd M, Wadsworth, Marc H, Hughes, Travis K, Bryson, Bryan D, Butler, Andrew, Satija, Rahul, Fortune, Sarah, Love, J Christopher, Shalek, Alex K

Journal:

Year:

2017

Language:

english

File:

PDF, 3.95 MB

english, 2017

8

Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits

Robinson, Jacob T., Jorgolli, Marsela, Shalek, Alex K., Yoon, Myung-Han, Gertner, Rona S., Park, Hongkun

Journal:

Nature Nanotechnology

Year:

2012

Language:

english

File:

PDF, 2.40 MB

english, 2012

9

Heterogeneity in immune responses: from populations to single cells

Satija, Rahul, Shalek, Alex K.

Journal:

Trends in Immunology

Year:

2014

Language:

english

File:

PDF, 4.67 MB

english, 2014

10

Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies

Martin-Gayo, Enrique, Gao, Ce, Chen, Hsiao Rong, Ouyang, Zhengyu, Kim, Dhohyung, Kolb, Kellie E., Shalek, Alex K., Walker, Bruce D., Lichterfeld, Mathias, Yu, Xu G.

Journal:

Year:

2020

Language:

english

File:

PDF, 4.57 MB

english, 2020

11

Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli

Gat-Viks, Irit, Chevrier, Nicolas, Wilentzik, Roni, Eisenhaure, Thomas, Raychowdhury, Raktima, Steuerman, Yael, Shalek, Alex K, Hacohen, Nir, Amit, Ido, Regev, Aviv

Journal:

Nature Biotechnology

Year:

2013

Language:

english

File:

PDF, 1.17 MB

english, 2013

12

Identification of a Master Regulator of Differentiation in Toxoplasma

Waldman, Benjamin S., Schwarz, Dominic, Wadsworth, Marc H., Saeij, Jeroen P., Shalek, Alex K., Lourido, Sebastian

Journal:

Year:

2020

Language:

english

File:

PDF, 10.74 MB

english, 2020

13

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

Lohr, Jens G, Adalsteinsson, Viktor A, Cibulskis, Kristian, Choudhury, Atish D, Rosenberg, Mara, Cruz-Gordillo, Peter, Francis, Joshua M, Zhang, Cheng-Zhong, Shalek, Alex K, Satija, Rahul, Trombetta,

Journal:

Nature Biotechnology

Year:

2014

Language:

english

File:

PDF, 1.10 MB

english, 2014

14

Probing Enzymatic Activity inside Living Cells Using a Nanowire–Cell “Sandwich” Assay

Na, Yu-Ran, Kim, So Yeon, Gaublomme, Jellert T., Shalek, Alex K., Jorgolli, Marsela, Park, Hongkun, Yang, Eun Gyeong

Journal:

Year:

2013

Language:

english

File:

PDF, 2.89 MB

english, 2013

15

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

Shalek, Alex K., Satija, Rahul, Shuga, Joe, Trombetta, John J., Gennert, Dave, Lu, Diana, Chen, Peilin, Gertner, Rona S., Gaublomme, Jellert T., Yosef, Nir, Schwartz, Schraga, Fowler, Brian, Weaver, S

Journal:

Year:

2014

Language:

english

File:

PDF, 12.73 MB

english, 2014

16

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM

Wong, Alan S. L., Choi, Gigi C. G., Cui, Cheryl H., Pregernig, Gabriela, Milani, Pamela, Adam, Miriam, Perli, Samuel D., Kazer, Samuel W., Gaillard, Aleth, Hermann, Mario, Shalek, Alex K., Fraenkel, E

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 916 KB

english, 2016

17

MERFISHing for spatial context

Shalek, Alex K., Satija, Rahul

Journal:

Trends in Immunology

Year:

2015

Language:

english

File:

PDF, 128 KB

english, 2015

18

Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses

Douam, Florian, Ziegler, Carly G. K., Hrebikova, Gabriela, Fant, Bruno, Leach, Robert, Parsons, Lance, Wang, Wei, Gaska, Jenna M., Winer, Benjamin Y., Heller, Brigitte, Shalek, Alex K., Ploss, Alexand

Journal:

Nature Communications

Year:

2018

Language:

english

File:

PDF, 2.91 MB

english, 2018

19

Systematic Discovery of TLR Signaling Components Delineates Viral-Sensing Circuits

Nicolas Chevrier, Philipp Mertins, Maxim N. Artyomov, Alex K. Shalek, Matteo Iannacone, Mark F. Ciaccio, Irit Gat-Viks, Elena Tonti, Marciela M. DeGrace, Karl R. Clauser, Manuel Garber, Thomas M. Eise

Journal:

Year:

2011

Language:

english

File:

PDF, 1.86 MB

english, 2011

20

Vertical Silicon Nanowires as a Universal Platform for Delivering Biomolecules into Living Cells

Alex K. Shalek, Jacob T. Robinson, Ethan S. Karp, Jin Seok Lee, Dae-Ro Ahn, Myung-Han Yoon, Amy Sutton, Marsela Jorgolli, Rona S. Gertner, Taranjit S. Gujral, Gavin MacBeath, Eun Gyeong Yang, Hongkun

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.88 MB

english, 2010

21

317 CYTOF ANALYSIS OF HUMAN COLON AND BLOOD REVEALS DISTINCT IMMUNE SIGNATURES OF ULCERATIVE COLITIS AND CROHN'S DISEASE

Mitsialis, Vanessa, Wall, Sarah, Liu, Peng, Ordovas-Montanes, Jose, Parmet, Tamar, Field, Michael, McCourt, Collin, Toothaker, Jessica, Goldsmith, Jeffrey D., Kean, Leslie, Shalek, Alex, Tseng, George

Journal:

Gastroenterology

Year:

2020

File:

PDF, 958 KB

2020

22

Revisiting Airway Epithelial Remodeling in Type 2 Immunity: Beyond Goblet Cell Metaplasia

Barrett, Nora A., Shalek, Alex K.

Journal:

Journal of Allergy and Clinical Immunology

Year:

2019

Language:

english

File:

PDF, 1.51 MB

english, 2019

23

TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures

Tu, Ang A., Gierahn, Todd M., Monian, Brinda, Morgan, Duncan M., Mehta, Naveen K., Ruiter, Bert, Shreffler, Wayne G., Shalek, Alex K., Love, J. Christopher

Journal:

Nature Immunology

Year:

2019

File:

PDF, 7.95 MB

2019

24

973. Single-cell RNA Sequencing Analysis of Zika Virus Infection in Human Stem Cell-Derived Cerebral Organoids

Ocwieja, Karen, Stanton, Alexandra, Richards, Alexsia, Antonucci, Jenna, Hughes, Travis, Shalek, Alex, Jaenisch, Rudolph, Gehrke, Lee

Journal:

Open Forum Infectious Diseases

Year:

2019

File:

PDF, 1.10 MB

2019

25

Nanowire-Mediated Delivery Enables Functional Interrogation of Primary Immune Cells: Application to the Analysis of Chronic Lymphocytic Leukemia

Shalek, Alex K., Gaublomme, Jellert T., Wang, Lili, Yosef, Nir, Chevrier, Nicolas, Andersen, Mette S., Robinson, Jacob T., Pochet, Nathalie, Neuberg, Donna, Gertner, Rona S., Amit, Ido, Brown, Jennife

Journal:

Year:

2012

Language:

english

File:

PDF, 1.78 MB

english, 2012

26

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

Gaublomme, Jellert T., Yosef, Nir, Lee, Youjin, Gertner, Rona S., Yang, Li V., Wu, Chuan, Pandolfi, Pier Paolo, Mak, Tak, Satija, Rahul, Shalek, Alex K., Kuchroo, Vijay K., Park, Hongkun, Regev, Aviv

Journal:

Year:

2015

Language:

english

File:

PDF, 3.27 MB

english, 2015

27

Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics

Wadsworth, Marc H., Hughes, Travis K., Shalek, Alex K.

Journal:

Year:

2015

Language:

english

File:

PDF, 323 KB

english, 2015

28

Regulation of X-linked gene expression during early mouse development by Rlim

Wang, Feng, Shin, JongDae, Shea, Jeremy M, Yu, Jun, Bošković, Ana, Byron, Meg, Zhu, Xiaochun, Shalek, Alex K, Regev, Aviv, Lawrence, Jeanne B, Torres, Eduardo M, Zhu, Lihua J, Rando, Oliver J, Bach, I

Journal:

Year:

2016

File:

PDF, 1.80 MB

2016

29

Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohnâs Disease

Mitsialis, Vanessa, Wall, Sarah, Liu, Peng, Ordovas-Montanes, Jose, Parmet, Tamar, Vukovic, Marko, Spencer, Dennis, Field, Michael, McCourt, Collin, Toothaker, Jessica, Bousvaros, Athos, Shalek, Alex

Journal:

Gastroenterology

Year:

2020

File:

PDF, 1.51 MB

2020

30

Dynamic regulatory network controlling TH17 cell differentiation

Yosef, Nir, Shalek, Alex K., Gaublomme, Jellert T., Jin, Hulin, Lee, Youjin, Awasthi, Amit, Wu, Chuan, Karwacz, Katarzyna, Xiao, Sheng, Jorgolli, Marsela, Gennert, David, Satija, Rahul, Shakya, Arvind

Journal:

Year:

2013

Language:

english

File:

PDF, 1.18 MB

english, 2013

31

High-Frequency, Functional HIV-Specific T-Follicular Helper and Regulatory Cells Are Present Within Germinal Centers in Children but Not Adults

Roider, Julia, Maehara, Takashi, Ngoepe, Abigail, Ramsuran, Duran, Muenchhoff, Maximilian, Adland, Emily, Aicher, Toby, Kazer, Samuel W., Jooste, Pieter, Karim, Farina, Kuhn, Warren, Shalek, Alex K.,

Journal:

Frontiers in Immunology

Year:

2018

Language:

english

File:

PDF, 2.76 MB

english, 2018

32

IL-5RÎ± marks nasal polyp IgG4 and IgE-expressing cells in aspirin-exacerbated respiratory disease

Buchheit, Kathleen M., Dwyer, Daniel F., Ordovas-Montanes, Jose, Katz, Howard R., Lewis, Erin, Vukovic, Marko, Lai, Juying, Bankova, Lora, Bhattacharyya, Neil, Shalek, Alex K., Barrett, Nora A., Boyce

Journal:

Journal of Allergy and Clinical Immunology

Year:

2020

Language:

english

File:

PDF, 8.71 MB

english, 2020

33

Inflammasomes within Hyperactive Murine Dendritic Cells Stimulate Long-Lived T Cell-Mediated Anti-tumor Immunity

Zhivaki, Dania, Borriello, Francesco, Chow, Ohn A., Doran, Benjamin, Fleming, Ira, Theisen, Derek J., Pallis, Paris, Shalek, Alex K., Sokol, Caroline L., Zanoni, Ivan, Kagan, Jonathan C.

Journal:

Year:

2020

File:

PDF, 60 KB

2020

34

Single-cell analyses to tailor treatments

Shalek, Alex K., Benson, Mikael

Journal:

Science Translational Medicine

Year:

2017

Language:

english

File:

PDF, 323 KB

english, 2017

35

Erratum: Deconstructing transcriptional heterogeneity in pluripotent stem cells

Kumar, Roshan M., Cahan, Patrick, Shalek, Alex K., Satija, Rahul, DaleyKeyser, A. Jay, Li, Hu, Zhang, Jin, Pardee, Keith, Gennert, David, Trombetta, John J., Ferrante, Thomas C., Regev, Aviv, Daley, G

Journal:

Year:

2015

File:

PDF, 27 KB

2015

36

Functional compensation precedes recovery of tissue mass following acute liver injury

Walesky, Chad M., Kolb, Kellie E., Winston, Carolyn L., Henderson, Jake, Kruft, Benjamin, Fleming, Ira, Ko, Sungjin, Monga, Satdarshan P., Mueller, Florian, Apte, Udayan, Shalek, Alex K., Goessling, W

Journal:

Nature Communications

Year:

2020

File:

PDF, 6.00 MB

2020

37

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices

Prakadan, Sanjay M., Shalek, Alex K., Weitz, David A.

Journal:

Nature Reviews Genetics

Year:

2017

Language:

english

File:

PDF, 2.02 MB

english, 2017

38

Erratum: Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

Gierahn, Todd M, Wadsworth, Marc H, Hughes, Travis K, Bryson, Bryan D, Butler, Andrew, Satija, Rahul, Fortune, Sarah, Love, J Christopher, Shalek, Alex K

Journal:

Year:

2017

Language:

english

File:

PDF, 68 KB

english, 2017

39

A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers

Martin-Gayo, Enrique, Cole, Michael B., Kolb, Kellie E., Ouyang, Zhengyu, Cronin, Jacqueline, Kazer, Samuel W., Ordovas-Montanes, Jose, Lichterfeld, Mathias, Walker, Bruce D., Yosef, Nir, Shalek, Alex

Journal:

Year:

2018

Language:

english

File:

PDF, 1.94 MB

english, 2018

40

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

Berger, Emily, Yorukoglu, Deniz, Zhang, Lillian, Nyquist, Sarah K., Shalek, Alex K., Kellis, Manolis, NumanagiÄ, Ibrahim, Berger, Bonnie

Journal:

Nature Communications

Year:

2020

File:

PDF, 871 KB

2020

41

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

Kimmerling, Robert J., Lee Szeto, Gregory, Li, Jennifer W., Genshaft, Alex S., Kazer, Samuel W., Payer, Kristofor R., de Riba Borrajo, Jacob, Blainey, Paul C., Irvine, Darrell J., Shalek, Alex K., Man

Journal:

Nature Communications

Year:

2016

Language:

english

File:

PDF, 824 KB

english, 2016

42

Evolution and Diversity of Immune Responses during Acute HIV Infection

Kazer, Samuel W., Walker, Bruce D., Shalek, Alex K.

Journal:

Year:

2020

File:

PDF, 716 KB

2020

43

Deconstructing transcriptional heterogeneity in pluripotent stem cells

Kumar, Roshan M., Cahan, Patrick, Shalek, Alex K., Satija, Rahul, Jay DaleyKeyser, A., Li, Hu, Zhang, Jin, Pardee, Keith, Gennert, David, Trombetta, John J., Ferrante, Thomas C., Regev, Aviv, Daley, G

Journal:

Year:

2014

Language:

english

File:

PDF, 9.46 MB

english, 2014

44

TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures

Tu, Ang A., Gierahn, Todd M., Monian, Brinda, Morgan, Duncan M., Mehta, Naveen K., Ruiter, Bert, Shreffler, Wayne G., Shalek, Alex K., Love, J. Christopher

Journal:

Nature Immunology

Year:

2019

Language:

english

File:

PDF, 7.95 MB

english, 2019

45

MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data

Finak, Greg, McDavid, Andrew, Yajima, Masanao, Deng, Jingyuan, Gersuk, Vivian, Shalek, Alex K., Slichter, Chloe K., Miller, Hannah W., McElrath, M. Juliana, Prlic, Martin, Linsley, Peter S., Gottardo,

Journal:

Year:

2015

Language:

english

File:

PDF, 3.57 MB

english, 2015

46

Single-Cell RNA-Seq Allows Deep Analysis of the Tumor Immune Microenvironment and Alterations Induced by Anti-PD-1 Treatment

Miller, Brian, Wadsworth, Marc, Bi, Kevin, Hughes, Travis, Sharpe, Arlene, Shalek, Alex, Haining, W.

Journal:

Clinical Lymphoma Myeloma and Leukemia

Year:

2016

Language:

english

File:

PDF, 60 KB

english, 2016

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