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

by Emily Berger, Deniz Yorukoglu, Lillian Zhang, Sarah K. Nyquist, Alex K. Shalek, Manolis Kellis, Ibrahim Numanagić, Bonnie Berger
Published 2020-09-01

Immunological Fingerprints of Controllers Developing Neutralizing HIV-1 Antibodies

by Enrique Martin-Gayo, Ce Gao, Hsiao Rong Chen, Zhengyu Ouyang, Dhohyung Kim, Kellie E. Kolb, Alex K. Shalek, Bruce D. Walker, Mathias Lichterfeld, Xu G. Yu
Published 2020-01-01

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

by Dania Zhivaki, Francesco Borriello, Ohn A. Chow, Benjamin Doran, Ira Fleming, Derek J. Theisen, Paris Pallis, Alex K. Shalek, Caroline L. Sokol, Ivan Zanoni, Jonathan C. Kagan
Published 2020-11-01

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

by Madhvi Menon, Shahin Mohammadi, Jose Davila-Velderrain, Brittany A. Goods, Tanina D. Cadwell, Yu Xing, Anat Stemmer-Rachamimov, Alex K. Shalek, John Christopher Love, Manolis Kellis, Brian P. Hafler
Published 2019-10-01

Functional compensation precedes recovery of tissue mass following acute liver injury

by Chad M. Walesky, Kellie E. Kolb, Carolyn L. Winston, Jake Henderson, Benjamin Kruft, Ira Fleming, Sungjin Ko, Satdarshan P. Monga, Florian Mueller, Udayan Apte, Alex K. Shalek, Wolfram Goessling
Published 2020-11-01

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

by Florian Douam, Carly G. K. Ziegler, Gabriela Hrebikova, Bruno Fant, Robert Leach, Lance Parsons, Wei Wang, Jenna M. Gaska, Benjamin Y. Winer, Brigitte Heller, Alex K. Shalek, Alexander Ploss
Published 2018-11-01

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

by Julia Roider, Julia Roider, Julia Roider, Julia Roider, Takashi Maehara, Abigail Ngoepe, Duran Ramsuran, Maximilian Muenchhoff, Maximilian Muenchhoff, Emily Adland, Toby Aicher, Toby Aicher, Toby Aicher, Samuel W. Kazer, Samuel W. Kazer, Samuel W. Kazer, Pieter Jooste, Farina Karim, Warren Kuhn, Alex K. Shalek, Alex K. Shalek, Alex K. Shalek, Thumbi Ndung'u, Thumbi Ndung'u, Thumbi Ndung'u, Thumbi Ndung'u, Thumbi Ndung'u, Lynn Morris, Lynn Morris, Lynn Morris, Penny L. Moore, Penny L. Moore, Penny L. Moore, Shiv Pillai, Henrik Kløverpris, Henrik Kløverpris, Henrik Kløverpris, Philip Goulder, Philip Goulder, Alasdair Leslie, Alasdair Leslie
Published 2018-09-01

MR1-Restricted MAIT Cells From The Human Lung Mucosal Surface Have Distinct Phenotypic, Functional, and Transcriptomic Features That Are Preserved in HIV Infection

by Sharon Khuzwayo, Sharon Khuzwayo, Maphe Mthembu, Maphe Mthembu, Erin W. Meermeier, Sanjay M. Prakadan, Sanjay M. Prakadan, Sanjay M. Prakadan, Samuel W. Kazer, Samuel W. Kazer, Samuel W. Kazer, Thierry Bassett, Kennedy Nyamande, Dilshaad Fakey Khan, Priya Maharaj, Mohammed Mitha, Moosa Suleman, Moosa Suleman, Zoey Mhlane, Dirhona Ramjit, Farina Karim, Alex K. Shalek, Alex K. Shalek, Alex K. Shalek, David M. Lewinsohn, David M. Lewinsohn, David M. Lewinsohn, Thumbi Ndung’u, Thumbi Ndung’u, Thumbi Ndung’u, Thumbi Ndung’u, Thumbi Ndung’u, Thumbi Ndung’u, Emily B. Wong, Emily B. Wong, Emily B. Wong, Emily B. Wong
Published 2021-04-01

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

by Enrique Martin-Gayo, Michael B. Cole, Kellie E. Kolb, Zhengyu Ouyang, Jacqueline Cronin, Samuel W. Kazer, Jose Ordovas-Montanes, Mathias Lichterfeld, Bruce D. Walker, Nir Yosef, Alex K. Shalek, Xu G. Yu
Published 2018-01-01

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

by Robert J. Kimmerling, Gregory Lee Szeto, Jennifer W. Li, Alex S. Genshaft, Samuel W. Kazer, Kristofor R. Payer, Jacob de Riba Borrajo, Paul C. Blainey, Darrell J. Irvine, Alex K. Shalek, Scott R. Manalis
Published 2016-01-01

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

by Feng Wang, JongDae Shin, Jeremy M Shea, Jun Yu, Ana Bošković, Meg Byron, Xiaochun Zhu, Alex K Shalek, Aviv Regev, Jeanne B Lawrence, Eduardo M Torres, Lihua J Zhu, Oliver J Rando, Ingolf Bach
Published 2016-09-01

A Single Human VH-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood

by Maya Sangesland, Ashraf S. Yousif, Larance Ronsard, Samuel W. Kazer, Alex Lee Zhu, G. James Gatter, Matthew R. Hayward, Ralston M. Barnes, Maricel Quirindongo-Crespo, Daniel Rohrer, Nils Lonberg, Douglas Kwon, Alex K. Shalek, Daniel Lingwood
Published 2020-08-01

Linking single-cell measurements of mass, growth rate, and gene expression

by Robert J. Kimmerling, Sanjay M. Prakadan, Alejandro J. Gupta, Nicholas L. Calistri, Mark M. Stevens, Selim Olcum, Nathan Cermak, Riley S. Drake, Kristine Pelton, Frederik De Smet, Keith L. Ligon, Alex K. Shalek, Scott R. Manalis
Published 2018-11-01

Publisher Correction: Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes

by Alex S. Genshaft, Carly G. K. Ziegler, Constantine N. Tzouanas, Benjamin E. Mead, Alex M. Jaeger, Andrew W. Navia, Ryan P. King, Miyeko D. Mana, Siyi Huang, Vanessa Mitsialis, Scott B. Snapper, Ömer H. Yilmaz, Tyler Jacks, Jeffrey F. Van Humbeck, Alex K. Shalek
Published 2021-09-01

Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes

by Alex S Genshaft, Carly G. K. Ziegler, Constantine N. Tzouanas, Benjamin E. Mead, Alex M. Jaeger, Andrew W. Navia, Ryan P. King, Miyeko D. Mana, Siyi Huang, Vanessa Mitsialis, Scott B. Snapper, Ömer H. Yilmaz, Tyler Jacks, Jeffrey F. Van Humbeck, Alex K. Shalek
Published 2021-08-01

Leukocyte dynamics after intracerebral hemorrhage in a living patient reveal rapid adaptations to tissue milieu

by Brittany A. Goods, Michael H. Askenase, Erica Markarian, Hannah E. Beatty, Riley S. Drake, Ira Fleming, Jonathan H. DeLong, Naomi H. Philip, Charles C. Matouk, Issam A. Awad, Mario Zuccarello, Daniel F. Hanley, J. Christopher Love, Alex K. Shalek, Lauren H. Sansing, the ICHseq Investigators
Published 2021-03-01

Targeting Treg cells with GITR activation alleviates resistance to immunotherapy in murine glioblastomas

by Zohreh Amoozgar, Jonas Kloepper, Jun Ren, Rong En Tay, Samuel W. Kazer, Evgeny Kiner, Shanmugarajan Krishnan, Jessica M. Posada, Mitrajit Ghosh, Emilie Mamessier, Christina Wong, Gino B. Ferraro, Ana Batista, Nancy Wang, Mark Badeaux, Sylvie Roberge, Lei Xu, Peigen Huang, Alex K. Shalek, Dai Fukumura, Hye-Jung Kim, Rakesh K. Jain
Published 2021-05-01

Harnessing single-cell genomics to improve the physiological fidelity of organoid-derived cell types

by Benjamin E. Mead, Jose Ordovas-Montanes, Alexandra P. Braun, Lauren E. Levy, Prerna Bhargava, Matthew J. Szucs, Dustin A. Ammendolia, Melanie A. MacMullan, Xiaolei Yin, Travis K. Hughes, Marc H. Wadsworth, Rushdy Ahmad, Seth Rakoff-Nahoum, Steven A. Carr, Robert Langer, James J. Collins, Alex K. Shalek, Jeffrey M. Karp
Published 2018-06-01

Measuring kinetics and metastatic propensity of CTCs by blood exchange between mice

by Bashar Hamza, Alex B. Miller, Lara Meier, Max Stockslager, Sheng Rong Ng, Emily M. King, Lin Lin, Kelsey L. DeGouveia, Nolawit Mulugeta, Nicholas L. Calistri, Haley Strouf, Christina Bray, Felicia Rodriguez, William A. Freed-Pastor, Christopher R. Chin, Grissel C. Jaramillo, Megan L. Burger, Robert A. Weinberg, Alex K. Shalek, Tyler Jacks, Scott R. Manalis
Published 2021-09-01

A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases

by Danuta R. Gawel, Jordi Serra-Musach, Sandra Lilja, Jesper Aagesen, Alex Arenas, Bengt Asking, Malin Bengnér, Janne Björkander, Sophie Biggs, Jan Ernerudh, Henrik Hjortswang, Jan-Erik Karlsson, Mattias Köpsen, Eun Jung Lee, Antonio Lentini, Xinxiu Li, Mattias Magnusson, David Martínez-Enguita, Andreas Matussek, Colm E. Nestor, Samuel Schäfer, Oliver Seifert, Ceylan Sonmez, Henrik Stjernman, Andreas Tjärnberg, Simon Wu, Karin Åkesson, Alex K. Shalek, Margaretha Stenmarker, Huan Zhang, Mika Gustafsson, Mikael Benson
Published 2019-07-01