PUBLICATIONS

Meromit Singer and Lior Pachter. Controlling for conservation in genome-wide DNA methylation studies. BMC Genomics 16.1 (2015): 1.

Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David I.K. Martin, Meromit Singer# and Lior Pachter#. Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 12.1 (2011): 1

David I.K. Martin*, Meromit Singer*, Joseph Dhahbi, Guanxiong Mao, Lu Zhang, Gary P. Schroth, Lior Pachter and Dario Boffelli. Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states . Genome Research 21.12 (2011): 2049-2057

Daria Bloch, Gabriele Monshausen, Meromit Singer, Simon Gilroy and Shaul Yalovsky. Nitrogen source interacts with ROP signaling in root hair tip-growth. Plant Cell and Environment. 2011 Jan;34(1):76-88

Meromit Singer, Dario Boffelli, Joseph Dhahbi, Alexander Schoenhuth, Gary P. Schroth, David I.K. Martin and Lior Pachter. MetMap enables genome-scale methyltyping for determining methylation states in populations. PLoS Computational Biology 2010 Aug 19; 6(8):e1000888

Alexandra Schnell*, Linglin Huang*, Meromit Singer*, Anvita Singaraju, Rocky M Barilla, Brianna M L Regan, Alina Bollhagen, Pratiksha I Thakore, Danielle Dionne, Toni M Delorey, Mathias Pawlak, Gerd Meyer Zu Horste, Orit Rozenblatt-Rosen, Rafael A Irizarry, Aviv Regev#, Vijay K Kuchroo#. Stem-like intestinal Th17 cells give rise to pathogenic effector T cells during autoimmunity. Cell. 2021 Dec 22;184(26).doi: 10.1016/j.cell.2021.11.018

Chen Zhu, Karen O Dixon, Kathleen Newcomer, Guangxiang Gu, Sheng Xiao, Sarah Zaghouani, Markus A Schramm, Chao Wang, Huiyuan Zhang, Kouichiro Goto, Elena Christian, Manu Rangachari, Orit Rosenblatt-Rosen, Hitoshi Okada, Tak Mak, Meromit Singer, Aviv Regev, Vijay Kuchroo. Tim-3 adaptor protein Bat3 is a molecular checkpoint of T cell terminal differentiation and exhaustion. Sci. Adv. 2021 Apr 30;7(18) doi: 10.1126/sciadv.abd2710.

2021 Apr 5;218(4):e20200921. doi: 10.1084/jem.20200921

Kristen E. Pauken*, Osmaan Shahid*, Kaitlyn A. Lagattuta*, Kelly M. Mahuron*, Jacob M. Luber*, Margaret M. Lowe, Linglin Huang, Conor Delaney, Jaclyn M. Long, Megan E. Fung, Kathleen Newcomer, Katy K. Tsai, Melissa Chow, Samantha Guinn, Juhi R. Kuchroo, Kelly P. Burke, Jason M. Schenkel, Michael D. Rosenblum#, Adil I. Daud#, Arlene H. Sharpe#, Meromit Singer#. Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment. J Exp Med. 2021 Apr 5;218(4):e20200920. doi: 10.1084/jem.20200920.

Liliana Lucca, Pierre-Paul Axisa, Benjamin Lu, Brian Harnett, Shlomit Jessel, Le Zhang, Khadir Raddassi, Lin Zhang, Kelly Olino, James Clune, Meromit Singer, Harriet M. Kluger#, David A. Hafler#. Circulating Clonally Expanded T Cells Reflect Functions of Tumor Infiltrating T Cells. J Exp Med. 2021 Apr 5;218(4):e20200921. doi: 10.1084/jem.20200921

Mahesh Raundhal, Shrestha Ghosh, Samuel A. Myers, Michael S. Cuoco, Meromit Singer, Steven A. Carr, Sushrut S. Waikar, Joseph V. Bonventre, Jerome Ritz, Richard M. Stone, David P. Steensma, Aviv Regev, Laurie H. Glimcher Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias. Nat Immunol 2021 Apr;22(4):520-529. doi: 10.1038/s41590-021-00895-4.

Ivy X. Chen, Kathleen Newcomer, Kristen E. Pauken, Vikram R. Juneja, Kamila Naxerova, Michelle W. Wu, Matthias Pinter, Debattama R. Sen, Meromit Singer#, Arlene H. Sharpe# and Rakesh Jain#. A bilateral tumor model identifies transcriptional programs that associated with patient response. PNAS (2020) 117(38):23684-23694

Nandini Acharya, Asaf Madi, Huiyuan Zhang, Max Klapholz, Giulia Escobar, Shai Dulberg, Elena Christian, Michelle Ferreira, Karen O Dixon, Geoffrey Fell, Katherine Tooley, Davide Mangani, Junrong Xia, Meromit Singer, Marcus Bosenberg, Donna Neuberg, Orit Rozenblatt-Rosen, Aviv Regev, Vijay K Kuchroo, Ana C Anderson. Endogenous Glucocorticoid Signaling Regulates CD8 + T Cell Differentiation and Development of Dysfunction in the Tumor Microenvironment., Immunity (2020) 53(3):658-671.e6

Conor Delaney*, Alexandra Schnell*, Louis V. Cammarata*, Aaron Yao-Smith, Aviv Regev, Vijay K. Kuchroo, and Meromit Singer. Combinatorial prediction of marker panels from single-cell transcriptomic data.

Molecular Systems Biology (2019) 15:e9005

The COMET interface is here, and the software package can be downloaded here.

Kelly M Mahuron, Joshua M Moreau, Jeff E Glasgow, Devi P Boda, Mariela L Pauli, Victoire Gouirand, Luv Panjabi, Robby Grewal, Jacob M Luber, Anubhav N Mathur, Renny M Feldman, Eric Shifrut, Pooja Mehta, Margaret M Lowe, Michael D Alvarado, Alexander Marson, Meromit Singer, Jim Wells, Ray Jupp, Adil I Daud, Michael D Rosenblum. Layilin augments integrin activation to promote antitumor immunity.,

J Exp. Med. (2020) 217(9):e20192080

Meromit Singer and Ana C. Anderson. Revolutionizing Cancer Immunology: The Power of Next-Generation Sequencing Technologies. Cancer Immunology Research (2019) 7(2):168-173

Chihara N, Madi A, Kondo T, Zhang H, Acharya N, Singer M, Nyman J, Marjanovic ND, Kowalczyk MS, Wang C, Kurtulus S, Law T, Etminan Y, Nevin J, Buckley CD, Burkett PR, Buenrostro JD, Rozenblatt-Rosen O, Anderson AC, Regev A and Kuchroo VK. Induction and transcriptional regulation of the co-inhibitory gene module in T cells. Nature (2018) DOI: 10.1038/s41586-018-0206-z

Chao Wang, Maria I. Edilova, Lisa E. Wagar, Shariq Mujib, Meromit Singer, Nicole F. Bernard, Th Croughs, Michael M. Lederman, Irini Sereti, Margaret A. Fischl, Elisabeth Kremmer, Mario Ostrowski, Jean-Pierre Routy and Tania H. Watts. Effect of IL-7 Therapy on Phospho-Ribosomal Protein S6 and TRAF1 Expression in HIV-Specific CD8 T Cells in Patients Receiving Antiretroviral Therapy. The Journal if Immunology (2018) DOI: 10.4049/jimmunol.1601254

Chao Wang, Meromit Singer and Ana C. Anderson. Molecular dissection of CD8+ T-cell dysfunction. Trends in Immunology (2017) Aug;38(8):567-576

Xiuxing Wang, Kailin Yang, Qi Xie, Qiulian Wu, Stephen C. Mack, Yu Shi, Leo Kim, Briana C. Prager, William A. Flavahan, Xiaojing Liu, Meromit Singer, Christopher G. Hubert, Tyler E. Miller, Wenchao Zhou, Zhi Huang, Xiaoguang Fang, Aviv Regev, Mario L. Suva, Tae Hyun Hwang, Jason W. Locasale, Shideng Bao and Jeremy N. Rich. Purine Synthesis Promotes Brain Tumor Initiating Cell Maintenance in Glioma. Nature Neuroscience. (2017) May;20(5):661-673.

Meromit Singer*, Chao Wang*, Le Cong, Nemanja D. Marjanovic, Monika S. Kowalczyk, Huiyuan Zhang, Jackson Nyman, Kaori Sakuishi, Sema Kurtulus, David Gennert, Junrong Xia, John Y.H. Kwon, James Nevin, Rebecca H. Herbst, Itai Yanai, Orit Rozenblatt-Rosen, Vijay K. Kuchroo#, Aviv Regev# and Ana C. Anderson#. A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells. Cell 166.6 (2016): 1500-1511

Meromit Singer and Lior Pachter. Controlling for conservation in genome-wide DNA methylation studies. BMC Genomics 16.1 (2015): 1.