Publications

Carina Lauson, Silvia Tiberti, Paola Corsetto, Federica Conte, Punit Tyagi, Markus Machwirth, Stefan Ebert, Alessia Loffreda, Lukas Scheller, Dalia Sheta, Zeinab Mokhtari, Timo Peters, Ayush Raman, et al (2023). Linoleic acid potentiates CD8+ T cell metabolic fitness and antitumor immunity. Cell Metabolism.

Elias Orouji, Ayush Raman (2022). Computational methods to explore chromatin state dynamics. Briefings in Bioinformatics.

S Carson Callahan, Veena Kochat, Zhiyi Liu, Ayush Raman, Jonathan Schulz, Christopher Terranova, Margarita Divenko, Archit Ghosh, Ming Tang, Curtis Pickering, Jeffrey Myers, Kunal Rai (2022). High Enhancer Activity is an Epigenetic Feature of HPV Negative Atypical Head and Neck Squamous Cell Carcinoma. Frontiers in Cell and Developmental Biology.

Christopher J Terranova, Kristina M Stemler, Praveen Barrodia, Sabrina L Jeter-Jones, Zhongqi Ge, Marimar de la Cruz Bonilla, Ayush Raman, Chia-Wei Cheng, Kendra L Allton, Emre Arslan, et al (2021). Reprogramming of H3K9bhb at regulatory elements is a key feature of fasting in the small intestine. Cell Reports.

Christopher J Terranova, Ming Tang, Mayinuer Maitituoheti, Ayush Raman, Archit K Ghosh, Jonathan Schulz, Samir B Amin, Elias Orouji, Katarzyna Tomczak, Sharmistha Sarkar, et al (2021). Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. Cell Reports.

Hongcang Gu, Ayush Raman, Xiaoxue Wang, Federico Gaiti, Ronan Chaligne, Arman W Mohammad, Aleksandra Arczewska, Zachary D Smith, Dan A Landau, Martin J Aryee, Alexander Meissner, Andreas Gnirke (2021). Smart-RRBS for single-cell methylome and transcriptome analysis. Nature Protocols.

Elias Orouji, Ayush Raman, Anand K Singh, Alexey Sorokin, Emre Arslan, Archit K Ghosh, Jonathan Schulz, Christopher J Terranova, Ming Tang, Mayinuer Maitituoheti, et al (2021). Chromatin State Dynamics Confers Specific Therapeutic Strategies in Enhancer Subtypes of Colorectal Cancer. Gut.

Sarah J Shareef, Samantha M Bevill, Ayush Raman, Martin J Aryee, Peter van Galen, Volker Hovestadt, Bradley E Bernstein (2021). Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells. Nature Biotechnology.

Ayush Raman (2021). A research parasite's perspective on establishing a baseline to avoid errors in secondary analyses. Gigascience.

Veena Kochat, Ayush Raman, Sharon M Landers, Ming Tang, Jonathan Schulz, Christopher Terranova, Jace P Landry, Angela D Bhalla, Hannah C Beird, Chia-Chin Wu, et al (2021). Enhancer reprogramming in PRC2-deficient malignant peripheral nerve sheath tumors induces a targetable de-differentiated state. Acta Neuropathologica.

Mayinuer Maitituoheti, Emily Z Keung, Ming Tang, Liang Yan, Hunain Alam, Guangchun Han, Anand K Singh, Ayush Raman, Christopher Terranova, Sharmistha Sarkar, et al (2020). Enhancer reprogramming confers dependence on glycolysis and IGF signaling in KMT2D mutant melanoma. Cell reports.

Teresa Manzo, Boone M Prentice, Kristin G Anderson, Ayush Raman, Aislyn Schalck, Gabriela S Codreanu, Carina B Nava Lauson, Silvia Tiberti, Andrea Raimondi, Marissa A Jones, et al (2020). Accumulation of long-chain fatty acids in the tumor microenvironment drives dysfunction in intrapancreatic CD8+ T cells. Journal of Experimental Medicine.

Chun-An Chen, Wei Wang, Steen Pedersen, Ayush Raman, Michelle Seymour, Fernanda Ruiz, Anping Xia, Meike E van der Heijden, Li Wang, Jiani Yin, Joanna Lopez, Megan Rech, Richard Lewis, Samuel Wu, Zhandong Liu, Fred Pereira, Robia Pautler, Huda Zoghbi, Christian P Schaaf (2019). Nr2f1 heterozygous knockout mice recapitulate neurological phenotypes of Bosch-Boonstra-Schaaf optic atrophy syndrome and show impaired hippocampal synaptic plasticity. Human Molecular Genetics.

Santanu Adhikary, Deepavali Chakravarti, Christopher Terranova, Isha Sengupta, Mayinuer Maitituoheti, Anirban Dasgupta, Dushyant Kumar Srivastava, Junsheng Ma, Ayush Raman, Emily Tarco, Aysegul Sahin, Roland Bassett, Fei Yang, Coya Tapia, Siddhartha Roy, Kunal Rai, Chandrima Das (2019). Atypical plant homeodomain of UBR7 functions as an H2BK120Ub ligase and breast tumor suppressor. Nature Communications.

Ayush Raman, Amy E Pohodich, Ying-Wooi Wan, Hari Krishna Yalamanchili, William E Lowry, Huda Y Zoghbi, Zhandong Liu (2018). Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations. Nature communications.

Christopher Terranova, Ming Tang, Elias Orouji, Mayinuer Maitituoheti, Ayush Raman, Samirkumar Amin, Zhiyi Liu, Kunal Rai (2018). An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-Throughput ChIP-sequencing in Tumor Tissues. J Vis Exp..

Amy E Pohodich, Hari Yalamanchili, Ayush Raman, Ying-Wooi Wan, Michael Gundry, Shuang Hao, Haijing Jin, Jianrong Tang, Zhandong Liu, Huda Y Zoghbi (2018). Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity. Elife.

Ayush Raman, Kunal Rai (2018). Loss of histone acetylation and H3K4 methylation promotes melanocytic malignant transformation. Molecular & Cellular Oncology.

Urszula Oleksiewicz, Marta Gladych, Ayush Raman, Holger Heyn, Elisabetta Mereu, Paula Chlebanowska, Anastazja Andrzejewska, Barbara Sozanska, Neha Samant, et al (2017). TRIM28 and Interacting KRAB-ZNFs Control Self-Renewal of Human Pluripotent Stem Cells through Epigenetic Repression of Pro-differentiation Genes. Stem cell reports.

Haidong Yi, Ayush Raman, Han Zhang, Genevera I Allen, Zhandong Liu (2017). Detecting hidden batch factors through data adaptive adjustment for biological effects. Bioinformatics.

The Cancer Genome Atlas Consortium (2015). Genomic classification of cutaneous melanoma. Cell.

Vladimir Litvak, Alexander V Ratushny, Aaron E Lampano, Frank Schmitz, Albert Huang, Ayush Raman, Alistair G Rust, Andreas Bergthaler, John D Aitchison, Alan Aderem (2012). A FOXO3--IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses. Nature.

Mycobacterium tuberculosis systems biology consortium (2009). Mycobacterium tuberculosis systems biology data in R. Biobytes.