Please note that my papers and citations are available online at: 👩‍💻

Please note my publications 🤓📚🧬 are as follows 📖 :

Revisions/Under Review/Preprints: ✏️

  • Raghu Ramesh, Saniya Khullar, Seogsik Won, Alena J. Hanson, Camila Lopez-Anido, Daifeng Wang, John Svaren, Integration of Nuclear Receptors into a Schwann cell-specific Gene Regulatory Network, submitted
  • Saniya Khullar, Xiang Huang, Raghu Ramesh, John Svaren, Daifeng Wang, NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation, under review, Biorxiv. Pre-print Link
  • Bo P. Lear, Elizabeth A.N. Thompson, Kendra Rodriguez, Zachary P. Arndt, Saniya Khullar, Payton Klosa, Ryan Lu, Christopher S. Morrow, Ryan Risgaard, Ella R. Peterson, Brian Teefy, Anita Bhattacharyya, Andre M.M. Sousa, Daifeng Wang, Berenice Benayoun, Darcie L. Moore, Age-specific imprinting through direct reprogramming reveals a developmental loss of intrinsic neurite growth ability in human neurons, in revision, Biorxiv. Pre-print Link

Published: 😺

2024: ⌛

  • Saniya Khullar, Biological-Network Guided Machine Learning for Understanding Gene Regulation in Human Brains and Disease Phenotypes From Multi-Omics Data Link to Dissertation at U.W.-Madison Library; Link to Dissertation on ProQuest
  • Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Pengyu Ni, Xiao Zhou, PsychENCODE Consortium, Trygve E Bakken, Jaroslav Bendl, Lucy Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panos Roussos, Nenad Sestan, Zhiping Weng, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel Geschwind, Mark Gerstein, Single-cell genomics and regulatory networks for 388 human brains, Science. Link Video

2023: ⌛

  • Pramod Bharadwaj Chandrashekar, Sayali Alatkar, Jiebiao Wang, Gabriel E. Hoffman, Chenfeng He, Ting Jin, Saniya Khullar, Jaroslav Bendl, John F. Fullard, Panagiotis Roussos, Daifeng Wang, DeepGAMI: Deep biologically guided auxiliary learning for multimodal integration and imputation to improve phenotype prediction, Genome Medicine. Link Video
  • Minjie Shen, Carissa L Sirois, Meng Li, Yu Guo, Qiping Dong, Natasha Mendez-Albelo, Yu Gao, Saniya Khullar, Lee Kissel, Jonathan Bryan, Soraya O Sandoval, Natalie Wolkoff, Amaya Contractor, Sabrina Huang, Tomer Korabelnikov, Birth Defects Research Laboratory BDRL, Jon Levine, Andre MM Sousa, Qiang Chang, Anita Bhattacharyya, Daifeng Wang, Donna Werling, Xinyu Zhao, Species-specific FMRP regulation of RACK1 is critical for prenatal cortical development, Neuron. Link
  • Chenfeng He, Noah Cohen Kalafut, Soraya O. Sandoval, Ryan Risgaard, Carissa L. Sirois, Chen Yang, Saniya Khullar, Marin Suzuki, Xiang Huang, Qiang Chang, Xinyu Zhao, Andre M.M. Sousa, Daifeng Wang, Brain and Organoid Manifold Alignment (BOMA), a machine learning framework for comparative gene expression analysis across brains and organoids, Cell Reports Methods. Link
  • Saniya Khullar, Daifeng Wang, Predicting brain-regional gene regulatory networks from multi-omics for Alzheimer’s disease phenotypes and Covid-19 severity, Human Molecular Genetics. Link

2022: ⌛

  • Shuang Liu, Hyejung Won, Declan Clarke, Nana Matoba, Saniya Khullar, Yudi Mu, Daifeng Wang, Mark Gerstein, Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex, Genome Medicine. Link
  • Chirag Gupta, Jielin Xu, Ting Jin, Saniya Khullar, Xiaoyu Liu, Sayali Alatkar, Feixiong Cheng, Daifeng Wang, Single-cell network biology characterizes cell-type gene regulation for drug repurposing and phenotype prediction in Alzheimer’s disease, PLOS Computational Biology. (Cover image of July 2022 issue) Link
  • Chirag Gupta, Pramod Chandrashekar, Chenfeng He, Ting Jin, Saniya Khullar, Qiang Chang, Daifeng Wang, Bringing artificial intelligence to research on intellectual and developmental disabilities: taking inspiration from neurological diseases IDDRC 2022 special issue on Computational Neuroscience, Journal of Neurodevelopmental Disorders. Link

2021: ⌛

  • Anna S. Heffron, Sean J. McIlwain, Maya F. Amjadi, David A. Baker, Saniya Khullar, Tammy Armbrust, Peter J. Halfmann, Yoshihiro Kawaoka, Ajay K. Sethi, Ann C. Palmenberg, Miriam A. Shelef, David H. O’Connor, Irene M. Ong, The landscape of antibody binding in SARS-CoV-2 infection, PLOS Biology. Link

2018: ⌛

  • Michala Skovlund Sørensen, Elizabeth C. Silvius, Saniya Khullar, Klaus Hindsø, Jonathan A. Forsberg, Michael Mørk Petersen, Biochemical Variables are Predictive for Patient Survival after Surgery for Skeletal Metastasis. A Prediction Model Development and External Validation Study, The Open Orthopaedics Journal. Link

Conference Abstracts: ✏️

2022: ⌛

  • Albert R. Wang, Saniya Khullar, Jared Brown, Andrew Baschnagel, Darya Buehler, Christina Kendziorski, Gopal Iyer. Remodeling the extracellular matrix environment enables the dissemination of primary tumor cells through a chemokine gradient to establish brain metastasis in non-small cell lung cancer adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3859. Link
  • Saniya Khullar, Daifeng Wang, Predicting gene regulatory networks from multi-omics to link genetic risk variants and neuroimmunology to Alzheimer’s disease phenotypes. Alzheimers Dementia. 2022;18:e068648. Link