Author

Emily Lee

Harvard University

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Cancer Biology· 2 Genomics· 2 Neuroscience· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Research Focus:differential expression· 3 Approach:experimental assay· 3 Organism:human· 3 Approach:statistical model· 3 Approach:machine learning (classical)· 2 Assay:scRNA-seq· 2 Assay:bulk RNA-seq· 1

Frequent Co-Authors

Benjamin L. de BivortiD· 2 shared Carolyn ElyaiD· 2 shared Jiajing ZhangiD· 2 shared Adam P Rosebrock· 1 shared Aidan C. DalyiD· 1 shared Andrew C. PattiD· 1 shared Andrew F. TeichiD· 1 shared Angie M. MaciasiD· 1 shared

Activity by Year

2016-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 10 mutual co-author links

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2 shared papersGenomics

Benjamin L. de BivortORCID

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Author profile →

7 papers

Recent·Most cited

CalFluxTools: An R package for analysis of high-throughput calcium oscillation screening data

Andrew C. Patt, William F. Borschel, John Braisted, Danyal Raza, Chia-Kuie Wu, Atena Farkhondeh, Caroline Strong, Jiajing Zhang, Emily Lee, Bryan J. Traynor, Ewy A. Mathé

CalFluxTools automates analysis of calcium flux data from high-throughput screens, providing quality control, statistical tests, and machine learning predictions for toxicity assessment.

bioRxiv · Sep 21, 2026 · PreprintBioinformatics

iPSC-derived NF1-CDKN2A-PRC2 deficient neural crest mimics MPNST glial-to-neuro-mesenchymal transition and uncover new therapeutic opportunities

Itziar Uriarte-Arrazola, Miriam Magallón‐Lorenz, Juana Fernández‐Rodríguez, Jiajing Zhang, Emily Lee, Sara Ortega‐Bertran, Edgar Creus‐Bachiller, Judit Farrés-Casas, Kelli M. Wilson, Crystal McKnight, Katlin Recabo, Ignacio Blanco, Héctor Salvador, Cleofé Romagosa, Conxi Lázaro, , Eduard Serra

This paper uses iPSC-derived neural crest models to mimic MPNST progression and identifies PARPi as a potential therapy for PRC2-deficient tumors.

bioRxiv · Aug 13, 2025 · PreprintCancer Biology

Single-cell transcriptomic landscape of the neuroimmune compartment in amyotrophic lateral sclerosis brain and spinal cord

John F. Tuddenham, Masashi Fujita, Emily Lee, Nivedita Nimmagadda, Anthony Khairallah, Claire Harbison, Xena E. Flowers, Guillermo Coronas‐Samano, Silas Maniatis, Aidan C. Daly, Julie A. Schneider, Andrew F. Teich, Jean Paul Vonsattel, Peter A. Sims, Wassim Elyaman, , Marta Olah

The paper identifies microglia subsets in ALS brain and spinal cord, finding an undifferentiated phenotype and enrichment of interferon response microglia in aggressive cases.

Acta Neuropathologica · Jul 29, 2025Peer-reviewedNeuroscience

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi

Jason Stajich, Brian Lovett, Emily Lee, Angie M. Macias, Ann E. Hajek, Benjamin L. de Bivort, Matt T. Kasson, Henrik H. De Fine Licht, Carolyn Elya

This paper presents a largely-complete genome of Entomophthora muscae, revealing insights into its large genome size, transposon activity, and unique biological features.

bioRxiv · Sep 13, 2023 · PreprintGenomics

Neural mechanisms of parasite-induced summiting behavior in 'zombie' Drosophila

Carolyn Elya, Danylo O. Lavrentovich, Emily Lee, Cassandra L. Pasadyn, Jasper Duval, Maya Basak, Valerie Saykina, Benjamin L. de Bivort

The paper identifies the neural and hormonal mechanisms underlying parasite-induced summiting behavior in Drosophila using a combination of behavioral assays, machine learning, and metabolomic analysis.

eLife · May 15, 2023Peer-reviewedNeuroscience

Molecular signatures associated with ZIKV exposure in human cortical neural progenitors

Feiran Zhang, Christy Hammack, Sarah Ogden, Yichen Cheng, Emily Lee, Zhexing Wen, Xuyu Qian, Ha Nam Nguyen, Yujing Li, Bing Yao, Miao Xu, Tianlei Xu, Li Chen, Zhiqin Wang, Hao Feng, , Peng Jin

This study identifies virus- and strain-specific molecular signatures of ZIKV infection in human cortical neural progenitors, showing distinct impacts on DNA replication and apoptosis.

bioRxiv · Aug 23, 2016Genomics

The mutational landscape of EGFR-, MYC-, and Kras- driven genetically-engineered mouse models of lung adenocarcinoma

David McFadden, Katerina Politi, Arjun Bhutkar, Frances K Chen, Xiaoling Song, Mono Pirun, Philip M Santiago, Caroline Kim, James T Platt, Emily Lee, Emily Hodges, Adam P Rosebrock, Roderick Bronson, Nicholas D Socci, Gregory Hannon, , Harold Varmus

This study compares the mutational landscapes of EGFR-, MYC-, and Kras-driven lung adenocarcinoma GEMMs to human cancers, finding simpler somatic genotypes in models that are useful for engineering studies.

bioRxiv · Apr 11, 2016Cancer Biology