HEART-GeN lab publications and pre-prints
Preprints
Kynon JM Benjamin. “RFMix-reader: Accelerated reading and processing for local ancestry studies.” bioRxiv. 2024. PMID: 39071265.
Benjamin, KJM, Sauler, M, Poonyagariyagorn, H, and Enid R Neptune. “Cell type-specific expression of angiotensin receptors in the human lung with implications for health, aging, and chronic disease.” bioRxiv. 2024. PMID: 38948835.
Evans, TA, Feltrin, AS, Benjamin, KJ, Katipalli, T, Hyde, TM, Kleinman, JE, Weinberger, DR, Paquola, ACM, and Jennifer A Erwin. “Lifespan analysis of repeat expression reveals age-dependent upregulation of HERV-K in the neurotypcial human brain.” medRxiv. 2024. PMID: 38797538.
Publications
2024
Benjamin, KJM, Chen, Q, Eagles, NJ, Huuki-Myers, LA, Collado-Torres, L, Stolz, JM, Shin, JH, Paquola, ACM, Hyde, TM, Kleinman, JE, Jaffe, AE, Han, S, and Daniel R Weinberger. “Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry.” Nature Neuroscience. 2024. PMID: 38769152. PDF.
Benjamin, KJM+, Arora, R+, Feltrin, AS, Pertea, G, Giles, H, Stolz, JM, D’Ignazio, L, Collado-Torres, L, Shin, JH, Hyde, TM, Kleinman, JE, Weinberger, DR, Paquola, ACM, and Jennifer A Erwin. “Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus.” Nature Communications. 2024. PMID: 38730231. PDF.
Tietze, E, Barbosa, AR, Araujo, BHS, Euclydes, V, Cho, HJ, Lee, YK, Feltrin, A, Spiegelberg, B, Lorenzetti, A, van de Leemput, J, Di Carlo, P, Sawada, T, Ursini, G, Benjamin, KJ, Brentani, H, Kleinman, JE, Hyde, TM, Weinberger, DR, McKay, R, Shin, JH, Paquola, ACM, and Jennifer A Erwin. “Human archetypal pluripotent stem cell differentiates into trophoblast stem cells via endogenous BMP5/7 induction without transitioning through a naive state.” Scientific Reports. 2024. PMID: 38332235.
2023
Benjamin, KJM, Katipalli, T and Apuã CM Paquola. “dRFEtools: dynamic recursive feature elimination for omics.” Bioinformatics. 2023. PMID: 37632789. PDF.
Sawada, T, Barbosa, A, Araujo, B, McCord, AE, D’Ignazio, L, Benjamin, KJM, Sheehan, B, Zabolocki, M, Feltrin, A, Arora, R, Brandtjen, A, Kleinman, JE, Hyde, TM, Bardy, C, Weinberger, DR, Paquola, ACM, and Jennifer A Erwin. “Recapitulation of perturbed striatal gene expression dynamics of donor’s brains with ventral forebrain organoids derived from the same individuals with schizophrenia.” American Journal of Psychiatry. 2023. PMID: 37915216.
2022
Benjamin, KJM, Chen, Q, Jaffe, AE, Stolz, JM, Collado-Torres, L, Huuki-Myers, LA, Burke, EE, Arora, R, Feltrin, AS, Barbosa, AR, Radulescu, E, Pergola, G, Shin, JH, Ulrich, WS, Deep-Soboslay, A, Tao, R, the BrainSeq Consortium, Hyde, TM, Kleinman, JE, Erwin, JA, Weinberger, DR, and Apuã CM Paquola. “Analysis of the caudate nucleus transcriptome in individuals with schizophrenia highlights effects of antipsychotics and novel risk genes.” Nature Neuroscience. 2022. PMID: 36319771. PDF.
D’Ignazio, L, Jacomini, RS, Qamar, B, Benjamin, KJM, Arora, R, Sawada, T, Diffenderfer, KE, Pankonin, AR, Hendriks, WT, Bragg, DC, Paquola, ACM, and Jennifer A Erwin. “Variation in TAF1 expression in female carrier induced pluripotent stem cells and human brain ontogeny has implications for adult neostriatum vulnerability in X-linked Dystonia Parkinsonism.” eNeuro. 2022. PMID: 35868859.
2020
Sawada, T, Benjamin, KJM, Brandtjen, AC, Tietze, E, Allen, SJ, Paquola, ACM, Kleinman, JE, Hyde, TM, and Jennifer A Erwin. “Generation of four postmortem dura-derived iPS cell lines from four control individuals with genotypic and brain-region-specific transcrptomic data available through the BrainSEQ consortium.” Stem Cell Research. 2020. PMID: 32446240.
Sawada, T, Chater, TE, Sasagawa, Y, Yoshimura, M, Fujimori, N, Tanaka, K, Benjamin, KJ, Paquola, ACM, Erwin, JA, Goda, Y, Nikaido, I, and Tadafumi Kato. “Developmental Excitation-Inhibition Imbalance Underlying Psychoses Revealed by Single-Cell Analyses of Discordant Twins-Derived Cerebral Organoids.” Molecular Psychiatry. 2020. PMID: 32764691.