Indicators of Successful Career Transitions from Physical Sciences and Engineering to Biomedical Research

Overview

Journal Curr Genomics

Publisher Bentham Science Publishers

Date 2022 Mar 11

PMID 35273460

Authors

Michael A Beer

Affiliations

Soon will be listed here.

References

Xi W, Beer M . Loop competition and extrusion model predicts CTCF interaction specificity. Nat Commun. 2021; 12(1):1046. PMC: 7886907. DOI: 10.1038/s41467-021-21368-0. View

Whalen S, Truty R, Pollard K . Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. Nat Genet. 2016; 48(5):488-96. PMC: 4910881. DOI: 10.1038/ng.3539. View

Beer M, Shigaki D, Huangfu D . Enhancer Predictions and Genome-Wide Regulatory Circuits. Annu Rev Genomics Hum Genet. 2020; 21:37-54. PMC: 7644210. DOI: 10.1146/annurev-genom-121719-010946. View

Kreimer A, Zeng H, Edwards M, Guo Y, Tian K, Shin S . Predicting gene expression in massively parallel reporter assays: A comparative study. Hum Mutat. 2017; 38(9):1240-1250. PMC: 5560998. DOI: 10.1002/humu.23197. View

Xi W, Beer M . Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy. PLoS Comput Biol. 2018; 14(12):e1006625. PMC: 6298642. DOI: 10.1371/journal.pcbi.1006625. View

Venter J, Adams M, Myers E, Li P, Mural R, Sutton G . The sequence of the human genome. Science. 2001; 291(5507):1304-51. DOI: 10.1126/science.1058040. View

Ferrell Jr J, Tsai T, Yang Q . Modeling the cell cycle: why do certain circuits oscillate?. Cell. 2011; 144(6):874-85. DOI: 10.1016/j.cell.2011.03.006. View

Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J . Initial sequencing and analysis of the human genome. Nature. 2001; 409(6822):860-921. DOI: 10.1038/35057062. View

Cao F, Fullwood M . Inflated performance measures in enhancer-promoter interaction-prediction methods. Nat Genet. 2019; 51(8):1196-1198. DOI: 10.1038/s41588-019-0434-7. View

10.

Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon W . Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome. J Proteomics Bioinform. 2011; 4(2):22-35. PMC: 3124146. DOI: 10.4172/jpb.1000163. View

11.

Barrangou R, Doudna J . Applications of CRISPR technologies in research and beyond. Nat Biotechnol. 2016; 34(9):933-941. DOI: 10.1038/nbt.3659. View

12.

Ghandi M, Mohammad-Noori M, Beer M . Robust k-mer frequency estimation using gapped k-mers. J Math Biol. 2013; 69(2):469-500. PMC: 3895138. DOI: 10.1007/s00285-013-0705-3. View

13.

Beer M . Predicting enhancer activity and variant impact using gkm-SVM. Hum Mutat. 2017; 38(9):1251-1258. PMC: 5526747. DOI: 10.1002/humu.23185. View

14.

Li Q, Dixon G, Verma N, Rosen B, Gordillo M, Luo R . Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation. Nat Genet. 2019; 51(6):999-1010. PMC: 6545159. DOI: 10.1038/s41588-019-0408-9. View

15.

Hawrylycz M, Lein E, Guillozet-Bongaarts A, Shen E, Ng L, Miller J . An anatomically comprehensive atlas of the adult human brain transcriptome. Nature. 2012; 489(7416):391-399. PMC: 4243026. DOI: 10.1038/nature11405. View

16.

Snyder M, Gingeras T, Moore J, Weng Z, Gerstein M, Ren B . Perspectives on ENCODE. Nature. 2020; 583(7818):693-698. PMC: 7410827. DOI: 10.1038/s41586-020-2449-8. View

17.

Gemayel R . Scientific career paths - part II. FEBS J. 2017; 284(17):2700-2704. DOI: 10.1111/febs.14178. View

18.

Mirny L . Nucleosome-mediated cooperativity between transcription factors. Proc Natl Acad Sci U S A. 2010; 107(52):22534-9. PMC: 3012490. DOI: 10.1073/pnas.0913805107. View

19.

Shigaki D, Adato O, Adhikari A, Dong S, Hawkins-Hooker A, Inoue F . Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay. Hum Mutat. 2019; 40(9):1280-1291. PMC: 6879779. DOI: 10.1002/humu.23797. View

20.

Weinstein J, Collisson E, Mills G, Mills Shaw K, Ozenberger B, Ellrott K . The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013; 45(10):1113-20. PMC: 3919969. DOI: 10.1038/ng.2764. View