Osnat Penn

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Osnat Penn (Hebrew: אסנת פן), born in 1981,[1] is an Israeli computational biologist whose work focuses on molecular evolution, cell research, and immunoinformatics.[2] She is the third Israeli scientist in three years to win the UNESCO-L’Oréal fellowship, which she received in 2013 for her work on the genetic origins of autism.[3] Penn is currently a postdoctorate fellow at the University of Washington in Seattle, where she has been working since 2012.[4][2]

Life and work[edit]

Penn holds three degrees from Tel-Aviv University in Israel. She completed a Bachelor of Science in Biology and Computer Science, specializing in bioinformatics.[5] She also completed a Master's degree in Molecular biology and a Ph.D. in Computational Biology, both with the department of cell research and immunology. Her Ph.D. thesis was titled "Computational methods for sequence analysis of HIV evolutionary dynamics," and was supervised by Tel-Aviv professor Tal Pupko.[5]

Penn previously worked at Tel-Aviv University as a teaching assistant for the course Introduction to Bioinformatics between 2006 and 2009. She also taught several bioinformatics and biological sequence analysis courses at Tel-Aviv between 2007 and 2011.[2]

Career[edit]

Penn has been responsible for several different computer programs developed at Tel Aviv University in order to aid in biological research.[2] She developed GUIDANCE, a web server used for estimating alignment confidence scores, with the support of the Converging Technologies Program.[2][6] RASER, the RAte Shift EstimatoR, is used to test site-specific evolutionary rate shifts and identify the specific sites and lineages in which the shifts likely occur.[7] The Pepitope Server is used to map epitopes using affinity-selected peptides.[2][8]

Her work with autism genetic sequencing, which won her the UNESCO-L’Oréal award and a grant of $40,000 to further her studies,[1] worked to identify genetic variations in autistic children that differed from genome sequences in allistic parents.[1] It contributed to research on the genetic complexity of autism, especially in instances where there is no family history of the condition (sporadic autism). Her work may lead to prenatal screening and early diagnosis of autism, as well as the development of gene therapy as an interventional treatment.[9]

Publications[edit]

Penn has been published in Cell,[10][11] Genome Research,[12] Molecular Biology and Evolution,[13] Nucleic Acids Research,[14] Systematic Biology,[15] BMC Evolutionary Biology,[16] PLoS Computational Biology,[17] Bioinformatics,[18] Proteins,[19] Genome Medicine,[20] Nature,[21] Frontiers in Molecular Biosciences,[22] Nature Ecology and Evolution,[23] Genome Biology,[24] American Journal of Human Genetics[25] and Protein Engineering, Design and Selection.[26]

References[edit]

  1. ^ a b c "Osnat Zomer-Penn". www.jewishvirtuallibrary.org. Retrieved 2022-11-24.
  2. ^ a b c d e f Penn, Osnat Zomer. "Osnat Penn (Osnat Zomer) Homepage". www.tau.ac.il. Retrieved 2022-11-24.
  3. ^ "Israeli Autism Researcher Wins UNESCO Fellowship". Algemeiner. 29 March 2013. Retrieved 26 November 2015.
  4. ^ "Osnat Penn". Eichler Lab. University of Washington. Archived from the original on 16 June 2016. Retrieved 26 November 2015.
  5. ^ a b "Eichler Lab". 2016-06-16. Archived from the original on 2016-06-16. Retrieved 2022-11-24.
  6. ^ "GUIDANCE Server - a web server for assessing alignment confidence score". guidance.tau.ac.il. Retrieved 2022-11-24.
  7. ^ "RASER - The RAte Shift EstimatoR". www.tau.ac.il. Retrieved 2022-11-24.
  8. ^ "Pepitope Server". pepitope.tau.ac.il. Retrieved 2022-11-24.
  9. ^ Shamah, David. "Israeli wins European women's science competition". www.timesofisrael.com. Retrieved 2022-11-24.
  10. ^ Bernier, Raphael; Golzio, Christelle; Xiong, Bo; Stessman, Holly A.; Coe, Bradley P.; Penn, Osnat; Witherspoon, Kali; Gerdts, Jennifer; Baker, Carl (2014-07-17). "Disruptive CHD8 Mutations Define a Subtype of Autism Early in Development". Cell. 158 (2): 263–276. doi:10.1016/j.cell.2014.06.017. ISSN 0092-8674. PMC 4136921. PMID 24998929.
  11. ^ Gouwens, Nathan W.; Sorensen, Staci A.; Baftizadeh, Fahimeh; Budzillo, Agata; Lee, Brian R.; Jarsky, Tim; Alfiler, Lauren; Baker, Katherine; Barkan, Eliza; Berry, Kyla; Bertagnolli, Darren; Bickley, Kris; Bomben, Jasmine; Braun, Thomas; Brouner, Krissy; Casper, Tamara; Crichton, Kirsten; Daigle, Tanya L.; Dalley, Rachel; de Frates, Rebecca A.; Dee, Nick; Desta, Tsega; Lee, Samuel Dingman; Dotson, Nadezhda; Egdorf, Tom; Ellingwood, Lauren; Enstrom, Rachel; Esposito, Luke; Farrell, Colin; Feng, David; Fong, Olivia; Gala, Rohan; Gamlin, Clare; Gary, Amanda; Glandon, Alexandra; Goldy, Jeff; Gorham, Melissa; Graybuck, Lucas; Gu, Hong; Hadley, Kristen; Hawrylycz, Michael J.; Henry, Alex M.; Hill, DiJon; Hupp, Madie; Kebede, Sara; Kim, Tae Kyung; Kim, Lisa; Kroll, Matthew; Lee, Changkyu; Link, Katherine E.; Mallory, Matthew; Mann, Rusty; Maxwell, Michelle; McGraw, Medea; McMillen, Delissa; Mukora, Alice; Ng, Lindsay; Ng, Lydia; Ngo, Kiet; Nicovich, Philip R.; Oldre, Aaron; Park, Daniel; Peng, Hanchuan; Penn, Osnat; Pham, Thanh; Pom, Alice; Popović, Zoran; Potekhina, Lydia; Rajanbabu, Ramkumar; Ransford, Shea; Reid, David; Rimorin, Christine; Robertson, Miranda; Ronellenfitch, Kara; Ruiz, Augustin; Sandman, David; Smith, Kimberly; Sulc, Josef; Sunkin, Susan M.; Szafer, Aaron; Tieu, Michael; Torkelson, Amy; Trinh, Jessica; Tung, Herman; Wakeman, Wayne; Ward, Katelyn; Williams, Grace; Zhou, Zhi; Ting, Jonathan T.; Arkhipov, Anton; Sümbül, Uygar; Lein, Ed S.; Koch, Christof; Yao, Zizhen; Tasic, Bosiljka; Berg, Jim; Murphy, Gabe J.; Zeng, Hongkui (November 2020). "Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells". Cell. 183 (4): 935–953.e19. doi:10.1016/j.cell.2020.09.057. PMC 7781065. PMID 33186530.
  12. ^ Gelfman, Sahar; Burstein, David; Penn, Osnat; Savchenko, Anna; Amit, Maayan; Schwartz, Schraga; Pupko, Tal; Ast, Gil (2012-01-01). "Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons". Genome Research. 22 (1): 35–50. doi:10.1101/gr.119834.110. ISSN 1088-9051. PMC 3246205. PMID 21974994.
  13. ^ Privman, Eyal; Penn, Osnat; Pupko, Tal (2012-01-01). "Improving the Performance of Positive Selection Inference by Filtering Unreliable Alignment Regions". Molecular Biology and Evolution. 29 (1): 1–5. doi:10.1093/molbev/msr177. ISSN 0737-4038. PMID 21772063.
  14. ^ Penn, Osnat; Privman, Eyal; Ashkenazy, Haim; Landan, Giddy; Graur, Dan; Pupko, Tal (2010-07-01). "GUIDANCE: a web server for assessing alignment confidence scores". Nucleic Acids Research. 38 (suppl 2): W23–W28. doi:10.1093/nar/gkq443. ISSN 0305-1048. PMC 2896199. PMID 20497997.
  15. ^ Stern, Adi; Mayrose, Itay; Penn, Osnat; Shaul, Shaul; Gophna, Uri; Pupko, Tal (2010-03-01). "An Evolutionary Analysis of Lateral Gene Transfer in Thymidylate Synthase Enzymes". Systematic Biology. 59 (2): 212–225. doi:10.1093/sysbio/syp104. ISSN 1063-5157. PMC 2826268. PMID 20525631.
  16. ^ Blanga-Kanfi, Shani; Miranda, Hector; Penn, Osnat; Pupko, Tal; DeBry, Ronald W.; Huchon, Dorothée (2009-04-02). "Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades". BMC Evolutionary Biology. 9 (1): 71. doi:10.1186/1471-2148-9-71. ISSN 1471-2148. PMC 2674048. PMID 19341461.
  17. ^ Penn, Osnat; Stern, Adi; Rubinstein, Nimrod D.; Dutheil, Julien; Bacharach, Eran; Galtier, Nicolas; Pupko, Tal (2008-11-07). "Evolutionary Modeling of Rate Shifts Reveals Specificity Determinants in HIV-1 Subtypes". PLOS Comput Biol. 4 (11): e1000214. Bibcode:2008PLSCB...4E0214P. doi:10.1371/journal.pcbi.1000214. PMC 2566816. PMID 18989394.
  18. ^ Mayrose, Itay; Penn, Osnat; Erez, Elana; Rubinstein, Nimrod D.; Shlomi, Tomer; Freund, Natalia Tarnovitski; Bublil, Erez M.; Ruppin, Eytan; Sharan, Roded (2007-12-01). "Pepitope: epitope mapping from affinity-selected peptides". Bioinformatics. 23 (23): 3244–3246. doi:10.1093/bioinformatics/btm493. ISSN 1367-4803. PMC 7110138. PMID 17977889.
  19. ^ Bublil, Erez M.; Freund, Natalia Tarnovitski; Mayrose, Itay; Penn, Osnat; Roitburd-Berman, Anna; Rubinstein, Nimrod D.; Pupko, Tal; Gershoni, Jonathan M. (2007-07-01). "Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm". Proteins: Structure, Function, and Bioinformatics. 68 (1): 294–304. CiteSeerX 10.1.1.124.9174. doi:10.1002/prot.21387. ISSN 1097-0134. PMID 17427229. S2CID 5322731.
  20. ^ Chow, Julie; Jensen, Matthew; Amini, Hajar; Hormozdiari, Farhad; Penn, Osnat; Shifman, Sagiv; Girirajan, Santhosh; Hormozdiari, Fereydoun (2019-10-25). "Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders". Genome Medicine. 11 (1): 65. doi:10.1186/s13073-019-0678-y. ISSN 1756-994X. PMC 6815046. PMID 31653223.
  21. ^ Tasic, Bosiljka; Yao, Zizhen; Graybuck, Lucas T.; Smith, Kimberly A.; Nguyen, Thuc Nghi; Bertagnolli, Darren; Goldy, Jeff; Garren, Emma; Economo, Michael N.; Viswanathan, Sarada; Penn, Osnat; Bakken, Trygve; Menon, Vilas; Miller, Jeremy; Fong, Olivia (November 2018). "Shared and distinct transcriptomic cell types across neocortical areas". Nature. 563 (7729): 72–78. doi:10.1038/s41586-018-0654-5. ISSN 1476-4687. PMC 6456269. PMID 30382198.
  22. ^ Xue, Ava Yuan; Di Pizio, Antonella; Levit, Anat; Yarnitzky, Tali; Penn, Osnat; Pupko, Tal; Niv, Masha Y. (2018). "Independent Evolution of Strychnine Recognition by Bitter Taste Receptor Subtypes". Frontiers in Molecular Biosciences. 5: 9. doi:10.3389/fmolb.2018.00009. ISSN 2296-889X. PMC 5840161. PMID 29552563.
  23. ^ Dennis, Megan Y.; Harshman, Lana; Nelson, Bradley J.; Penn, Osnat; Cantsilieris, Stuart; Huddleston, John; Antonacci, Francesca; Penewit, Kelsi; Denman, Laura; Raja, Archana; Baker, Carl; Mark, Kenneth; Malig, Maika; Janke, Nicolette; Espinoza, Claudia (2017-02-17). "The evolution and population diversity of human-specific segmental duplications". Nature Ecology & Evolution. 1 (3): 1–10. doi:10.1038/s41559-016-0069. hdl:11586/203935. ISSN 2397-334X.
  24. ^ Dougherty, Max L.; Nuttle, Xander; Penn, Osnat; Nelson, Bradley J.; Huddleston, John; Baker, Carl; Harshman, Lana; Duyzend, Michael H.; Ventura, Mario; Antonacci, Francesca; Sandstrom, Richard; Dennis, Megan Y.; Eichler, Evan E. (2017-03-09). "The birth of a human-specific neural gene by incomplete duplication and gene fusion". Genome Biology. 18 (1): 49. doi:10.1186/s13059-017-1163-9. ISSN 1474-760X. PMC 5345166. PMID 28279197.
  25. ^ Stessman, Holly A. F.; Willemsen, Marjolein H.; Fenckova, Michaela; Penn, Osnat; Hoischen, Alexander; Xiong, Bo; Wang, Tianyun; Hoekzema, Kendra; Vives, Laura; Vogel, Ida; Brunner, Han G.; van der Burgt, Ineke; Ockeloen, Charlotte W.; Schuurs-Hoeijmakers, Janneke H.; Klein Wassink-Ruiter, Jolien S. (2016-03-03). "Disruption of POGZ Is Associated with Intellectual Disability and Autism Spectrum Disorders". American Journal of Human Genetics. 98 (3): 541–552. doi:10.1016/j.ajhg.2016.02.004. ISSN 1537-6605. PMC 4890241. PMID 26942287.
  26. ^ Bar-Rogovsky, Hagit; Stern, Adi; Penn, Osnat; Kobl, Iris; Pupko, Tal; Tawfik, Dan S. (November 2015). "Assessing the prediction fidelity of ancestral reconstruction by a library approach". Protein Engineering, Design & Selection. 28 (11): 507–518. doi:10.1093/protein/gzv038. ISSN 1741-0134. PMID 26275856.

External links[edit]

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