Noah Rosenberg

Last updated
Noah A. Rosenberg
Noah rosenberg 2023 06.jpg
Alma mater Rice University
Spouse(s)Donna Zulman, MD
AwardsFellow of the American Association for the Advancement of Science
Scientific career
Fields Population genetics
Phylogenetics
Mathematical and theoretical biology
Thesis Statistical modeling of genetic histories and relationships of populations  (2001)
Doctoral advisor Marcus Feldman [1]
Website rosenberglab.stanford.edu

Noah Aubrey Rosenberg is a geneticist working in evolutionary biology, mathematical phylogenetics, and population genetics, and is the Stanford Professor of Population Genetics and Society. [2] His research focuses on mathematical modeling and statistical methods for genetics and evolution [3] and he is the editor-in-chief of Theoretical Population Biology . [4]

Contents

Education

Rosenberg graduated from the Illinois Mathematics and Science Academy in 1993, where he began the mathematical reference known as The Noah Sheets. [5] He earned a BA in mathematics from Rice University in 1997, where he scored among the top 100 students in the Putnam Competition. [6] Rosenberg earned an MS in mathematics from Stanford University in 1999 and a PhD in biology from Stanford University in 2001 under the supervision of Marcus Feldman. [7] His dissertation was titled "Statistical modeling of genetic histories and relationships of populations." [8] Part of his dissertation work was recognized as The Lancet's 2003 paper of the year. [9] From 2001 to 2005, Rosenberg was a postdoctoral fellow at the University of Southern California. [7]

Career

Rosenberg was a professor at the University of Michigan from 2005 to 2011, where he held appointments in the Department of Human Genetics, the Department of Ecology and Evolutionary Biology, and the Department of Biostatistics. He joined the Stanford University Department of Biology as an associate professor in 2011 and was promoted to full professor in 2014, when he was named the Stanford Professor of Population Genetics and Society. [2] He is a member of Stanford's Institute for Computational and Mathematical Engineering (ICME) and Stanford Bio-X. [10] [11] Rosenberg was elected as a fellow of the American Association for the Advancement of Science in 2018. [12]

Rosenberg has published more than 150 peer-reviewed articles and has advised more than 35 doctoral students and postdoctoral fellows. [6] His trainees have gone on to professorships at universities including Cornell University, [13] Duke University, [14] the MD Anderson Cancer Center, [15] and the University of Southern California. [16] [17]

Rosenberg has served as the editor-in-chief of the journal Theoretical Population Biology since 2013 [4] and has served as an associate editor for scientific journals including Genetics and Evolution, Medicine, and Public Health. [18] He is also a co-director of the Stanford Center for Computational, Evolutionary, and Human Genomics. [19] In 2018, Rosenberg started the Stanford X-Tree Project, a website illustrating concepts from phylogenetics using photographs of real trees from the Stanford campus. [20]

Research

Much of Rosenberg's work has analyzed global patterns of genetic and linguistic variation, [9] [21] [22] [23] including developing software for the analysis and visualization of population ancestry data. [24] [25] [ non-primary source needed ] He has also studied the genetic histories of specific people groups, such as the Ohlone Indigenous population of California, [26] African Americans, [27] and Jewish populations. [28]

Rosenberg's work in forensic genetics has explored the implications of imputation techniques for genetic privacy. [29] [30] His work in coalescent theory has characterized the effects of consanguinity, [31] founder events, [32] and migration [33] on patterns of genetic variation. And his work in human genetics has investigated the implications of population history for association studies and polygenic scores. [34] [35]

Rosenberg has contributed to the understanding of mathematical properties of objects and quantities used in evolutionary biology. His work includes combinatorial enumeration of phylogenetic trees and coalescent histories, [36] [37] [38] [39] analysis of evolutionary models, [40] [41] [42] and derivation of mathematical bounds on population-genetic statistics. [43] [44] [45] He has also applied population-genetic statistics to other fields, such as his 2020 paper bridging health care efficiency research and population-genetic statistics which he co-authored with his wife, Donna Zulman. [46]

Rosenberg is a regular contributor to the On-Line Encyclopedia of Integer Sequences. [47] [48] [49]

Related Research Articles

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Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.

In biology, phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference, methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.

<span class="mw-page-title-main">Mitochondrial Eve</span> Matrilineal most recent common ancestor of all living humans

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A phylogenetic tree, phylogeny or evolutionary tree is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.

<span class="mw-page-title-main">Computational biology</span> Branch of biology

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Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.

<span class="mw-page-title-main">Mathematical and theoretical biology</span> Branch of biology

Mathematical and theoretical biology, or biomathematics, is a branch of biology which employs theoretical analysis, mathematical models and abstractions of living organisms to investigate the principles that govern the structure, development and behavior of the systems, as opposed to experimental biology which deals with the conduction of experiments to test scientific theories. The field is sometimes called mathematical biology or biomathematics to stress the mathematical side, or theoretical biology to stress the biological side. Theoretical biology focuses more on the development of theoretical principles for biology while mathematical biology focuses on the use of mathematical tools to study biological systems, even though the two terms are sometimes interchanged.

In biology and genetic genealogy, the most recent common ancestor (MRCA), also known as the last common ancestor (LCA), of a set of organisms is the most recent individual from which all the organisms of the set are descended. The term is also used in reference to the ancestry of groups of genes (haplotypes) rather than organisms.

Coalescent theory is a model of how alleles sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next. The model looks backward in time, merging alleles into a single ancestral copy according to a random process in coalescence events. Under this model, the expected time between successive coalescence events increases almost exponentially back in time. Variance in the model comes from both the random passing of alleles from one generation to the next, and the random occurrence of mutations in these alleles.

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Masatoshi Nei was a Japanese-born American evolutionary biologist.

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Genetic admixture occurs when previously isolated populations interbreed resulting in a population that is descended from multiple sources. It can occur between species, such as with hybrids, or within species, such as when geographically distant individuals migrate to new regions. It results in gene pool that is a mix of the source populations.

A genetic lineage includes all descendants of a given genetic sequence, typically following a new mutation. It is not the same as an allele because it excludes cases where different mutations give rise to the same allele, and includes descendants that differ from the ancestor by one or more mutations. The genetic sequence can be of different sizes, e.g. a single gene or a haplotype containing multiple adjacent genes along a chromosome. Given recombination, each gene can have a separate genetic lineages, even as the population shares a single organismal lineage. In asexual microbes or somatic cells, cell lineages exactly match genetic lineages, and can be traced.

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Incomplete lineage sorting, also termed hemiplasy, deep coalescence, retention of ancestral polymorphism, or trans-species polymorphism, describes a phenomenon in population genetics when ancestral gene copies fail to coalesce into a common ancestral copy until deeper than previous speciation events. It is caused by lineage sorting of genetic polymorphisms that were retained across successive nodes in the species tree. In other words, the tree produced by a single gene differs from the population or species level tree, producing a discordant tree. Whatever the mechanism, the result is that a generated species level tree may differ depending on the selected genes used for assessment. This is in contrast to complete lineage sorting, where the tree produced by the gene is the same as the population or species level tree. Both are common results in phylogenetic analysis, although it depends on the gene, organism, and sampling technique.

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References

  1. ↑ Noah Rosenberg at the Mathematics Genealogy Project
  2. 1 2 "People | Center for Computational, Evolutionary and Human Genomics (CEHG)". cehg.stanford.edu. Retrieved 2023-11-01.
  3. ↑ University, Stanford (2020-06-01). "Where mathematics and biology meet". Stanford News. Retrieved 2023-11-02.
  4. 1 2 "Theoretical Population Biology Editorial Board". Elsevier. Retrieved 2018-04-26.
  5. ↑ The Noah Sheets
  6. 1 2 "Noah Rosenberg CV" (PDF).
  7. 1 2 "Noah Rosenberg's Profile | Stanford Profiles". profiles.stanford.edu. Retrieved 2023-11-02.
  8. ↑ Rosenberg, Noah Aubrey (2001). Statistical modeling of genetic histories and relationships of populations (Thesis). OCLC   81533899. ProQuest   304727329.[ page needed ][ non-primary source needed ]
  9. 1 2 Horton, Richard (2003). "Read all about it: The Lancet 's Paper of the Year, 2003". The Lancet. 362 (9401): 2101–2103. doi:10.1016/s0140-6736(03)15110-0. ISSN   0140-6736. PMC   7123340 . PMID   14697815.
  10. ↑ "Noah Rosenberg | Stanford Institute for Computational & Mathematical Engineering". profiles.stanford.edu. Retrieved 2023-11-02.
  11. ↑ University, © Stanford; Stanford; California 94305 (2014-06-20). "Noah Rosenberg - Professor of Biology". Welcome to Bio-X. Retrieved 2023-11-02.{{cite web}}: CS1 maint: numeric names: authors list (link)
  12. ↑ Korte, Andrea (27 November 2018). "AAAS Honors Accomplished Scientists as 2018 Elected Fellows". AAAS.
  13. ↑ "Jaehee Kim". jaeheekimlab.github.io. Retrieved 2023-11-02.
  14. ↑ "Amy Goldberg, PhD - People". www.goldberglab.org. Retrieved 2023-11-02.
  15. ↑ "Scheet Lab". scheet.org. Retrieved 2023-11-02.
  16. ↑ "Edge Lab - Team". edgepopgen.github.io. Retrieved 2023-11-02.
  17. ↑ "Mooney Lab". mooney-lab.github.io. Retrieved 2023-11-02.
  18. ↑ "Editorial Board". Evolution, Medicine, and Public Health. Retrieved 2023-11-02.
  19. ↑ "Co-Directors | Center for Computational, Evolutionary and Human Genomics (CEHG)". cehg.stanford.edu. Retrieved 2023-11-02.
  20. ↑ Prillaman, McKenzie (2021-12-07). "Stanford professor spotlights evolutionary tree concepts with campus trees". Stanford News. Retrieved 2023-11-02.
  21. ↑ Brown, David (2008-02-22). "Genetic Mutations Offer Insights on Human Diversity". The Washington Post . ISSN   0190-8286 . Retrieved 2023-11-02.
  22. ↑ Balter, Michael (2011-09-23). "Tracing the Paths of the First Americans" . Science. 333 (6050): 1692. Bibcode:2011Sci...333.1692B. doi:10.1126/science.333.6050.1692. ISSN   0036-8075.
  23. ↑ Hunley, Keith (2015-02-17). "Reassessment of global gene–language coevolution". Proceedings of the National Academy of Sciences. 112 (7): 1919–1920. doi: 10.1073/pnas.1425000112 . ISSN   0027-8424. PMC   4343119 . PMID   25675520.
  24. ↑ Rosenberg, Noah A. (2004). "distruct : a program for the graphical display of population structure". Molecular Ecology Notes. 4 (1): 137–138. doi:10.1046/j.1471-8286.2003.00566.x.
  25. ↑ Kopelman, Naama M.; Mayzel, Jonathan; Jakobsson, Mattias; Rosenberg, Noah A.; Mayrose, Itay (2015). "Clumpak : a program for identifying clustering modes and packaging population structure inferences across K". Molecular Ecology Resources. 15 (5): 1179–1191. doi:10.1111/1755-0998.12387. PMC   4534335 . PMID   25684545.
  26. ↑ Imbler, Sabrina (12 April 2022). "New DNA Analysis Supports an Unrecognized Tribe's Ancient Roots in California". The New York Times .
  27. ↑ MacCormick, Holly Alyssa (2023-07-10). "New genealogy method helps fill gaps in African American ancestry". Stanford News. Retrieved 2023-11-02.
  28. ↑ Rosenberg, Noah A.; Weitzman, Steven P. (2013). "From Generation to Generation: The Genetics of Jewish Populations". Human Biology. 85 (6): 817–823. doi:10.1353/hub.2013.a548063. Project MUSE   548063.[ non-primary source needed ]
  29. ↑ Collins, Nathan (2017-05-15). "Gene matches could aid science, but raise privacy concerns". Stanford News. Retrieved 2023-11-02.
  30. ↑ Collins, Nathan (2018-10-17). "New way to find relatives from forensic DNA". Stanford News. Retrieved 2023-11-02.
  31. ↑ Severson, Alissa L; Carmi, Shai; Rosenberg, Noah A (2019). "The Effect of Consanguinity on Between-Individual Identity-by-Descent Sharing". Genetics. 212 (1): 305–316. doi:10.1534/genetics.119.302136. PMC   6499533 . PMID   30926583.[ non-primary source needed ]
  32. ↑ DeGiorgio, Michael; Degnan, James H; Rosenberg, Noah A (2011). "Coalescence-Time Distributions in a Serial Founder Model of Human Evolutionary History". Genetics. 189 (2): 579–593. doi:10.1534/genetics.111.129296. PMC   3189793 . PMID   21775469.[ non-primary source needed ]
  33. ↑ Alcala, Nicolas; Goldberg, Amy; Ramakrishnan, Uma; Rosenberg, Noah A (2019). Heyer, Evelyne (ed.). "Coalescent Theory of Migration Network Motifs". Molecular Biology and Evolution. 36 (10): 2358–2374. doi:10.1093/molbev/msz136. PMC   6759081 . PMID   31165149.[ non-primary source needed ]
  34. ↑ Edge, Michael D.; Gorroochurn, Prakash; Rosenberg, Noah A. (2013). "Windfalls and pitfalls". Evolution, Medicine, and Public Health. 2013 (1): 254–272. doi:10.1093/emph/eot021. ISSN   2050-6201. PMC   3868415 . PMID   24481204.[ non-primary source needed ]
  35. ↑ Rosenberg, Noah A; Edge, Michael D; Pritchard, Jonathan K; Feldman, Marcus W (2019-01-01). "Interpreting polygenic scores, polygenic adaptation, and human phenotypic differences". Evolution, Medicine, and Public Health. 2019 (1): 26–34. doi:10.1093/emph/eoy036. PMC   6393779 . PMID   30838127.[ non-primary source needed ]
  36. ↑ Rosenberg, Noah A. (2007). "Counting Coalescent Histories". Journal of Computational Biology. 14 (3): 360–377. doi:10.1089/cmb.2006.0109. hdl: 2027.42/63175 . PMID   17563317.[ non-primary source needed ]
  37. ↑ Rosenberg, Noah A.; Degnan, James H. (2010). "Coalescent histories for discordant gene trees and species trees". Theoretical Population Biology. 77 (3): 145–151. doi:10.1016/j.tpb.2009.12.004. PMID   20064540.[ non-primary source needed ]
  38. ↑ Disanto, Filippo; Rosenberg, Noah A. (2015). "Coalescent Histories for Lodgepole Species Trees". Journal of Computational Biology. 22 (10): 918–929. arXiv: 1503.03560 . doi:10.1089/cmb.2015.0015. PMID   25973633.[ non-primary source needed ]
  39. ↑ Rosenberg, Noah A. (2019). "Enumeration of lonely pairs of gene trees and species trees by means of antipodal cherries". Advances in Applied Mathematics. 102: 1–17. doi: 10.1016/j.aam.2018.09.001 . PMC   6456302 . PMID   30983650.[ non-primary source needed ]
  40. ↑ Rosenberg, Noah A. (2006). "The Mean and Variance of the Numbers of r-Pronged Nodes and r-Caterpillars in Yule-Generated Genealogical Trees". Annals of Combinatorics. 10 (1): 129–146. doi:10.1007/s00026-006-0278-6. S2CID   2484974.[ non-primary source needed ]
  41. ↑ Mehta, Rohan S.; Bryant, David; Rosenberg, Noah A. (2016). "The probability of monophyly of a sample of gene lineages on a species tree". Proceedings of the National Academy of Sciences. 113 (29): 8002–8009. Bibcode:2016PNAS..113.8002M. doi: 10.1073/pnas.1601074113 . PMC   4961160 . PMID   27432988.[ non-primary source needed ]
  42. ↑ Disanto, Filippo; Fuchs, Michael; Paningbatan, Ariel R.; Rosenberg, Noah A. (2022). "The distributions under two species-tree models of the number of root ancestral configurations for matching gene trees and species trees". The Annals of Applied Probability. 32 (6): 4426–4458. arXiv: 2006.09106 . doi: 10.1214/22-AAP1791 .[ non-primary source needed ]
  43. ↑ Edge, Michael D.; Rosenberg, Noah A. (2014). "Upper bounds on FST in terms of the frequency of the most frequent allele and total homozygosity: The case of a specified number of alleles". Theoretical Population Biology. 97: 20–34. doi:10.1016/j.tpb.2014.08.001. PMC   4180022 . PMID   25132646.[ non-primary source needed ]
  44. ↑ Alcala, Nicolas; Rosenberg, Noah A (2017). "Mathematical Constraints on F ST: Biallelic Markers in Arbitrarily Many Populations". Genetics. 206 (3): 1581–1600. doi:10.1534/genetics.116.199141. ISSN   1943-2631. PMC   5500152 . PMID   28476869.[ non-primary source needed ]
  45. ↑ Morrison, Maike L.; Rosenberg, Noah A. (2023). "Mathematical bounds on Shannon entropy given the abundance of the ith most abundant taxon". Journal of Mathematical Biology. 87 (5): 76. doi:10.1007/s00285-023-01997-3. PMC   10603011 . PMID   37884812.[ non-primary source needed ]
  46. ↑ Armitage, Hanae (2020-02-13). "Formula for an "aha" moment: Pair up with your spouse". Scope. Retrieved 2023-11-02.
  47. ↑ "A354690 - OEIS". oeis.org. Retrieved 2023-11-02.
  48. ↑ "A355108 - OEIS". oeis.org. Retrieved 2023-11-02.
  49. ↑ "A354970 - OEIS". oeis.org. Retrieved 2023-11-02.
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