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Article ; Online: FDA Approval Summary: Enfortumab Vedotin plus Pembrolizumab for Cisplatin-Ineligible Locally Advanced or Metastatic Urothelial Carcinoma.

Maguire, William F / Lee, Daniel / Weinstock, Chana / Gao, Xin / Bulik, Catharine C / Agrawal, Sundeep / Chang, Elaine / Hamed, Salaheldin S / Bloomquist, Erik W / Tang, Shenghui / Pazdur, Richard / Kluetz, Paul G / Amiri-Kordestani, Laleh / Suzman, Daniel L

Clinical cancer research : an official journal of the American Association for Cancer Research

2024 Volume 30, Issue 10, Page(s) 2011–2016

Abstract: On April 3, 2023, the FDA granted accelerated approval to enfortumab vedotin-ejfv (EV) plus pembrolizumab for treatment of patients with locally advanced or metastatic urothelial carcinoma who are ineligible for cisplatin-containing chemotherapy. ... ...

Abstract	On April 3, 2023, the FDA granted accelerated approval to enfortumab vedotin-ejfv (EV) plus pembrolizumab for treatment of patients with locally advanced or metastatic urothelial carcinoma who are ineligible for cisplatin-containing chemotherapy. Substantial evidence of effectiveness was obtained from EV-103/KEYNOTE-869 (NCT03288545), a multicohort study. Across cohorts, a total of 121 patients received EV 1.25 mg/kg (maximum of 125 mg) intravenously on days 1 and 8 of a 21-day cycle plus pembrolizumab 200 mg intravenously on day 1 of each 21-day cycle until disease progression or unacceptable toxicity. The major efficacy outcome measures were objective response rate (ORR) and duration of response (DoR), determined by blinded independent central review using RECIST v1.1. The confirmed ORR in 121 patients was 68% (95% confidence interval, 59-76), including 12% with complete responses. The median DoR for the 82 responders was 22 months (range: 1+ to 46+). The safety profile of the combination comprised adverse reactions expected to occur with the corresponding monotherapies, but with overall increased frequency of adverse reactions, including skin toxicity, pneumonitis, and peripheral neuropathy. The article summarizes the data and the FDA thought process supporting accelerated approval of EV + pembrolizumab, as well as additional exploratory analyses conducted by the FDA.
MeSH term(s)	Humans ; Antibodies, Monoclonal, Humanized/administration & dosage ; Antibodies, Monoclonal, Humanized/adverse effects ; Antibodies, Monoclonal, Humanized/therapeutic use ; Drug Approval ; United States ; Male ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Aged ; Female ; Antibodies, Monoclonal/administration & dosage ; Antibodies, Monoclonal/adverse effects ; Antibodies, Monoclonal/therapeutic use ; United States Food and Drug Administration ; Middle Aged ; Cisplatin/administration & dosage ; Cisplatin/adverse effects ; Cisplatin/therapeutic use ; Aged, 80 and over ; Urinary Bladder Neoplasms/drug therapy ; Urinary Bladder Neoplasms/pathology ; Carcinoma, Transitional Cell/drug therapy ; Carcinoma, Transitional Cell/pathology ; Urologic Neoplasms/drug therapy ; Urologic Neoplasms/pathology ; Treatment Outcome
Language	English
Publishing date	2024-03-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-23-3738
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Article ; Online: Regulatory implications of ctDNA in immuno-oncology for solid tumors.

Vellanki, Paz J / Ghosh, Soma / Pathak, Anand / Fusco, Michael J / Bloomquist, Erik W / Tang, Shenghui / Singh, Harpreet / Philip, Reena / Pazdur, Richard / Beaver, Julia A

Journal for immunotherapy of cancer

2023 Volume 11, Issue 2

Abstract: In the era of precision oncology, use of circulating tumor DNA (ctDNA) is emerging as a minimally invasive approach for the diagnosis and management of patients with cancer and as an enrichment tool in clinical trials. In recent years, the US Food and ... ...

Abstract	In the era of precision oncology, use of circulating tumor DNA (ctDNA) is emerging as a minimally invasive approach for the diagnosis and management of patients with cancer and as an enrichment tool in clinical trials. In recent years, the US Food and Drug Administration has approved multiple ctDNA-based companion diagnostic assays for the safe and effective use of targeted therapies and ctDNA-based assays are also being developed for use with immuno-oncology-based therapies. For early-stage solid tumor cancers, ctDNA may be particularly important to detect molecular residual disease (MRD) to support early implementation of adjuvant or escalated therapy to prevent development of metastatic disease. Clinical trials are also increasingly using ctDNA MRD for patient selection and stratification, with an ultimate goal of improving trial efficiency through use of an enriched patient population. Standardization and harmonization of ctDNA assays and methodologies, along with further clinical validation of ctDNA as a prognostic and predictive biomarker, are necessary before ctDNA may be considered as an efficacy-response biomarker to support regulatory decision making.
MeSH term(s)	United States ; Humans ; Precision Medicine/methods ; Circulating Tumor DNA/genetics ; Medical Oncology ; Prognosis ; Neoplasm, Residual
Chemical Substances	Circulating Tumor DNA
Language	English
Publishing date	2023-01-27
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2719863-7
ISSN	2051-1426 ; 2051-1426
ISSN (online)	2051-1426
ISSN	2051-1426
DOI	10.1136/jitc-2022-005344
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Article ; Online: FDA Approval Summary: Ribociclib Indicated for Male Patients with Hormone Receptor-Positive, HER2-Negative Advanced or Metastatic Breast Cancer.

Gao, Jennifer J / Osgood, Christy L / Feng, Zhou / Bloomquist, Erik W / Tang, Shenghui / Chang, C J George / Ricks, Tiffany K / Hou, Sherry C / Pierce, William F / Rivera, Donna R / Pazdur, Richard / Kluetz, Paul G / Amiri-Kordestani, Laleh

Clinical cancer research : an official journal of the American Association for Cancer Research

2023 Volume 29, Issue 24, Page(s) 5008–5011

Abstract: On December 10, 2021, the FDA expanded the indications for ribociclib to include male patients for the treatment of hormone receptor-positive, HER2-negative advanced or metastatic breast cancer. Ribociclib is now indicated in combination with an ... ...

Abstract	On December 10, 2021, the FDA expanded the indications for ribociclib to include male patients for the treatment of hormone receptor-positive, HER2-negative advanced or metastatic breast cancer. Ribociclib is now indicated in combination with an aromatase inhibitor (AI) as initial endocrine-based therapy in adult patients, or with fulvestrant as initial endocrine-based therapy or following disease progression on endocrine therapy (ET), in postmenopausal women or in men. The efficacy of ribociclib + AI for male patients was primarily based on previous favorable benefit-risk assessments of ribociclib from MONALEESA-2 and MONALEESA-7 trials, and supported by COMPLEEMENT-1, an open-label, single-arm, multicenter clinical trial, in which 39 male patients (n = 3,246 total patients) received ribociclib + letrozole + goserelin/leuprolide. The overall response rate (ORR) based on confirmed responses in male patients with measurable disease at baseline was 46.9% [95% confidence interval (CI), 29.1-65.3], consistent with an ORR of 43.6% (95% CI, 41.5-45.8) in the overall population. Overall, adverse reactions occurring in male patients were similar to those occurring in female patients treated with ribociclib + ET. The efficacy of ribociclib + fulvestrant for male patients was primarily based on the previous findings of a favorable benefit-risk assessment from the MONALEESA-3 trial, supported by FDA review of clinical data of a limited number of male patients treated in clinical practice receiving ribociclib + fulvestrant. The known mechanism of action, biologic rationale, and clinical information available adequately demonstrate that the efficacy and safety of ribociclib + AI/fulvestrant are similar in male and female patients. This article summarizes the FDA's decision-making and data supporting the approval of ribociclib in male patients with breast cancer, and discusses regulatory insights.
MeSH term(s)	Adult ; Female ; Humans ; Male ; Letrozole ; Fulvestrant/therapeutic use ; Receptors, Estrogen ; Breast Neoplasms/drug therapy ; Breast Neoplasms/pathology ; Aminopyridines ; Aromatase Inhibitors/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Receptor, ErbB-2/therapeutic use
Chemical Substances	ribociclib (TK8ERE8P56) ; Letrozole (7LKK855W8I) ; Fulvestrant (22X328QOC4) ; Receptors, Estrogen ; Aminopyridines ; Aromatase Inhibitors ; Receptor, ErbB-2 (EC 2.7.10.1)
Language	English
Publishing date	2023-08-17
Publishing country	United States
Document type	Multicenter Study ; Journal Article
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-23-1133
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Article ; Online: Unifying vertical and nonvertical evolution: a stochastic ARG-based framework.

Bloomquist, Erik W / Suchard, Marc A

Systematic biology

2009 Volume 59, Issue 1, Page(s) 27–41

Abstract: Evolutionary biologists have introduced numerous statistical approaches to explore nonvertical evolution, such as horizontal gene transfer, recombination, and genomic reassortment, through collections of Markov-dependent gene trees. These tree ... ...

Abstract	Evolutionary biologists have introduced numerous statistical approaches to explore nonvertical evolution, such as horizontal gene transfer, recombination, and genomic reassortment, through collections of Markov-dependent gene trees. These tree collections allow for inference of nonvertical evolution, but only indirectly, making findings difficult to interpret and models difficult to generalize. An alternative approach to explore nonvertical evolution relies on phylogenetic networks. These networks provide a framework to model nonvertical evolution but leave unanswered questions such as the statistical significance of specific nonvertical events. In this paper, we begin to correct the shortcomings of both approaches by introducing the "stochastic model for reassortment and transfer events" (SMARTIE) drawing upon ancestral recombination graphs (ARGs). ARGs are directed graphs that allow for formal probabilistic inference on vertical speciation events and nonvertical evolutionary events. We apply SMARTIE to phylogenetic data. Because of this, we can typically infer a single most probable ARG, avoiding coarse population dynamic summary statistics. In addition, a focus on phylogenetic data suggests novel probability distributions on ARGs. To make inference with our model, we develop a reversible jump Markov chain Monte Carlo sampler to approximate the posterior distribution of SMARTIE. Using the BEAST phylogenetic software as a foundation, the sampler employs a parallel computing approach that allows for inference on large-scale data sets. To demonstrate SMARTIE, we explore 2 separate phylogenetic applications, one involving pathogenic Leptospirochete and the other Saccharomyces.
MeSH term(s)	Algorithms ; Bayes Theorem ; Classification/methods ; Evolution, Molecular ; Gene Transfer, Horizontal/genetics ; Leptospiraceae/genetics ; Likelihood Functions ; Markov Chains ; Models, Genetic ; Monte Carlo Method ; Phylogeny ; Saccharomyces/genetics
Language	English
Publishing date	2009-11-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syp076
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Article ; Online: Inferring species-level phylogenies and taxonomic distinctiveness using multilocus data in Sistrurus rattlesnakes.

Kubatko, Laura S / Gibbs, H Lisle / Bloomquist, Erik W

Systematic biology

2011 Volume 60, Issue 4, Page(s) 393–409

Abstract: Phylogenetic relationships and taxonomic distinctiveness of closely related species and subspecies are most accurately inferred from data derived from multiple independent loci. Here, we apply several approaches for understanding species-level ... ...

Abstract	Phylogenetic relationships and taxonomic distinctiveness of closely related species and subspecies are most accurately inferred from data derived from multiple independent loci. Here, we apply several approaches for understanding species-level relationships using data from 18 nuclear DNA loci and 1 mitochondrial DNA locus within currently described species and subspecies of Sistrurus rattlesnakes. Collectively, these methods provide evidence that a currently described species, the massasauga rattlesnake (Sistrurus catenatus), consists of two well-supported clades, one composed of the two western subspecies (S. c. tergeminus and S. c. edwardsii) and the other the eastern subspecies (S. c. catenatus). Within pigmy rattlesnakes (S. miliarius), however, there is not strong support across methods for any particular grouping at the subspecific level. Monophyly based tests for taxonomic distinctiveness show evidence for distinctiveness of all subspecies but this support is strongest by far for the S. c. catenatus clade. Because support for the distinctiveness of S. c. catenatus is both strong and consistent across methods, and due to its morphological distinctiveness and allopatric distribution, we suggest that this subspecies be elevated to full species status, which has significant conservation implications. Finally, most divergence time estimates based upon a fossil-calibrated species tree are > 50% younger than those from a concatenated gene tree analysis and suggest that an active period of speciation within Sistrurus occurred within the late Pliocene/Pleistocene eras.
MeSH term(s)	Animals ; Crotalus/classification ; Crotalus/genetics ; DNA/chemistry ; DNA, Mitochondrial/chemistry ; Genetic Speciation ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Species Specificity
Chemical Substances	DNA, Mitochondrial ; DNA (9007-49-2)
Language	English
Publishing date	2011-07
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1482572-7
ISSN	1076-836X ; 1063-5157
ISSN (online)	1076-836X
ISSN	1063-5157
DOI	10.1093/sysbio/syr011
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Article ; Online: FDA Approval Summary: Belzutifan for von Hippel-Lindau Disease-Associated Tumors.

Clinical cancer research : an official journal of the American Association for Cancer Research

2022 Volume 28, Issue 22, Page(s) 4843–4848

Abstract: On August 13, 2021, the FDA approved belzutifan (WELIREG, Merck), a first-in-class hypoxia-inducible factor (HIF) inhibitor for adult patients with von Hippel-Lindau (VHL) disease who require therapy for associated renal cell carcinoma (RCC), central ... ...

Abstract	On August 13, 2021, the FDA approved belzutifan (WELIREG, Merck), a first-in-class hypoxia-inducible factor (HIF) inhibitor for adult patients with von Hippel-Lindau (VHL) disease who require therapy for associated renal cell carcinoma (RCC), central nervous system (CNS) hemangioblastomas, or pancreatic neuroendocrine tumors (pNET), not requiring immediate surgery. The FDA granted approval based on the clinically meaningful effects on overall response rate (ORR) observed in patients enrolled in Study MK-6482-004. All 61 patients had VHL-associated RCC; some also had CNS hemangioblastomas and/or pNET. For VHL disease-associated RCC, ORR was 49% [95% confidence interval (CI), 36-62], median duration of response (DoR) was not reached, 56% of responders had DoR ≥12 months, and median time to response was 8 months. Twenty-four patients had measurable CNS hemangioblastomas with an ORR of 63% (95% CI, 41-81), and 12 patients had measurable pNET with an ORR of 83% (95% CI, 52-98). For these tumors, median DoR was not reached, with 73% and 50% of patients having response durations ≥12 months for CNS hemangioblastomas and pNET, respectively. The most common adverse reactions, including laboratory abnormalities, reported in ≥20% were anemia, fatigue, increased creatinine, headache, dizziness, increased glucose, and nausea. Belzutifan can render some hormonal contraceptives ineffective and can cause embryo-fetal harm during pregnancy. This article summarizes the data and the FDA thought process supporting traditional approval of belzutifan for this indication.
MeSH term(s)	Adult ; Humans ; Pregnancy ; Female ; von Hippel-Lindau Disease/complications ; von Hippel-Lindau Disease/drug therapy ; von Hippel-Lindau Disease/pathology ; Hemangioblastoma/complications ; Hemangioblastoma/pathology ; Carcinoma, Renal Cell/complications ; Central Nervous System Neoplasms ; Antineoplastic Agents ; Kidney Neoplasms ; Neuroectodermal Tumors, Primitive/complications
Chemical Substances	Antineoplastic Agents
Language	English
Publishing date	2022-06-20
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-22-1054
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Article: Three roads diverged? Routes to phylogeographic inference.

Bloomquist, Erik W / Lemey, Philippe / Suchard, Marc A

Trends in ecology & evolution

2010 Volume 25, Issue 11, Page(s) 626–632

Abstract: Phylogeographic methods facilitate inference of the geographical history of genetic lineages. Recent examples explore human migration and the origins of viral pandemics. There is longstanding disagreement over the use and validity of certain ... ...

Abstract	Phylogeographic methods facilitate inference of the geographical history of genetic lineages. Recent examples explore human migration and the origins of viral pandemics. There is longstanding disagreement over the use and validity of certain phylogeographic inference methodologies. In this paper, we highlight three distinct frameworks for phylogeographic inference to give a taste of this disagreement. Each of the three approaches presents a different viewpoint on phylogeography, most fundamentally on how we view the relationship between the inferred history of a sample and the history of the population the sample is embedded in. Satisfactory resolution of this relationship between history of the tree and history of the population remains a challenge for all but the most trivial models of phylogeographic processes. Intriguingly, we believe that some recent methods that entirely avoid inference about the history of the population will eventually help to reach a resolution.
MeSH term(s)	Animals ; Demography ; Genetic Variation ; Models, Biological ; Phylogeography
Language	English
Publishing date	2010-09-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	284965-3
ISSN	1872-8383 ; 0169-5347
ISSN (online)	1872-8383
ISSN	0169-5347
DOI	10.1016/j.tree.2010.08.010
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Article ; Online: Regulatory Considerations for Contribution of Effect of Drugs Used in Combination Regimens: Renal Cell Cancer Case Studies.

Brewer, Jamie R / Chang, Elaine / Agrawal, Sundeep / Singh, Harpreet / Suzman, Daniel L / Xu, James / Weinstock, Chana / Fernandes, Laura L / Cheng, Joyce / Zhang, Lijun / Xie, Diqiong / Goldberg, Kirsten B / Bloomquist, Erik W / Tang, Shenghui / Sridhara, Rajeshwari / Theoret, Marc R / Pazdur, Richard / Ibrahim, Amna / Beaver, Julia A

Clinical cancer research : an official journal of the American Association for Cancer Research

2020 Volume 26, Issue 24, Page(s) 6406–6411

Abstract: The development and review of combination drug regimens in oncology may present unique challenges to investigators and regulators. For regulatory approval of combination regimens, it is necessary to demonstrate the contribution of effect of each ... ...

Abstract	The development and review of combination drug regimens in oncology may present unique challenges to investigators and regulators. For regulatory approval of combination regimens, it is necessary to demonstrate the contribution of effect of each monotherapy to the overall combination. Alternative approaches to traditional designs may be needed to accelerate oncology drug development, for example, when combinations are substantially superior to available therapy, to reduce exposure to less effective therapies, and for drugs that are inactive as single agents and that in combination potentiate activity of another drug. These approaches include demonstration of activity in smaller randomized trials and/or monotherapy trials conducted in a similar disease setting. This article will discuss alternative approaches used in the development of approved drugs in combination, based on examples of recent approvals of combination regimens in renal cell carcinoma.
MeSH term(s)	Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Carcinoma, Renal Cell/drug therapy ; Drug Approval/legislation & jurisprudence ; Drug Combinations ; Drug Development ; Humans ; Kidney Neoplasms/drug therapy ; Prognosis ; Survival Rate ; United States ; United States Food and Drug Administration
Chemical Substances	Drug Combinations
Language	English
Publishing date	2020-07-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-19-4229
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Article ; Online: StepBrothers: inferring partially shared ancestries among recombinant viral sequences.

Bloomquist, Erik W / Dorman, Karin S / Suchard, Marc A

Biostatistics (Oxford, England)

2008 Volume 10, Issue 1, Page(s) 106–120

Abstract: Phylogeneticists have developed several statistical methods to infer recombination among molecular sequences that are evolutionarily related. Of these methods, Markov change-point models currently provide the most coherent framework. Yet, the Markov ... ...

Abstract	Phylogeneticists have developed several statistical methods to infer recombination among molecular sequences that are evolutionarily related. Of these methods, Markov change-point models currently provide the most coherent framework. Yet, the Markov assumption is faulty in that the inferred relatedness of homologous sequences across regions divided by recombinant events is not independent, particularly for nonrecombinant sequences as they share the same history. To correct this limitation, we introduce a novel random tips (RT) model. The model springs from the idea that a recombinant sequence inherits its characters from an unknown number of ancestral full-length sequences, of which one only observes the incomplete portions. The RT model decomposes recombinant sequences into their ancestral portions and then augments each portion onto the data set as unique partially observed sequences. This data augmentation generates a random number of sequences related to each other through a single inferable tree with the same random number of tips. While intuitively pleasing, this single tree corrects the independence assumptions plaguing previous methods while permitting the detection of recombination. The single tree also allows for inference of the relative times of recombination events and generalizes to incorporate multiple recombinant sequences. This generalization answers important questions with which previous models struggle. For example, we demonstrate that a group of human immunodeficiency type 1 recombinant viruses from Argentina, previously thought to have the same recombinant history, actually consist of 2 groups: one, a clonal expansion of a reference sequence and another that predates the formation of the reference sequence. In another example, we demonstrate that 2 hepatitis B virus recombinant strains share similar splicing locations, suggesting a common descent of the 2 viruses. We implement and run both examples in a software package called StepBrothers, freely available to interested parties.
MeSH term(s)	Argentina ; Base Sequence ; Bayes Theorem ; China ; Computational Biology/methods ; DNA, Recombinant/classification ; DNA, Recombinant/genetics ; DNA, Viral/classification ; DNA, Viral/genetics ; Evolution, Molecular ; HIV-1/genetics ; Hepatitis B virus/genetics ; Humans ; Neural Networks, Computer ; Phylogeny ; Recombination, Genetic ; Sequence Analysis, DNA ; Stochastic Processes
Chemical Substances	DNA, Recombinant ; DNA, Viral
Language	English
Publishing date	2008-06-18
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2031500-4
ISSN	1468-4357 ; 1465-4644
ISSN (online)	1468-4357
ISSN	1465-4644
DOI	10.1093/biostatistics/kxn019
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Article ; Online: Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics.

Minin, Vladimir N / Bloomquist, Erik W / Suchard, Marc A

Molecular biology and evolution

2008 Volume 25, Issue 7, Page(s) 1459–1471

Abstract: Kingman's coalescent process opens the door for estimation of population genetics model parameters from molecular sequences. One paramount parameter of interest is the effective population size. Temporal variation of this quantity characterizes the ... ...

Abstract	Kingman's coalescent process opens the door for estimation of population genetics model parameters from molecular sequences. One paramount parameter of interest is the effective population size. Temporal variation of this quantity characterizes the demographic history of a population. Because researchers are rarely able to choose a priori a deterministic model describing effective population size dynamics for data at hand, nonparametric curve-fitting methods based on multiple change-point (MCP) models have been developed. We propose an alternative to change-point modeling that exploits Gaussian Markov random fields to achieve temporal smoothing of the effective population size in a Bayesian framework. The main advantage of our approach is that, in contrast to MCP models, the explicit temporal smoothing does not require strong prior decisions. To approximate the posterior distribution of the population dynamics, we use efficient, fast mixing Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. In a simulation study, we demonstrate that the proposed temporal smoothing method, named Bayesian skyride, successfully recovers "true" population size trajectories in all simulation scenarios and competes well with the MCP approaches without evoking strong prior assumptions. We apply our Bayesian skyride method to 2 real data sets. We analyze sequences of hepatitis C virus contemporaneously sampled in Egypt, reproducing all key known aspects of the viral population dynamics. Next, we estimate the demographic histories of human influenza A hemagglutinin sequences, serially sampled throughout 3 flu seasons.
MeSH term(s)	Bayes Theorem ; Egypt ; Genetics, Population ; Hepacivirus/genetics ; Humans ; Markov Chains ; Mathematics ; Models, Genetic ; Models, Statistical ; Orthomyxoviridae/genetics ; Phylogeny ; Population Density ; Population Dynamics
Language	English
Publishing date	2008-04-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	998579-7
ISSN	1537-1719 ; 0737-4038
ISSN (online)	1537-1719
ISSN	0737-4038
DOI	10.1093/molbev/msn090
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