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@ARTICLE{Davidsen2019-uw,
title = "Deep generative models for {T} cell receptor protein sequences",
author = "Davidsen, Kristian and Olson, Branden J and DeWitt, III, William S and Feng, Jean and Harkins, Elias and Bradley, Philip and Matsen, IV, Frederick A",
journal = "Elife",
publisher = "eLife Sciences Publications, Ltd",
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pages = "e46935",
month = sep,
year = 2019,
url = "https://doi.org/10.7554/eLife.46935",
issn = "2050-084X",
doi = "10.7554/eLife.46935"
}
@ARTICLE{Jiang2017-xs,
title = "LEARNING SUMMARY STATISTIC FOR APPROXIMATE BAYESIAN COMPUTATION VIA DEEP NEURAL NETWORK",
author = "Jiang, Bai and Wu, Tung-Yu and Zheng, Charles and Wong, Wing H",
journal = "Stat. Sin.",
publisher = "Institute of Statistical Science, Academia Sinica",
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year = 2017,
url = "http://www.jstor.org/stable/26384090",
issn = "1017-0405, 1996-8507"
}
@UNPUBLISHED{Chan2018-qq,
title = "A {Likelihood-Free} Inference Framework for Population Genetic Data using Exchangeable Neural Networks",
author = "Chan, Jeffrey and Perrone, Valerio and Spence, Jeffrey P and Jenkins, Paul A and Mathieson, Sara and Song, Yun S",
journal = "bioRxiv",
pages = "267211",
month = feb,
year = 2018,
url = "https://www.biorxiv.org/content/early/2018/02/18/267211",
language = "en",
doi = "10.1101/267211"
}
@ARTICLE{Cui2016-wz,
title = "A Model of Somatic Hypermutation Targeting in Mice Based on {High-Throughput} Ig Sequencing Data",
author = "Cui, Ang and Di Niro, Roberto and Vander Heiden, Jason A and Briggs, Adrian W and Adams, Kris and Gilbert, Tamara and O'Connor, Kevin C and Vigneault, Francois and Shlomchik, Mark J and Kleinstein, Steven H",
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number = 9,
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month = nov,
year = 2016,
url = "http://dx.doi.org/10.4049/jimmunol.1502263",
language = "en",
issn = "0022-1767, 1550-6606",
pmid = "27707999",
doi = "10.4049/jimmunol.1502263",
pmc = "PMC5161250"
}
@ARTICLE{Yaari2013-dg,
title = "Models of somatic hypermutation targeting and substitution based on synonymous mutations from high-throughput immunoglobulin sequencing data",
author = "Yaari, Gur and Vander Heiden, Jason A and Uduman, Mohamed and Gadala-Maria, Daniel and Gupta, Namita and Stern, Joel N H and O'Connor, Kevin C and Hafler, David A and Laserson, Uri and Vigneault, Francois and Kleinstein, Steven H",
journal = "Front. Immunol.",
volume = 4,
pages = "358",
month = nov,
year = 2013,
url = "http://dx.doi.org/10.3389/fimmu.2013.00358",
language = "en",
issn = "1664-3224",
pmid = "24298272",
doi = "10.3389/fimmu.2013.00358",
pmc = "PMC3828525"
}
@ARTICLE{Rogozin1992-xv,
title = "Somatic hypermutagenesis in immunoglobulin genes. {II}. Influence of neighbouring base sequences on mutagenesis",
author = "Rogozin, I B and Kolchanov, N A",
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month = nov,
year = 1992,
url = "http://www.ncbi.nlm.nih.gov/pubmed/1420357",
issn = "0006-3002",
pmid = "1420357"
}
@ARTICLE{Jardine2013-yt,
title = "Rational {HIV} immunogen design to target specific germline {B} cell receptors",
author = "Jardine, Joseph and Julien, Jean-Philippe and Menis, Sergey and Ota, Takayuki and Kalyuzhniy, Oleksandr and McGuire, Andrew and Sok, Devin and Huang, Po-Ssu and MacPherson, Skye and Jones, Meaghan and Nieusma, Travis and Mathison, John and Baker, David and Ward, Andrew B and Burton, Dennis R and Stamatatos, Leonidas and Nemazee, David and Wilson, Ian A and Schief, William R",
journal = "Science",
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volume = 340,
number = 6133,
pages = "711--716",
month = may,
year = 2013,
url = "http://dx.doi.org/10.1126/science.1234150",
language = "en",
issn = "0036-8075, 1095-9203",
pmid = "23539181",
doi = "10.1126/science.1234150",
pmc = "PMC3689846"
}
@ARTICLE{Wiehe2018-of,
title = "Functional Relevance of Improbable Antibody Mutations for {HIV} Broadly Neutralizing Antibody Development",
author = "Wiehe, Kevin and Bradley, Todd and Ryan Meyerhoff, R and Hart, Connor and Williams, Wilton B and Easterhoff, David and Faison, William J and Kepler, Thomas B and Saunders, Kevin O and Munir Alam, S and Bonsignori, Mattia and Haynes, Barton F",
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year = 2018,
url = "http://www.cell.com/article/S1931312818302191/abstract",
language = "en",
issn = "1931-3128",
pmid = "29861171",
doi = "10.1016/j.chom.2018.04.018"
}
@ARTICLE{Hwang2017-tt,
title = "Sequence intrinsic somatic mutation mechanisms contribute to affinity maturation of {VRC01-class} {HIV-1} broadly neutralizing antibodies",
author = "Hwang, Joyce K and Wang, Chong and Du, Zhou and Meyers, Robin M and Kepler, Thomas B and Neuberg, Donna and Kwong, Peter D and Mascola, John R and Joyce, M Gordon and Bonsignori, Mattia and Haynes, Barton F and Yeap, Leng-Siew and Alt, Frederick W",
journal = "Proc. Natl. Acad. Sci. U. S. A.",
month = jul,
year = 2017,
url = "http://dx.doi.org/10.1073/pnas.1709203114",
language = "en",
issn = "0027-8424, 1091-6490",
pmid = "28747530",
doi = "10.1073/pnas.1709203114"
}
@ARTICLE{Bonsignori2017-nj,
title = "Staged induction of {HIV-1} glycan-dependent broadly neutralizing antibodies",
author = "Bonsignori, Mattia and Kreider, Edward F and Fera, Daniela and Meyerhoff, R Ryan and Bradley, Todd and Wiehe, Kevin and Alam, S Munir and Aussedat, Baptiste and Walkowicz, William E and Hwang, Kwan-Ki and Saunders, Kevin O and Zhang, Ruijun and Gladden, Morgan A and Monroe, Anthony and Kumar, Amit and Xia, Shi-Mao and Cooper, Melissa and Louder, Mark K and McKee, Krisha and Bailer, Robert T and Pier, Brendan W and Jette, Claudia A and Kelsoe, Garnett and Williams, Wilton B and Morris, Lynn and Kappes, John and Wagh, Kshitij and Kamanga, Gift and Cohen, Myron S and Hraber, Peter T and Montefiori, David C and Trama, Ashley and Liao, Hua-Xin and Kepler, Thomas B and Moody, M Anthony and Gao, Feng and Danishefsky, Samuel J and Mascola, John R and Shaw, George M and Hahn, Beatrice H and Harrison, Stephen C and Korber, Bette T and Haynes, Barton F",
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number = 381,
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year = 2017,
url = "http://dx.doi.org/10.1126/scitranslmed.aai7514",
language = "en",
issn = "1946-6234, 1946-6242",
pmid = "28298420",
doi = "10.1126/scitranslmed.aai7514"
}
@ARTICLE{Cui2016-wz,
title = "A Model of Somatic Hypermutation Targeting in Mice Based on {High-Throughput} Ig Sequencing Data",
author = "Cui, Ang and Di Niro, Roberto and Vander Heiden, Jason A and Briggs, Adrian W and Adams, Kris and Gilbert, Tamara and O'Connor, Kevin C and Vigneault, Francois and Shlomchik, Mark J and Kleinstein, Steven H",
journal = "J. Immunol.",
publisher = "Am Assoc Immnol",
volume = 197,
number = 9,
pages = "3566--3574",
month = nov,
year = 2016,
url = "http://dx.doi.org/10.4049/jimmunol.1502263",
language = "en",
issn = "0022-1767, 1550-6606",
pmid = "27707999",
doi = "10.4049/jimmunol.1502263",
pmc = "PMC5161250"
}
@ARTICLE{Emerson2017-co,
title = "Immunosequencing identifies signatures of cytomegalovirus exposure history and {HLA-mediated} effects on the {T} cell repertoire",
author = "Emerson, Ryan O and DeWitt, William S and Vignali, Marissa and Gravley, Jenna and Hu, Joyce K and Osborne, Edward J and Desmarais, Cindy and Klinger, Mark and Carlson, Christopher S and Hansen, John A and Rieder, Mark and Robins, Harlan S",
journal = "Nat. Genet.",
publisher = "Nature Research",
month = apr,
year = 2017,
url = "http://dx.doi.org/10.1038/ng.3822",
language = "en",
issn = "1061-4036, 1546-1718",
doi = "10.1038/ng.3822"
}
@INPROCEEDINGS{Kingma2014-mo,
title = "{Auto-Encoding} Variational Bayes",
booktitle = "International Conference on Learning Representations",
author = "Kingma, Diederik P and Welling, Max",
editor = "Bengio, Yoshua and Lecun, Yann",
publisher = "arxiv.org",
year = 2014,
url = "http://arxiv.org/abs/1312.6114v10"
}
@ARTICLE{Bouckaert2014-ra,
title = "{BEAST} 2: a software platform for Bayesian evolutionary analysis",
author = "Bouckaert, Remco and Heled, Joseph and K{\"{u}}hnert, Denise and Vaughan, Tim and Wu, Chieh-Hsi and Xie, Dong and Suchard, Marc A and Rambaut, Andrew and Drummond, Alexei J",
journal = "PLoS Comput. Biol.",
publisher = "dx.plos.org",
volume = 10,
number = 4,
pages = "e1003537",
month = apr,
year = 2014,
url = "http://dx.doi.org/10.1371/journal.pcbi.1003537",
issn = "1553-734X, 1553-7358",
pmid = "24722319",
doi = "10.1371/journal.pcbi.1003537",
pmc = "PMC3985171"
}
@ARTICLE{Drummond2007-co,
title = "{BEAST}: Bayesian evolutionary analysis by sampling trees",
author = "Drummond, Alexei J and Rambaut, Andrew",
affiliation = "Bioinformatics Institute, University of Auckland, Auckland, New Zealand. alexei@cs.auckland.ac.nz",
journal = "BMC Evol. Biol.",
publisher = "biomedcentral.com",
volume = 7,
pages = "214",
month = "8~" # nov,
year = 2007,
url = "http://dx.doi.org/10.1186/1471-2148-7-214",
issn = "1471-2148",
pmid = "17996036",
doi = "10.1186/1471-2148-7-214",
pmc = "PMC2247476"
}
@ARTICLE{Drummond2012-ek,
title = "Bayesian Phylogenetics with {BEAUti} and the {BEAST} 1.7",
author = "Drummond, Alexei J. and Suchard, Marc A. and Xie, Dong and Rambaut, Andrew",
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publisher = "SMBE",
volume = 29,
number = 8,
pages = "1969--1973",
month = aug,
year = 2012,
url = "http://dx.doi.org/10.1093/molbev/mss075",
issn = "0737-4038",
doi = "10.1093/molbev/mss075"
}
@ARTICLE{Wu2015-uw,
title = "Maturation and Diversity of the {VRC01-Antibody} Lineage over 15 Years of Chronic {HIV-1} Infection",
author = "Wu, Xueling and Zhang, Zhenhai and Schramm, Chaim A and Joyce, M Gordon and Do Kwon, Young and Zhou, Tongqing and Sheng, Zizhang and Zhang, Baoshan and O'Dell, Sijy and McKee, Krisha and Georgiev, Ivelin S and Chuang, Gwo-Yu and Longo, Nancy S and Lynch, Rebecca M and Saunders, Kevin O and Soto, Cinque and Srivatsan, Sanjay and Yang, Yongping and Bailer, Robert T and Louder, Mark K and {NISC Comparative Sequencing Program} and Mullikin, James C and Connors, Mark and Kwong, Peter D and Mascola, John R and Shapiro, Lawrence",
journal = "Cell",
month = "8~" # apr,
year = 2015,
url = "http://dx.doi.org/10.1016/j.cell.2015.03.004",
issn = "0092-8674, 1097-4172",
pmid = "25865483",
doi = "10.1016/j.cell.2015.03.004"
}
@ARTICLE{Doria-Rose2014-vi,
title = "Developmental pathway for potent {V1V2-directed} {HIV-neutralizing} antibodies",
author = "Doria-Rose, Nicole A. and Schramm, Chaim A. and Gorman, Jason and Moore, Penny L. and Bhiman, Jinal N. and DeKosky, Brandon J. and Ernandes, Michael J. and Georgiev, Ivelin S. and Kim, Helen J. and Pancera, Marie and Staupe, Ryan P. and Altae-Tran, Han R. and Bailer, Robert T. and Crooks, Ema T. and Cupo, Albert and Druz, Aliaksandr and Garrett, Nigel J. and Hoi, Kam H. and Kong, Rui and Louder, Mark K. and Longo, Nancy S. and McKee, Krisha and Nonyane, Molati and O'Dell, Sijy and Roark, Ryan S. and Rudicell, Rebecca S. and Schmidt, Stephen D. and Sheward, Daniel J. and Soto, Cinque and Wibmer, Constantinos Kurt and Yang, Yongping and Zhang, Zhenhai and Sequencing, Nisc Comparative and Mullikin, James C. and Binley, James M. and Sanders, Rogier W. and Wilson, Ian A. and Moore, John P. and Ward, Andrew B. and Georgiou, George and Williamson, Carolyn and Abdool Karim, Salim S. and Morris, Lynn and Kwong, Peter D. and Shapiro, Lawrence and Mascola, John R.",
journal = "Nature",
publisher = "Nature Publishing Group",
month = "2~" # mar,
year = 2014,
url = "http://dx.doi.org/10.1038/nature13036",
issn = "0028-0836, 1476-4687",
doi = "10.1038/nature13036"
}
@ARTICLE{Yeap2015-nl,
title = "{Sequence-Intrinsic} Mechanisms that Target {AID} Mutational Outcomes on Antibody Genes",
author = "Yeap, Leng-Siew and Hwang, Joyce K and Du, Zhou and Meyers, Robin M and Meng, Fei-Long and Jakubauskait{\.e}, Agn{\.e} and Liu, Mengyuan and Mani, Vinidhra and Neuberg, Donna and Kepler, Thomas B and Wang, Jing H and Alt, Frederick W",
journal = "Cell",
publisher = "Elsevier",
volume = 163,
number = 5,
pages = "1124--1137",
month = nov,
year = 2015,
url = "http://dx.doi.org/10.1016/j.cell.2015.10.042",
language = "en",
issn = "0092-8674, 1097-4172",
pmid = "26582132",
doi = "10.1016/j.cell.2015.10.042",
pmc = "PMC4751889"
}
@ARTICLE{Marcou2018-sm,
title = "High-throughput immune repertoire analysis with {IGoR}",
author = "Marcou, Quentin and Mora, Thierry and Walczak, Aleksandra M",
journal = "Nat. Commun.",
volume = 9,
number = 1,
pages = "561",
month = feb,
year = 2018,
url = "http://dx.doi.org/10.1038/s41467-018-02832-w",
language = "en",
issn = "2041-1723",
pmid = "29422654",
doi = "10.1038/s41467-018-02832-w",
pmc = "PMC5805751"
}
@ARTICLE{Dhar2019-qg,
title = "A Bayesian Phylogenetic Hidden Markov Model for {B} Cell Receptor Sequence Analysis",
author = "Dhar, Amrit and Ralph, Duncan K and Minin, Vladimir N and Matsen, IV, Frederick A",
month = jun,
year = 2019,
url = "http://arxiv.org/abs/1906.11982",
archivePrefix = "arXiv",
eprint = "1906.11982",
primaryClass = "stat.ME",
arxivid = "1906.11982"
}
@ARTICLE{Simonich2019-nn,
title = "Kappa chain maturation helps drive rapid development of an infant {HIV-1} broadly neutralizing antibody lineage",
author = "Simonich, Cassandra A and Doepker, Laura and Ralph, Duncan and Williams, James A and Dhar, Amrit and Yaffe, Zak and Gentles, Lauren and Small, Christopher T and Oliver, Brian and Vigdorovich, Vladimir and Mangala Prasad, Vidya and Nduati, Ruth and Sather, D Noah and Lee, Kelly K and Matsen, Iv, Frederick A and Overbaugh, Julie",
journal = "Nat. Commun.",
volume = 10,
number = 1,
pages = "2190",
month = may,
year = 2019,
url = "http://dx.doi.org/10.1038/s41467-019-09481-7",
issn = "2041-1723",
pmid = "31097697",
doi = "10.1038/s41467-019-09481-7"
}
@ARTICLE{Shaw2019-qi,
title = "Joint maximum likelihood of phylogeny and ancestral states is not consistent",
author = "Shaw, David A and Dinh, Vu C and Matsen IV, Frederick A",
journal = "Mol. Biol. Evol.",
month = may,
year = 2019,
url = "http://dx.doi.org/10.1093/molbev/msz128",
issn = "0737-4038, 1537-1719",
pmid = "31119293",
doi = "10.1093/molbev/msz128"
}
@ARTICLE{Feng2019-lw,
title = "Estimation of cell lineage trees by maximum-likelihood phylogenetics",
author = "Feng, Jean and DeWitt, III, William S and McKenna, Aaron and Simon, Noah and Willis, Amy and Matsen, IV, Frederick A",
month = mar,
year = 2019,
note = "\url{http://arxiv.org/abs/1904.00117}",
archivePrefix = "arXiv",
eprint = "1904.00117",
primaryClass = "q-bio.QM",
arxivid = "1904.00117"
}
@ARTICLE{Ho2019-lf,
title = "On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model",
author = "Ho, Lam Si Tung and Dinh, Vu and Matsen, IV, Frederick A and Suchard, Marc A",
month = mar,
year = 2019,
note = "\url{http://arxiv.org/abs/1903.03919}",
archivePrefix = "arXiv",
eprint = "1903.03919",
primaryClass = "q-bio.PE",
arxivid = "1903.03919"
}
@ARTICLE{Fourment2018-xx,
title = "19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology",
author = "Fourment, Mathieu and Magee, Andrew F and Whidden, Chris and Bilge, Arman and Matsen IV, Frederick A and Minin, Vladimir N",
month = nov,
year = 2018,
note = "\url{http://arxiv.org/abs/1811.11804}",
journal = "in press, Systematic Biology",
eprint = "1811.11804",
primaryClass = "q-bio.PE",
arxivid = "1811.11804",
post = "general/2019-06-01-pt.md"
}
@ARTICLE{Whidden2018-db,
title = "Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies",
author = "Whidden, Chris and Claywell, Brian C and Fisher, Thayer and Magee, Andrew F and Fourment, Mathieu and Matsen IV, Frederick A",
month = nov,
year = 2018,
note = "\url{http://arxiv.org/abs/1811.11007}",
journal = "in press, Systematic Biology",
eprint = "1811.11007",
primaryClass = "q-bio.PE",
arxivid = "1811.11007",
post = "general/2019-06-01-pt.md"
}
@ARTICLE{Zhang2018-gn,
title = "Non-bifurcating phylogenetic tree inference via the adaptive {LASSO}",
author = "Zhang, Cheng and Dinh, Vu and Matsen IV, Frederick A",
month = may,
year = 2018,
note = "\url{http://arxiv.org/abs/1805.11073}",
journal = "in revision for JASA",
eprint = "1805.11073",
primaryClass = "q-bio.PE",
arxivid = "1805.11073"
}
@ARTICLE{Ralph2017-ih,
title = "Per-sample immunoglobulin germline inference from {B} cell receptor deep sequencing data",
author = "Ralph, Duncan K and Matsen IV, Frederick A",
month = nov,
year = 2017,
note = "\url{http://arxiv.org/abs/1711.05843}",
journal = "arXiv",
eprint = "1711.05843",
primaryClass = "q-bio.PE",
arxivid = "1711.05843",
post = "general/2017-12-01-gl-inf.md"
}
@ARTICLE{Whidden2016-ig,
title = "Chain Reduction Preserves the Unrooted Subtree {Prune-and-Regraft} Distance",
author = "Whidden, Chris and Matsen IV, Frederick A",
month = "8~" # nov,
year = 2016,
note = "\url{http://arxiv.org/abs/1611.02351}",
journal = "arXiv",
eprint = "1611.02351",
primaryClass = "cs.DM",
arxivid = "1611.02351",
post = "general/2015-11-25-uspr.md"
}
@ARTICLE{Whidden2015-zr,
title = "Calculating the Unrooted Subtree Prune-and-Regraft Distance",
author = "Whidden, Chris and Matsen IV, Frederick A",
month = "24~" # nov,
year = 2015,
journal = "arXiv",
note = "\url{http://arxiv.org/abs/1511.07529}",
archivePrefix = "arXiv",
eprint = "1511.07529",
primaryClass = "cs.DS",
arxivid = "1511.07529",
post = "general/2015-11-25-uspr.md"
}
% published
% for i in %first %middle %last; do grep $i my_papers.bib | wc -l; done
% first author: 8
% middle author: 17
% senior author: 25
% since joining Fred Hutch
%last
@ARTICLE{Feng2019-sj,
title = "Survival analysis of {DNA} mutation motifs with penalized proportional hazards",
author = "Feng, Jean and Shaw, David A and Minin, Vladimir N and Simon, Noah and Matsen, IV, Frederick A",
journal = "Ann. Appl. Stat.",
publisher = "Institute of Mathematical Statistics",
volume = 13,
number = 2,
pages = "1268--1294",
month = jun,
year = 2019,
url = "https://projecteuclid.org/euclid.aoas/1560758446",
issn = "1932-6157, 1941-7330",
doi = "10.1214/18-AOAS1233",
post = "general/2017-11-14-motif.md"
}
%last
@INPROCEEDINGS{Zhang2018-lw,
title = "Variational Bayesian Phylogenetic Inference",
booktitle = "International Conference on Learning Representations ({ICLR})",
author = "Zhang, Cheng and Matsen, IV, Frederick A",
year = 2018,
url = "https://openreview.net/pdf?id=SJVmjjR9FX"
}
%last
@INCOLLECTION{Zhang2018-mm,
title = "Generalizing Tree Probability Estimation via {B}ayesian Networks",
booktitle = "Advances in Neural Information Processing Systems 31",
author = "Zhang, Cheng and Matsen IV, Frederick A",
editor = "Bengio, S and Wallach, H and Larochelle, H and Grauman, K and Cesa-Bianchi, N and Garnett, R",
publisher = "Curran Associates, Inc.",
pages = "1449--1458",
year = 2018,
note = "\url{http://papers.nips.cc/paper/7418-generalizing-tree-probability-estimation-via-bayesian-networks.pdf}",
arxivid = "1805.07834"
}
%last
@ARTICLE{Dhar2018-ne,
title = "Predicting {B} cell receptor substitution profiles using public repertoire data",
author = "Dhar, Amrit and Davidsen, Kristian and Matsen, 4th, Frederick A and Minin, Vladimir N",
journal = "PLoS Comput. Biol.",
volume = 14,
number = 10,
pages = "e1006388",
month = oct,
year = 2018,
url = "http://dx.doi.org/10.1371/journal.pcbi.1006388",
issn = "1553-734X, 1553-7358",
pmid = "30332400",
doi = "10.1371/journal.pcbi.1006388",
post = "general/2018-04-19-spurf.md"
}
%last
@ARTICLE{Davidsen2018-gn,
title = "Benchmarking Tree and Ancestral Sequence Inference for {B} Cell Receptor Sequences",
author = "Davidsen, Kristian and Matsen, Frederick A",
journal = "Front. Immunol.",
volume = 9,
pages = "2451",
year = 2018,
url = "https://www.frontiersin.org/article/10.3389/fimmu.2018.02451",
issn = "1664-3224",
doi = "10.3389/fimmu.2018.02451"
}
%middle
@ARTICLE{DeWitt2018-ar,
title = "Human {T} cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity",
author = "DeWitt, William S and Smith, Anajane and Schoch, Gary and Hansen, John A and Matsen, Frederick A and Bradley, Philip",
journal = "Elife",
publisher = "eLife Sciences Publications, Ltd",
volume = 7,
pages = "e38358",
month = aug,
year = 2018,
url = "https://doi.org/10.7554/eLife.38358",
issn = "2050-084X",
doi = "10.7554/eLife.38358",
post = "general/2018-05-15-pubtcr.md"
}
%last
@ARTICLE{Olson2018-lw,
title = "The {B}ayesian optimist's guide to adaptive immune receptor repertoire analysis",
author = "Olson, Branden J and Matsen IV, Frederick A",
journal = "Immunol. Rev.",
volume = 284,
number = 1,
pages = "148--166",
month = jun,
year = 2018,
url = "https://onlinelibrary.wiley.com/doi/abs/10.1111/imr.12664",
archivePrefix = "arXiv",
eprint = "1804.10964",
primaryClass = "q-bio.PE",
issn = "0105-2896",
arxivid = "1804.10964",
doi = "10.1111/imr.12664",
post = "general/2018-05-12-bayesian-optimist.md"
}
%last
@ARTICLE{Dinh2018-xe,
title = "Consistency and convergence rate of phylogenetic inference via regularization",
author = "Dinh, Vu and Ho, Lam Si Tung and Suchard, Marc A and Matsen IV, Frederick A",
journal = "Ann. Stat.",
publisher = "Institute of Mathematical Statistics",
volume = 46,
number = 4,
pages = "1481--1512",
month = aug,
year = 2018,
url = "https://projecteuclid.org/euclid.aos/1530086423",
issn = "0090-5364, 2168-8966",
doi = "10.1214/17-AOS1592",
post = "general/2016-06-05-regularization.md",
arxivid = "1606.03059"
}
%middle
@ARTICLE{Fourment2017-an,
title = "Effective online {Bayesian} phylogenetics via {Sequential} {Monte} {Carlo} with guided proposals",
author = "Fourment, Mathieu and Claywell, Brian C and Dinh, Vu and McCoy, Connor and Matsen IV, Frederick A and Darling, Aaron E",
journal = "Syst. Biol.",
month = nov,
year = 2017,
url = "http://dx.doi.org/10.1093/sysbio/syx090",
issn = "1063-5157, 1076-836X",
pmid = "29186587",
doi = "10.1093/sysbio/syx090",
post = "general/2017-06-07-sts.md"
}
%last
@ARTICLE{Dinh2017-sh,
title = "Online {Bayesian} phylogenetic inference: theoretical foundations via {Sequential} {Monte} {Carlo}",
author = "Dinh, Vu and Darling, Aaron E and Matsen IV, Frederick A",
journal = "Syst. Biol.",
month = dec,
year = 2017,
url = "http://dx.doi.org/10.1093/sysbio/syx087",
issn = "1063-5157, 1076-836X",
pmid = "29244177",
doi = "10.1093/sysbio/syx087",
post = "general/2016-10-26-smc-theory.md"
}
%last
@ARTICLE{DeWitt2018-el,
title = "Using genotype abundance to improve phylogenetic inference",
author = "DeWitt, William S and Mesin, Luka and Victora, Gabriel D and Minin, Vladimir N and Matsen IV, Frederick A",
journal = "Mol. Biol. Evol.",
month = feb,
year = 2018,
url = "https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msy020/4893244",
issn = "0737-4038",
post = "general/2017-09-05-gctree-phylo.md",
doi = "10.1093/molbev/msy020",
arxivid = "1708.08944"
}
%first
@ARTICLE{Matsen2018-bg,
title = "Tanglegrams: A Reduction Tool for Mathematical Phylogenetics",
author = "Matsen IV, F A and Billey, S C and Kas, A and Konvalinka, M",
journal = "IEEE/ACM Trans. Comput. Biol. Bioinform.",
volume = 15,
number = 1,
pages = "343--349",
month = jan,
year = 2018,
url = "http://dx.doi.org/10.1109/TCBB.2016.2613040",
issn = "1545-5963",
post = "general/2015-07-22-tanglegrams.md",
doi = "10.1109/TCBB.2016.2613040"
}
%last
@INCOLLECTION{Whidden2018-tl,
title = "Efficiently Inferring Pairwise Subtree Prune-and-Regraft Adjacencies between Phylogenetic Trees",
booktitle = "2018 Proceedings of the Fifteenth Workshop on Analytic Algorithmics and Combinatorics ({ANALCO})",
author = "Whidden, C and Matsen IV, F",
publisher = "Society for Industrial and Applied Mathematics",
pages = "77--91",
series = "Proceedings",
month = jan,
year = 2018,
url = "https://doi.org/10.1137/1.9781611975062.8",
doi = "10.1137/1.9781611975062.8"
}
%last
@ARTICLE{Claywell2018-zg,
title = "A Surrogate Function for One-Dimensional Phylogenetic Likelihoods",
author = "Claywell, Brian C and Dinh, Vu and Fourment, Mathieu and McCoy, Connor O and Matsen IV, Frederick A",
journal = "Mol. Biol. Evol.",
volume = 35,
number = 1,
pages = "242--246",
month = jan,
year = 2018,
url = "http://dx.doi.org/10.1093/molbev/msx253",
issn = "0737-4038, 1537-1719",
pmid = "29029199",
doi = "10.1093/molbev/msx253",
pmc = "PMC5850616"
}
%last
@ARTICLE{Whidden2017-rg,
title = "{Ricci--Ollivier} curvature of the rooted phylogenetic subtree--prune--regraft graph",
author = "Whidden, Chris and Matsen IV, Frederick A",
journal = "Theor. Comput. Sci.",
volume = 699,
number = "Supplement C",
pages = "1--20",
month = nov,
year = 2017,
url = "http://www.sciencedirect.com/science/article/pii/S0304397517301081",
issn = "0304-3975",
doi = "10.1016/j.tcs.2017.02.006",
post = "general/2015-04-02-rspr-curvature-nodata.md"
}
%middle
@ARTICLE{Breden2017-td,
title = "Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data",
author = "Breden, Felix and Luning Prak, Eline T and Peters, Bjoern and Rubelt, Florian and Schramm, Chaim A and Busse, Christian E and Vander Heiden, Jason A and Christley, Scott and Bukhari, Syed Ahmad Chan and Thorogood, Adrian and Matsen IV, Frederick A and Wine, Yariv and Laserson, Uri and Klatzmann, David and Douek, Daniel C and Lefranc, Marie-Paule and Collins, Andrew M and Bubela, Tania and Kleinstein, Steven H and Watson, Corey T and Cowell, Lindsay G and Scott, Jamie K and Kepler, Thomas B",
journal = "Front. Immunol.",
volume = 8,
pages = "1418",
year = 2017,
url = "https://www.frontiersin.org/article/10.3389/fimmu.2017.01418",
issn = "1664-3224",
doi = "10.3389/fimmu.2017.01418"
}
%middle
@ARTICLE{Watson2017-fg,
title = "Comment on ``{A} Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data''",
author = "Watson, Corey T and Matsen IV, Frederick A and Jackson, Katherine J L and Bashir, Ali and Smith, Melissa Laird and Glanville, Jacob and Breden, Felix and Kleinstein, Steven H and Collins, Andrew M and Busse, Christian E",
journal = "The Journal of Immunology",
publisher = "American Association of Immunologists",
volume = 198,
number = 9,
pages = "3371--3373",
month = may,
year = 2017,
url = "http://www.jimmunol.org/content/198/9/3371?etoc",
issn = "0022-1767, 1550-6606",
pmid = "28416712",
doi = "10.4049/jimmunol.1700306"
}
%last
@ARTICLE{Gavryushkin2017-pq,
title = "The combinatorics of discrete time-trees: theory and open problems",
author = "Gavryushkin, Alex and Whidden, Chris and Matsen IV, Frederick A",
affiliation = "Department of Biosystems Science and Engineering, ETH Z{\"u}rich, 4058, Basel, Switzerland. alex@gavruskin.com. Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.",
journal = "J. Math. Biol.",
month = "29~" # jul,
year = 2017,
url = "http://dx.doi.org/10.1007/s00285-017-1167-9",
issn = "0303-6812, 1432-1416",
pmid = "28756523",
post = "general/2016-07-11-discrete-time-tree.md",
doi = "10.1007/s00285-017-1167-9"
}
%last
@INPROCEEDINGS{Dinh2017-oj,
title = "Probabilistic Path {H}amiltonian {M}onte {C}arlo",
booktitle = "International Conference on Machine Learning",
author = "Dinh, Vu and Bilge, Arman and Zhang, Cheng and Matsen IV, Frederick A",
pages = "1009--1018",
month = "17~" # jul,
year = 2017,
url = "http://proceedings.mlr.press/v70/dinh17a.html",
post = "general/2017-06-26-pphmc.md",
publisher = "PMLR",
conference = "International Conference on Machine Learning"
}
%last
@ARTICLE{Dinh2017-lt,
title = "The shape of the one-dimensional phylogenetic likelihood function",
author = "Dinh, Vu and Matsen IV, Frederick A",
journal = "Ann. Appl. Probab.",
publisher = "Institute of Mathematical Statistics",
volume = 27,
number = 3,
pages = "1646--1677",
month = jun,
year = 2017,
url = "http://projecteuclid.org/euclid.aoap/1500451237",
issn = "1050-5164, 2168-8737",
post = "general/2015-07-15-stationary.md",
arxiv = "1507.03647",
doi = "10.1214/16-AAP1240"
}
%last
@ARTICLE{Billey2017-ci,
title = "On the enumeration of tanglegrams and tangled chains",
author = "Billey, Sara C and Konvalinka, Matja{\v z} and Matsen IV, Frederick A",
journal = "J. Combin. Theory Ser. A",
volume = 146,
pages = "239--263",
year = 2017,
url = "http://www.sciencedirect.com/science/article/pii/S0097316516301029",
keywords = "Tanglegrams; Enumeration; Binary trees; Binary partitions",
issn = "0097-3165",
post = "general/2015-07-22-tanglegrams.md",
doi = "10.1016/j.jcta.2016.10.003"
}
%last
@ARTICLE{Ralph2016-yl,
title = "{Likelihood-Based} Inference of {B} Cell Clonal Families",
author = "Ralph, Duncan K and Matsen IV, Frederick A",
journal = "PLoS Comput. Biol.",
publisher = "Public Library of Science",
volume = 12,
number = 10,
pages = "e1005086",
month = "17~" # oct,
year = 2016,
url = "http://journals.plos.org/ploscompbiol/article/asset?id=10.1371/journal.pcbi.1005086.PDF",
issn = "1553-734X, 1553-7358",
doi = "10.1371/journal.pcbi.1005086",
post = "general/2016-04-16-partis-clustering.md"
}
%middle
@ARTICLE{Weis2016-sw,
title = "Preexposure prophylaxis-selected drug resistance decays rapidly after drug cessation",
author = "Weis, Julie F and Baeten, Jared M and McCoy, Connor O and Warth, Chris and Donnell, Deborah and Thomas, Katherine K and Hendrix, Craig W and Marzinke, Mark A and Mugo, Nelly and Matsen IV, Frederick A and Celum, Connie and Lehman, Dara A and {for Partners PrEP Study Team}",
journal = "AIDS",
volume = 30,
number = 1,
pages = "31",
month = jan,
year = 2016,
url = "http://journals.lww.com/aidsonline/Abstract/2016/01020/Preexposure_prophylaxis_selected_drug_resistance.4.aspx",
issn = "0269-9370",
doi = "10.1097/QAD.0000000000000915"
}
%last
@ARTICLE{McCoy2015-qi,
title = "Quantifying evolutionary constraints on {B}-cell affinity maturation",
author = "McCoy, Connor O and Bedford, Trevor and Minin, Vladimir N and Bradley, Philip and Robins, Harlan and Matsen IV, Frederick A",
journal = "Philos. Trans. R. Soc. Lond. B Biol. Sci.",
volume = 370,
number = 1676,
month = "5~" # sep,
year = 2015,
url = "http://dx.doi.org/10.1098/rstb.2014.0244",
keywords = "B cell; affinity maturation; antibody; immunoglobulin; molecular evolution; natural selection",
issn = "0962-8436, 1471-2970",
pmid = "26194758",
doi = "10.1098/rstb.2014.0244",
post = "site/_posts/general/2014-03-23-mebcell.md"
}
%last
@ARTICLE{Ralph2016-kr,
title = "Consistency of {VDJ} Rearrangement and Substitution Parameters Enables Accurate {B} Cell Receptor Sequence Annotation",
author = "Ralph, Duncan K and Matsen IV, Frederick A",
affiliation = "Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America. Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.",
journal = "PLOS Comput. Biol.",
volume = 12,
number = 1,
pages = "e1004409",
month = jan,
year = 2016,
url = "http://dx.doi.org/10.1371/journal.pcbi.1004409",
archivePrefix = "arXiv",
eprint = "1503.04224",
primaryClass = "q-bio.PE",
issn = "1553-734X, 1553-7358",
pmid = "26751373",
arxivid = "1503.04224",
doi = "10.1371/journal.pcbi.1004409",
pmc = "PMC4709141",
post = "general/2015-03-23-partis-annotation.md"
}
%last
@ARTICLE{Cobey2015-dn,
title = "The evolution within us",
author = "Cobey, Sarah and Wilson, Patrick and Matsen IV, Frederick A",
journal = "Philos. Trans. R. Soc. Lond. B Biol. Sci.",
volume = 370,
number = 1676,
month = "5~" # sep,
year = 2015,
url = "http://dx.doi.org/10.1098/rstb.2014.0235",
keywords = "B-cell sequencing; antibody repertoires; vaccine design",
issn = "0962-8436, 1471-2970",
pmid = "26194749",
doi = "10.1098/rstb.2014.0235"
}
%middle
@ARTICLE{Gall2015-id,
title = "Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a {Barrett}'s Esophagus Cohort",
author = "Gall, Alevtina and Fero, Jutta and McCoy, Connor and Claywell, Brian C and Sanchez, Carissa A and Blount, Patricia L and Li, Xiaohong and Vaughan, Thomas L and Matsen, Frederick A and Reid, Brian J and Salama, Nina R",
journal = "PLoS One",
volume = 10,
number = 6,
pages = "e0129055",
month = "15~" # jun,
year = 2015,
url = "http://dx.doi.org/10.1371/journal.pone.0129055",
issn = "1932-6203",
pmid = "26076489",
doi = "10.1371/journal.pone.0129055"
}
%last
@ARTICLE{Whidden2015-eq,
title = "Quantifying {MCMC} exploration of phylogenetic tree space",
author = "Whidden, Chris and Matsen IV, Frederick A",
journal = "Systematic Biology",
volume = 64,
number = 3,
pages = "472--491",
month = may,
year = 2015,
url = "http://dx.doi.org/10.1093/sysbio/syv006",
post = "general/2014-05-13-sprmix.md",
keywords = "Markov chain Monte Carlo; phylogenetic methods; subtree prune-and-regraft; topological peaks; tree space",
issn = "1063-5157, 1076-836X",
pmid = "25631175",
doi = "10.1093/sysbio/syv006",
pmc = "PMC4395846"
}
%middle
@ARTICLE{Lehman2015-qs,
title = "Risk of Drug Resistance Among Persons Acquiring {HIV} Within a Randomized Clinical Trial of Single- or {Dual-Agent} Preexposure Prophylaxis",
author = "Lehman, Dara A and Baeten, Jared M and McCoy, Connor O and Weis, Julie F and Peterson, Dylan and Mbara, Gerald and Donnell, Deborah and Thomas, Katherine K and Hendrix, Craig W and Marzinke, Mark A and Frenkel, Lisa and Ndase, Patrick and Mugo, Nelly R and Celum, Connie and Overbaugh, Julie and Matsen, Frederick A and {The Partners PrEP study team}",
journal = "J. Infect. Dis.",
month = "13~" # jan,
year = 2015,
url = "http://jid.oxfordjournals.org/content/early/2015/01/13/infdis.jiu677.abstract",
issn = "0022-1899",
doi = "10.1093/infdis/jiu677",
post = "general/2015-01-15-prep.md"
}
%last
@INCOLLECTION{Hoffman2014-vc,
title = "Computational Tools for Taxonomic Assignment",
booktitle = "Encyclopedia of Metagenomics",
author = "Hoffman, Noah G and Matsen, Frederick A",
publisher = "Springer New York",
pages = "1--6",
month = "3~" # apr,
year = 2014,
url = "http://dx.doi.org/10.1007/978-1-4614-6418-1_89-5",
isbn = "9781461464181",
doi = "10.1007/978-1-4614-6418-1\_89-5"
}
%last
@ARTICLE{Matsen2015-sp,
title = "Phylogenetics and the human microbiome",
author = "Matsen IV, Frederick A",
journal = "Syst. Biol. (invited review)",
publisher = "sysbio.oxfordjournals.org",
volume = 64,
number = 1,
pages = "e26--41",
month = jan,
year = 2015,
arxiv = "1407.1794",
doi = "10.1093/sysbio/syu053",
pmc = "PMC4265140"
}
%middle
@ARTICLE{Darling2014-ux,
title = "{PhyloSift}: phylogenetic analysis of genomes and metagenomes",
author = "Darling, Aaron E and Jospin, Guillaume and Lowe, Eric and Matsen IV, Frederick A and Bik, Holly M and Eisen, Jonathan A",
affiliation = "ithree institute, University of Technology Sydney , Sydney , Australia ; Genome Center, University of California , Davis, CA , United States of America.Genome Center, University of California , Davis, CA , United States of America.Genome Center, University of California , Davis, CA , United States of America.Fred Hutchinson Cancer Research Center , Seattle, WA , United States of America.Genome Center, University of California , Davis, CA , United States of America.Department of Evolution and Ecology, University of California , Davis, CA , United States of America ; Department of Medical Microbiology and Immunology, University of California , Davis, CA , United States of America.",
journal = "PeerJ",
volume = 2,
pages = "e243",
month = "9~" # jan,
year = 2014,
url = "http://dx.doi.org/10.7717/peerj.243",
issn = "2167-8359",
pmid = "24482762",
doi = "10.7717/peerj.243",
pmc = "PMC3897386",
note = "Selected as one of the top 20 articles from 2014 in PeerJ (\url{http://peerj.com/collections/5-peerjpicks/})"
}
%first
@article{matsen2013apobec3g,
title = "A Novel {B}ayesian Method for Detection of {APOBEC3-Mediated} Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses",
author = "Matsen IV, Frederick A and Small, Christopher T and Soliven, Khanh and Engel, Gregory A and Feeroz, Mostafa M and Wang, Xiaoxing and Craig, Karen L and Hasan, M Kamrul and Emerman, Michael and Linial, Maxine L and Jones-Engel, Lisa",
journal = "PLoS Comput. Biol.",
publisher = "dx.plos.org",
volume = 10,
number = 2,
pages = "e1003493",
month = "27~" # feb,
year = "2014",
url = "http://dx.doi.org/10.1371/journal.pcbi.1003493",
issn = "1553-734X",
pmid = "24586139",
doi = "10.1371/journal.pcbi.1003493",
post={general/2014-02-27-sfv-apobec.md},
pmc = "PMC3937129"
}
%middle
@article{soliven2013simian,
title={Simian Foamy Virus Infection of Rhesus Macaques in {B}angladesh: Relationship of latent proviruses and transcriptionally active viruses},
author={Soliven, Khanh and Wang, Xiaoxing and Small, Christopher T and Feeroz, Mostafa M and Lee, Eun-Gyung and Craig, Karen L and Hasan, Kamrul and Engel, Gregory A and Jones-Engel, Lisa and Matsen, Frederick A and Maxine L. Linial},
journal={Journal of virology},
volume={87},
number={24},
pages={13628--13639},
year={2013},
publisher={Am Soc Microbiol},
doi={10.1128/JVI.01989-13}
}
%middle
@article{engel2013zoonotic,
title={Zoonotic simian foamy virus in {B}angladesh reflects diverse patterns of transmission and co-infection},
author={L. Jones-Engel and G. Engel and C. Small and K. Soliven and M. Feeroz and X. Wang and M. Hasan and G. Oh and S. M. R. Alam and K. Craig and D. Jackson and F. Matsen IV and M. L. Linial},
journal={Emerging Microbes and Infections},
volume={2},
number={9},
pages={e58},
year={2013},
publisher={Nature Publishing Group},
doi={10.1038/emi.2013.60},