Works by Howison, Mark

Results: 24

Incorporating Within-Host Diversity in Phylogenetic Analyses for Detecting Clusters of New HIV Diagnoses.

Published in:

Frontiers in Microbiology, 2022, v. 12, p. 1, doi. 10.3389/fmicb.2021.803190

By:

Guang, August;
Howison, Mark;
Ledingham, Lauren;
D'Antuono, Matthew;
Chan, Philip A.;
Lawrence, Charles;
Dunn, Casey W.;
Kantor, Rami

Publication type:

Article

Empirical comparison of analytical approaches for identifying molecular HIV-1 clusters.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41598-020-75560-1

By:

Novitsky, Vlad;
Steingrimsson, Jon A.;
Howison, Mark;
Gillani, Fizza S.;
Li, Yuanning;
Manne, Akarsh;
Fulton, John;
Spence, Matthew;
Parillo, Zoanne;
Marak, Theodore;
Chan, Philip A.;
Bertrand, Thomas;
Bandy, Utpala;
Alexander-Scott, Nicole;
Dunn, Casey W.;
Hogan, Joseph;
Kantor, Rami

Publication type:

Article

Acquired Human Immunodeficiency Virus Type 1 Drug Resistance in Rhode Island, USA, 2004–2021.

Published in:

Journal of Infectious Diseases, 2024, v. 230, n. 6, p. 1422, doi. 10.1093/infdis/jiae344

By:

Aung, Su;
Novitsky, Vlad;
Steingrimsson, Jon;
Gillani, Fizza S;
Howison, Mark;
Nagel, Katherine;
Solomon, Matthew;
Bertrand, Thomas;
Bhattarai, Lila;
Fulton, John;
Bandy, Utpala;
Kantor, Rami

Publication type:

Article

Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora.

Published in:

Molecular Biology & Evolution, 2022, v. 39, n. 2, p. 1, doi. 10.1093/molbev/msac027

By:

Munro, Catriona;
Zapata, Felipe;
Howison, Mark;
Siebert, Stefan;
Dunn, Casey W

Publication type:

Article

Prospective Evaluation of Routine Statewide Integration of Molecular Epidemiology and Contact Tracing to Disrupt Human Immunodeficiency Virus Transmission.

Published in:

Open Forum Infectious Diseases, 2024, v. 11, n. 10, p. 1, doi. 10.1093/ofid/ofae599

By:

Kantor, Rami;
Steingrimsson, Jon;
Fulton, John;
Novitsky, Vladimir;
Howison, Mark;
Gillani, Fizza;
Bhattarai, Lila;
MacAskill, Meghan;
Hague, Joel;
Guang, August;
Khanna, Aditya;
Dunn, Casey;
Hogan, Joseph;
Bertrand, Thomas;
Bandy, Utpala

Publication type:

Article

NOT ALL CLUSTERS ARE EQUAL: STATEWIDE MOLECULAR HIV CLUSTER DYNAMICS IN RHODE ISLAND.

Published in:

Topics in Antiviral Medicine, 2023, v. 31, n. 2, p. 341

By:

Novitsky, Vlad;
Steingrimsson, Jon A.;
Howison, Mark;
Dunn, Casey;
Gillani, Fizza;
Fulton, John;
Bertrand, Thomas;
Howe, Katharine;
Bhattarai, Lila;
Ronquillo, Guillermo;
Macaskill, Meghan;
Bandy, Utpala;
Hogan, Joseph W.;
Kantor, Rami

Publication type:

Article

STATEWIDE TRENDS OF ACQUIRED HIV-1 DRUG RESISTANCE IN RHODE ISLAND: 2004-2021.

Published in:

Topics in Antiviral Medicine, 2023, v. 31, n. 2, p. 230

By:

Su Aung;
Novitsky, Vlad;
Steingrimsson, Jon A.;
Gillani, Fizza;
Howison, Mark;
Nagel, Katherine;
Solomon, Matthew;
Bertrand, Thomas;
Howe, Katharine;
Bhattarai, Lila;
Fulton, John;
Bandy, Utpala;
Hogan, Joseph W.;
Kantor, Rami

Publication type:

Article

Multi-core and many-core shared-memory parallel raycasting volume rendering optimization and tuning.

Published in:

International Journal of High Performance Computing Applications, 2012, v. 26, n. 4, p. 399, doi. 10.1177/1094342012440466

By:

Bethel, E Wes;
Howison, Mark

Publication type:

Article

Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-58544-z

By:

Lee, Emma R.;
Parkin, Neil;
Jennings, Cheryl;
Brumme, Chanson J.;
Enns, Eric;
Casadellà, Maria;
Howison, Mark;
Coetzer, Mia;
Avila-Rios, Santiago;
Capina, Rupert;
Marinier, Eric;
Van Domselaar, Gary;
Noguera-Julian, Marc;
Kirkby, Don;
Knaggs, Jeff;
Harrigan, Richard;
Quiñones-Mateu, Miguel;
Paredes, Roger;
Kantor, Rami;
Sandstrom, Paul

Publication type:

Article

SARS-CoV-2 Variants in Rhode Island; May 2022 Update.

Published in:

Rhode Island Medical Journal, 2022, v. 105, n. 6, p. 7

By:

SINGH, MANJOT;
NOVITSKY, VLADIMIR;
CARPENTER-AZEVEDO, KRISTIN;
HOWISON, MARK;
HUARD, RICHARD C.;
KING, EWA;
KANTOR, RAMI

Publication type:

Article

SARS-CoV-2 Variants in Rhode Island.

Published in:

Rhode Island Medical Journal, 2021, v. 104, n. 7, p. 50

By:

KANTOR, RAMI;
NOVITSKY, VLADIMIR;
CARPENTER-AZEVEDO, KRISTIN;
HOWISON, MARK;
MANNE, AKARSH;
DARPOLOR, JOSEPHINE K.;
BOBENCHIK, APRIL;
TRIPATHI, ANUBHAV;
HUARD, RICHARD C.;
KING, EWA

Publication type:

Article

Toward a statistically explicit understanding of de novo sequence assembly.

Published in:

Bioinformatics, 2013, v. 29, n. 23, p. 2959, doi. 10.1093/bioinformatics/btt525

By:

Howison, Mark;
Zapata, Felipe;
Dunn, Casey W.

Publication type:

Article

Agalma: an automated phylogenomics workflow.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-330

By:

Dunn, Casey W.;
Howison, Mark;
Zapata, Felipe

Publication type:

Article

Measurement error and variant-calling in deep Illumina sequencing of HIV.

Published in:

Bioinformatics, 2019, v. 35, n. 12, p. 2029, doi. 10.1093/bioinformatics/bty919

By:

Howison, Mark;
Coetzer, Mia;
Kantor, Rami

Publication type:

Article

Statewide Longitudinal Trends in Transmitted HIV-1 Drug Resistance in Rhode Island, USA.

Published in:

Open Forum Infectious Diseases, 2022, v. 9, n. 1, p. 1, doi. 10.1093/ofid/ofab587

By:

Novitsky, Vlad;
Steingrimsson, Jon;
Gillani, Fizza S;
Howison, Mark;
Aung, Su;
Solomon, Matthew;
Won, Cindy Y;
Brotherton, Amy;
Shah, Rajeev;
Dunn, Casey;
Fulton, John;
Bertrand, Thomas;
Civitarese, Anna;
Howe, Katharine;
Marak, Theodore;
Chan, Philip;
Bandy, Utpala;
Alexander-Scott, Nicole;
Hogan, Joseph;
Kantor, Rami

Publication type:

Article

Revising transcriptome assemblies with phylogenetic information.

Published in:

PLoS ONE, 2021, v. 16, n. 1, p. 1, doi. 10.1371/journal.pone.0244202

By:

Guang, August;
Howison, Mark;
Zapata, Felipe;
Lawrence, Charles;
Dunn, Casey W.

Publication type:

Article

Added Value of Next Generation Sequencing in Characterizing the Evolution of HIV-1 Drug Resistance in Kenyan Youth.

Published in:

Viruses (1999-4915), 2023, v. 15, n. 7, p. 1416, doi. 10.3390/v15071416

By:

Novitsky, Vlad;
Nyandiko, Winstone;
Vreeman, Rachel;
DeLong, Allison K.;
Howison, Mark;
Manne, Akarsh;
Aluoch, Josephine;
Chory, Ashley;
Sang, Festus;
Ashimosi, Celestine;
Jepkemboi, Eslyne;
Orido, Millicent;
Hogan, Joseph W.;
Kantor, Rami

Publication type:

Article

An Automated Bioinformatics Pipeline Informing Near-Real-Time Public Health Responses to New HIV Diagnoses in a Statewide HIV Epidemic.

Published in:

Viruses (1999-4915), 2023, v. 15, n. 3, p. 737, doi. 10.3390/v15030737

By:

Howison, Mark;
Gillani, Fizza S.;
Novitsky, Vlad;
Steingrimsson, Jon A.;
Fulton, John;
Bertrand, Thomas;
Howe, Katharine;
Civitarese, Anna;
Bhattarai, Lila;
MacAskill, Meghan;
Ronquillo, Guillermo;
Hague, Joel;
Dunn, Casey W.;
Bandy, Utpala;
Hogan, Joseph W.;
Kantor, Rami

Publication type:

Article

Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping.

Published in:

Viruses (1999-4915), 2020, v. 12, n. 7, p. 694, doi. 10.3390/v12070694

By:

Parkin, Neil T.;
Avila-Rios, Santiago;
Bibby, David F.;
Brumme, Chanson J.;
Eshleman, Susan H.;
Harrigan, P. Richard;
Howison, Mark;
Hunt, Gillian;
Ji, Hezhao;
Kantor, Rami;
Ledwaba, Johanna;
Lee, Emma R.;
Matías-Florentino, Margarita;
Mbisa, Jean L.;
Noguera-Julian, Marc;
Paredes, Roger;
Rivera-Amill, Vanessa;
Swanstrom, Ronald;
Zaccaro, Daniel J.;
Zhang, Yinfeng

Publication type:

Article

Bioinformatic data processing pipelines in support of next‐generation sequencing‐based HIV drug resistance testing: the Winnipeg Consensus.

Published in:

Journal of the International AIDS Society, 2018, v. 21, n. 10, p. N.PAG, doi. 10.1002/jia2.25193

By:

Ji, Hezhao;
Enns, Eric;
Brumme, Chanson J.;
Parkin, Neil;
Howison, Mark;
Lee, Emma R.;
Capina, Rupert;
Marinier, Eric;
Avila‐Rios, Santiago;
Sandstrom, Paul;
Van Domselaar, Gary;
Harrigan, Richard;
Paredes, Roger;
Kantor, Rami;
Noguera‐Julian, Marc

Publication type:

Article

Phylogenomic Analyses Support Traditional Relationships within Cnidaria.

Published in:

PLoS ONE, 2015, v. 10, n. 10, p. 1, doi. 10.1371/journal.pone.0139068

By:

Zapata, Felipe;
Goetz, Freya E.;
Smith, Stephen A.;
Howison, Mark;
Siebert, Stefan;
Church, Samuel H.;
Sanders, Steven M.;
Ames, Cheryl Lewis;
McFadden, Catherine S.;
France, Scott C.;
Daly, Marymegan;
Collins, Allen G.;
Haddock, Steven H. D.;
Dunn, Casey W.;
Cartwright, Paulyn

Publication type:

Article

Bayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling.

Published in:

PLoS ONE, 2014, v. 9, n. 6, p. 1, doi. 10.1371/journal.pone.0099497

By:

Howison, Mark;
Zapata, Felipe;
Edwards, Erika J.;
Dunn, Casey W.

Publication type:

Article

Challenges in evaluating the use of viral sequence data to identify HIV transmission networks for public health.

Published in:

Statistical Communications in Infectious Diseases, 2020, v. 12, p. 1, doi. 10.1515/scid-2019-0019

By:

Kantor, Rami;
Fulton, John P.;
Steingrimsson, Jon;
Novitsky, Vladimir;
Howison, Mark;
Gillani, Fizza;
Li, Yuanning;
Manne, Akarsh;
Parillo, Zoanne;
Spence, Matthew;
Marak, Theodore;
Chan, Philip;
Dunn, Casey W.;
Bertrand, Thomas;
Bandy, Utpala;
Alexander-Scott, Nicole;
Hogan, Joseph W.

Publication type:

Article

Challenges in evaluating the use of viral sequence data to identify HIV transmission networks for public health.

Published in:

Statistical Communications in Infectious Diseases, 2020, v. 12, n. 1, p. 1, doi. 10.1515/scid-2019-0019

By:

Kantor, Rami;
Fulton, John P.;
Steingrimsson, Jon;
Novitsky, Vladimir;
Howison, Mark;
Gillani, Fizza;
Li, Yuanning;
Manne, Akarsh;
Parillo, Zoanne;
Spence, Matthew;
Marak, Theodore;
Chan, Philip;
Dunn, Casey W.;
Bertrand, Thomas;
Bandy, Utpala;
Alexander-Scott, Nicole;
Hogan, Joseph W.

Publication type:

Article