Search Results - "Danko, David C."

Ariadne: synthetic long read deconvolution using assembly graphs by Mak, Lauren, Meleshko, Dmitry, Danko, David C., Barakzai, Waris N., Maharjan, Salil, Belchikov, Natan, Hajirasouliha, Iman

“…Abstract Synthetic long read sequencing techniques such as UST’s TELL-Seq and Loop Genomics’ LoopSeq combine 3 $$'$$ ′ barcoding with standard short-read…”
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The Microbiomes of Seven Lichen Genera Reveal Host Specificity, a Reduced Core Community and Potential as Source of Antimicrobials by Sierra, Maria A, Danko, David C, Sandoval, Tito A, Pishchany, Gleb, Moncada, Bibiana, Kolter, Roberto, Mason, Christopher E, Zambrano, Maria Mercedes

“…The High Andean Paramo ecosystem is a unique neotropical mountain biome considered a diversity and evolutionary hotspot. Lichens, which are complex symbiotic…”
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A comprehensive metagenomics framework to characterize organisms relevant for planetary protection by Danko, David C, Sierra, Maria A, Benardini, James N, Guan, Lisa, Wood, Jason M, Singh, Nitin, Seuylemezian, Arman, Butler, Daniel J, Ryon, Krista, Kuchin, Katerina, Meleshko, Dmitry, Bhattacharya, Chandrima, Venkateswaran, Kasthuri J, Mason, Christopher E

“…Clean rooms of the Space Assembly Facility (SAF) at the Jet Propulsion Laboratory (JPL) at NASA are the final step of spacecraft cleaning and assembly before…”
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Minerva: an alignment- and reference-free approach to deconvolve Linked-Reads for metagenomics by Danko, David C, Meleshko, Dmitry, Bezdan, Daniela, Mason, Christopher, Hajirasouliha, Iman

“…Emerging Linked-Read technologies (aka read cloud or barcoded short-reads) have revived interest in short-read technology as a viable approach to understand…”
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Sequencing of Circulating Microbial Cell-Free DNA Can Identify Pathogens in Periprosthetic Joint Infections by Echeverria, Adriana P., Cohn, Ian S., Danko, David C., Shanaj, Sara, Blair, Lily, Hollemon, Desiree, Carli, Alberto V., Sculco, Peter K., Ho, Carine, Meshulam-Simon, Galit, Mironenko, Christine, Ivashkiv, Lionel B., Goodman, Susan M., Grizas, Alexandra, Westrich, Geoffrey H., Padgett, Douglas E., Figgie, Mark P., Bostrom, Mathias P., Sculco, Thomas P., Hong, David K., Hepinstall, Matthew S., Bauer, Thomas W., Blauwkamp, Timothy A., Brause, Barry D., Miller, Andy O., Henry, Michael W., Ahmed, Asim A., Cross, Michael B., Mason, Christopher E., Donlin, Laura T.

“…Over 1 million Americans undergo joint replacement each year, and approximately 1 in 75 will incur a periprosthetic joint infection. Effective treatment…”
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System-wide transcriptome damage and tissue identity loss in COVID-19 patients by Park, Jiwoon, Foox, Jonathan, Hether, Tyler, Danko, David C., Warren, Sarah, Kim, Youngmi, Reeves, Jason, Butler, Daniel J., Mozsary, Christopher, Rosiene, Joel, Shaiber, Alon, Afshin, Evan E., MacKay, Matthew, Rendeiro, André F., Bram, Yaron, Chandar, Vasuretha, Geiger, Heather, Craney, Arryn, Velu, Priya, Melnick, Ari M., Hajirasouliha, Iman, Beheshti, Afshin, Taylor, Deanne, Saravia-Butler, Amanda, Singh, Urminder, Wurtele, Eve Syrkin, Schisler, Jonathan, Fennessey, Samantha, Corvelo, André, Zody, Michael C., Germer, Soren, Salvatore, Steven, Levy, Shawn, Wu, Shixiu, Tatonetti, Nicholas P., Shapira, Sagi, Salvatore, Mirella, Westblade, Lars F., Cushing, Melissa, Rennert, Hanna, Kriegel, Alison J., Elemento, Olivier, Imielinski, Marcin, Rice, Charles M., Borczuk, Alain C., Meydan, Cem, Schwartz, Robert E., Mason, Christopher E.

“…The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal…”
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Characterizing the Urban Microbiome and Human Response to the Ecosystem of the Built Environment by Danko, David C

“…The urban environment contains a diverse set of microorganisms that survive on surfaces and suspended in the air. Using metagenomics and related technologies…”
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322. Clinical-Grade Metagenomics in Urinary Tract Infections: Improving Performance of Next-Generation Sequencing Assays Using Internal Controls and Machine Learning by Couto-Rodriguez, Mara, Danko, David C, Jirau Serrano, Xavier O, Paisie, Taylor, Papciak, John C, Szollosi, Eszter, Mason, Christopher E, Otto, Caitlin, O’Hara, Niamh B, Nagy-Szakal, Dorottya

“…Abstract Background Shotgun sequencing-based metagenomics is a useful approach to profiling microbiomes in environmental and patient samples. In a clinical…”
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Sequencing of Circulating Microbial Cell-Free DNA Can Identify Pathogens in Periprosthetic Joint Infections by Echeverria, Adriana P., Cohn, Ian S., Danko, David C., Shanaj, Sara, Blair, Lily, Hollemon, Desiree, Carli, Alberto V., Sculco, Peter K., Ho, Carine, Meshulam-Simon, Galit, Mironenko, Christine, Ivashkiv, Lionel B., Goodman, Susan M., Grizas, Alexandra, Westrich, Geoffrey H., Padgett, Douglas E., Figgie, Mark P., Bostrom, Mathias P., Sculco, Thomas P., Hong, David K., Hepinstall, Matthew S., Bauer, Thomas W., Blauwkamp, Timothy A., Brause, Barry D., Miller, Andy O., Henry, Michael W., Ahmed, Asim A., Cross, Michael B., Mason, Christopher E., Donlin, Laura T.

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2835. Utilization of Clinical-Grade Metagenomics in Urinary Tract Infection Diagnostics: Improving High-Risk Patients’ Outcomes with a Genomic-Based Assay by Romero, Eduardo J Morfa, Augenbraun, Michael, Rivera, Tiara, Rey, Sol, Serrano, Xavier O Jirau, Papciak, John C, Patel, Suraj S, Harrison, Bridget, Plourde, Anna, Otto, Caitlin, Mason, Chris, Wells, Heather L, Danko, David C, O’Hara, Niamh B, Couto-Rodriguez, Mara, Nagy-Szakal, Dorottya

“…Abstract Background Immunosuppressed patients and those experiencing complicated UTIs are more susceptible to misdiagnosis by outdated standard of care (SOC)…”
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The MetaSUB Microbiome Core Analysis Pipeline Enables Large Scale Metagenomic Analysis by Danko, David C, Mason, Chris

“…Motivation: Accurate data analysis and quality control is critical for metagenomic studies. Though many tools exist to analyze metagenomic data there is no…”
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The Challenges and Opportunities in Creating an Early Warning System for Global Pandemics by Danko, David C, Golden, James, Vorosmarty, Charles, Cak, Anthony, Corsi, Fabio, Mason, Christopher E, Maciel-de-Freitas, Rafael, Nagy-Szakal, Dorottya, OHara, Niamh B

“…The COVID-19 pandemic revealed that global health, social systems, and economies can be surprisingly fragile in an increasingly interconnected and…”
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