2024
A De Novo Whole Genome Assembly and Annotation of Parelaphostrongylus tenuis
Tyler J. Garwood, Jessie E. Richards, Marissa G. Macchietto, Richard W. Gerhold, Stephen A. Kania, John R. Garbe, Nicholas M. Fountain-Jones, Peter A. Larsen, Tiffany M. Wolf.
J Nematol., doi.org/10.2478/jofnem-2024-0009. 2024 March 14.
High-throughput genetic manipulation of multi-cellular organisms using a machine-vision guided embryonic microinjection robot
Andrew D Alegria, Amey S Joshi, Jorge Blanco Mendana, Kanav Khosla, Kieran T Smith, Benjamin Auch, Margaret Donovan, John Bischof, Daryl M Gohl, Suhasa B Kodandaramaiah.
Genetics, doi.org/10.1093/genetics/iyae025. 2024 Feb 19.
2023
Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiome
Asako Tan, Senthil Murugapiran, Alaya Mikalauskas, Jeff Koble, Drew Kennedy, Fred Hyde, Victor Ruotti, Emily Law, Jordan Jensen, Gary P. Schroth, Jean M. Macklaim, Scott Kuersten, Brice LeFrançois, Daryl M. Gohl.
BMC Microbiology, doi.org/10.1186/s12866-023-03037-y. 2023 Oct 20.
Novel insights into the whole blood DNA methylome of asthma in ethnically diverse children and youth
Esther Herrera-Luis, Carlos de la Rosa-Baez, Scott Huntsman, Celeste Eng, Kenneth B Beckman, Michael A Lenoir, Jose Rodriguez-Santana, Jesús Villar, Catherine Laprise, Luisa N Borrell, Elad Ziv, Esteban G Burchard, Maria Pino-Yanes
Eur Respir J., doi: 10.1183/13993003.00714-2023. 2023 Oct 6.
Epigenomic response to albuterol treatment in asthma-relevant airway epithelial cells
Javier Perez-Garcia, Maria Pino-Yanes, Elizabeth G. Plender, Jamie L. Everman, Celeste Eng, Nathan D. Jackson, Camille M. Moore, Kenneth B. Beckman, Vivian Medina, Sunita Sharma, Daniel Efrain Winnica, Fernando Holguin, José Rodríguez-Santana, Jesús Villar, Elad Ziv, Max A. Seibold & Esteban G. Burchard
Clinical Epigenetics, doi: 10.1186/s13148-023-01571-0. 2023 Oct 3.
Toward invasive mussel genetic biocontrol: Approaches, challenges, and perspectives
Víctor H. Hernández Elizárraga, Scott Ballantyne, Lindsey G. O'Brien, Juliana A. Americo, Steven T. Suhr, Marie-Claude Senut, Ben Minerich, Christopher M. Merkes, Thea M. Edwards, Katy Klymus, Catherine A. Richter, Diane L. Waller, Yale J. Passamaneck, Mauro F. Rebelo, Daryl M. Gohl
iScience, doi: 10.1016/j.isci.2023.108027. 2023 Sept 28.
More than bad luck: Cancer and aging are linked to replication-driven changes to the epigenome
Christopher Minteer, Kyra Thrush, John Gonzalez, Peter Niimi, Mariya Rozenblit, Joel Rozowsky, Jason Liu, Mor Frank, Thomas McCabe, Albert Higgins-Chen, Erin Hofstatter, Lajos Pusztai, Kenneth Beckman, Mark Ferstein, Morgan Levine
Science Advances, doi: 10.1126/sciadv.adf4163. 2023 July 19.
Outpatient treatment of COVID-19 and incidence of post-COVID-19 condition over 10 months (COVID-OUT): a multicentre, randomised, quadruple-blind, parallel-group, phase 3 trial
Carolyn T. Bramante, MD, MPH; John B. Buse, MD, PhD; David Liebovitz, MD; Jacinda
Nicklas, MD, MPH; Michael A. Puskarich, MD; Ken Cohen, MD; Hrishikesh Belani, MD,
MS; Blake Anderson, MS; Jared D. Huling, PhD; Christopher Tignanelli, MD, MS; Jennifer
Thompson, MD, MPH; Matthew Pullen, MD; Esteban Lemus Wirtz, BS; Lianne Siegel,
PhD; Jennifer Proper, PhD; David J. Odde, PhD; Nichole Klatt, PhD; Nancy Sherwood,
PhD; Sarah Lindberg, MPH; Amy Karger, MD, PhD; Kenny Beckman, PhD; et al.
Lancet Infect Dis 2023, doi.org/10.1016/ S1473-3099(23)00299-2. 2023 June 8.
Metformin reduces SARS-CoV-2 in a Phase 3 Randomized Placebo Controlled Clinical Trial
Carolyn T Bramante, Kenneth B Beckman, Tanvi Mehta, Amy B Krager, David J Odde, Christopher J Tignanelli, John B Buse, Darrell M Johnson, Ray H B Watson, Jerry J Daniel, David M Liebovitz, Jacinda M Nicklas, Kenneth Cohen, Michael A Puskarich, Hrishikesh K Belani, Lianne K Siegel, Nichole R Klatt, Blake Anderson, Katrina M Hartman, Via Rao, Aubrey A Hagan, et al.
medRxiv, doi.org/10.1101/2023.06.06.23290989. 2023 June 7.
Methods in Nutrition & Gut Microbiome Research: An American Society for Nutrition Satellite Session
Riley L. Hughes, Cara L. Frankenfeld, Daryl M. Gohl, Curtis Huttenhower, Scott A. Jackson, Doris Vandeputte, Emily Vogtmann, Sarah S. Comstock, Mary E. Kable
MPDI, doi.org/10.3390/nu15112451. 2023 May 24.
Variability and Bias in Microbiome Metagenomic Sequencing: an Interlaboratory Study Comparing Experimental Protocols
Samuel P. Forry, Stephanie L. Servetas, Jason G. Kralj, Keng Soh, Michalis Hadjithomas, Raul Cano, Martha Carlin, Maria G de Amorim, Benjamin Auch, Matthew G Bakker, Thais F Bartelli, Juan P. Bustamante, Ignacio Cassol, Mauricio Chalita, Emmanuel Dias-Neto, Aaron Del Duca, Daryl M. Gohl, et al.
bioRxiv, doi.org/10.1101/2023.04.28.538741. 2023 May 3.
A machine vision guided robot for fully automated embryonic microinjection
Andrew David Alegria Mr., Amey Sanjay Joshi Dr., Jorge Blanco Mendana Dr., Kanav Khosla Dr., Kieran Smith Mr., Benjamin Tiberius Auch Mr., Margaret Donovan Ms., John Bischof Dr., Daryl Gohl Dr., Suhasa Bangalore Kodandaramaiah Dr.
bioRxiv, doi.org/10.1101/2023.04.25.538280. 2023 Apr 25.
Deterministic Genetic Barcoding for Multiplexed Behavioral and Single-Cell Transcriptomic Studies
Jorge Blanco Mendana, Margaret Donovan, Lindsey Gengelbach, Benjamin Auch, John Garbe, Daryl M. Gohl
bioRxiv, doi.org/10.1101/2023.03.29.534817. 2023 Apr 1.
Multi-Omic Approach Associates Blood Methylome with Bronchodilator Drug Response in Pediatric Asthma
Javier Perez-Garcia, Esther Herrera-Luis, Annie Li, Angel C.Y. Mak, Scott Huntsman, Sam S. Oh, Jennifer R. Elhawary, Celeste Eng, Kenneth B. Beckman, Donglei Hu, Fabian Lorenzo-Diaz PhD, Michael A. Lenoir, Jose Rodriguez-Santana, Noah Zaitlen, Jesús Villar, Luisa N. Borrell, Esteban G. Burchard, Maria Pino-Yanes
Journal of Allergy and Clinical Immunology, doi.org/10.1016/j.jaci.2023.01.026. 2023 Feb 14.
Genetic variants associated with post-traumatic stress symptoms in patients with gynecologic cancer
Andrea M. Johnson, Deanna Teoh, Patricia Jewett, Burcu F. Darst, Jordan Mattson, Cody Hoffmann, Katherine Brown, Aditi Makaram, Ciana Keller, Anne H. Blaes, Susan A. Everson-Rose, Rachel I. Vogel
Gynecologic Oncology, doi.org/10.1016/j.ygyno.2023.01.006. 2023 Jan 19.
Associations between CES1 variants and dosing and adverse effects in children taking methylphenidate
Jacob T. Brown, Nancy Beery, Allise Taran, Tyler Stevens, Christine Henzler, Jonathan Badalamenti, Ron Regal and Catherine A. McCarty
Frontiers in Pediatrics, doi.org/10.3389/fped.2022.958622. 2023 Jan 18.
Mycobacterium tuberculosis requires the outer membrane lipid phthiocerol dimycocerosate for starvation-induced antibiotic tolerance
Alisha M. Block, Sarah B. Namugenyi, Nagendra P. Palani, Alyssa M. Brokaw, Leanne Zhang, Kenneth B. Beckman, Anna D. Tischler
mSystems, doi.org/10.1128/msystems.00699-22. 2023 Jan 4.
2022
Robotic platform for automated microinjection of zebrafish embryos for cryopreservation application
Amey S. Joshi, Andrew D. Alegria, Kieran Smith, Daryl M. Gohl, Kanav Khosla, John Bischof, Suhasa B. Kodandaramaiah
Cryobiology, doi.org/10.1016/j.cryobiol.2022.11.143. 2022 Dec 15.
Admixture mapping of severe asthma exacerbations in Hispanic/Latino children and youth
Esther Herrera-Luis, Angel C Y Mak, Javier Perez-Garcia, Elena Martin-Gonzalez, Celeste Eng, Kenneth B Beckman, Scott Huntsman, Donglei Hu, Ruperto González-Pérez, José M Hernández-Pérez, Elena Mederos-Luis, et al.
Thorax, doi: 10.1136/thorax-2022-218755. 2022 Sep 30.
Revisiting the bad luck hypothesis: Cancer risk and aging are linked to replication-driven changes to the epigenome
Christopher J. Minteer, Kyra Thrush, Peter Niimi, Joel Rozowsky, Jason Liu, Mor Frank, Thomas McCabe, Erin Hofstatter, Mariya Rozenblit, Lajos Pusztai, Kenneth Beckman, Mark Gerstein, Morgan E. Levine
bioRxiv, doi.org/10.1101/2022.09.14.507975. 2022 Sept 17.
Health inequities in SARS-CoV-2 infection, seroprevalence, and COVID-19 vaccination: Results from the East Bay COVID-19 study
Cameron Adams, Mary Horton, Olivia Solomon, Marcus Wong, Sean L. Wu, Sophia Fuller, Xiaorong Shao, Indro Fedrigo, Hong L. Quach, Diana L. Quach, Michelle Meas, Luis Lopez, Abigail Broughton, Anna L. Barcellos, Joan Shim, Yusef Seymens, Samantha Hernandez, Magelda Montoya, Darrell M. Johnson, Kenneth B. Beckman, Michael P. Busch, Josefina Coloma, Joseph A. Lewnard, Eva Harris, Lisa F. Barcellos
PLOS Global Public Health, doi.org/10.1371/journal.pgph.0000647. 2022 Aug 15.
Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes
Asako Tan, Senthil Murugapiran, Alaya Mikalauskas, Jeff Koble, Drew Kennedy, Fred Hyde, Victor Ruotti, Emily Law, Jordan Jensen, Gary P Schroth, Jean Macklaim, Scott Kuersten,
Brice Le Francois, Daryl M Gohl
bioRxiv, doi.org/10.1101/2022.08.08.502835. 2022 Aug 8.
Mycobacterium tuberculosis requires the outer membrane lipid phthiocerol dimycocerosate for starvation-induced antibiotic tolerance
Alisha M. Block, Sarah B. Namugenyi, Nagendra P. Palani, Alyssa M. Brokaw, Leanne Zhang, Kenneth B. Beckman, Anna D. Tischler
bioRxiv, doi.org/10.1101/2022.07.07.499240. 2022 July 8.
Diagnostic capabilities of nanopore long-read sequencing in muscular dystrophy
Christine C Bruels, Hannah R Littel, Audrey L Daugherty, Seth Stafki, Elicia A Estrella, Emily S McGaughy, Don Truong, Jonathan P Badalamenti, Lynn Pais, Vijay S Ganesh, Anne O'Donnell-Luria, Heather J Stalker, Yang Wang, Christin Collins, Andrea Behlmann, Richard J L F Lemmers, Silvère M van der Maarel, Regina Laine, Partha S Ghosh, Basil T Darras, Carla D Zingariello, Christina A Pacak, Louis M Kunkel, Peter B Kang
Ann Clin Transl Neurol., doi: 10.1002/acn3.51612. 2022 June 23.
The potential for bacteria from carbon-limited deep terrestrial environments to participate in chlorine cycling
Susma Bhattarai, Hanna Temme, Abhiney Jain, Jonathan P Badalamenti, Jeffrey A Gralnick, Paige J Novak
FEMS Microbiol Ecol., doi: 10.1093/femsec/fiac054. 2022 May 3.
Epigenome-wide association study of lung function in Latino children and youth with asthma
Esther Herrera-Luis, Annie Li, Angel C Y Mak, Javier Perez-Garcia, Jennifer R Elhawary, Sam S Oh, Donglei Hu, Celeste Eng, Kevin L Keys, Scott Huntsman, Kenneth B Beckman, Luisa N Borrell, Jose Rodriguez-Santana, Esteban G Burchard, Maria Pino-Yane
Clin Epigenetics.14(1):9. doi: 10.1186/s13148-022-01227-5. 2022 Jan 15.
Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii
Inge Holm, Luisa Nardini, Adrien Pain, Emmanuel Bischoff, Cameron E. Anderson, Soumanaba Zongo, Wamdaogo M. Guelbeogo, N’Fale Sagnon, Daryl M. Gohl, Ronald J. Nowling, Kenneth D. Vernick* and Michelle M. Riehl
Front. Genet., doi.org/10.3389/fgene.2021.785934. 2022 Jan 10.
2021
The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Comparative Genomics, Invasion Genetics, and Biocontrol
Michael A McCartney, Benjamin Auch, Thomas Kono, Sophie Mallez, Ying Zhang, Angelico Obille, Aaron Becker, Juan E Abrahante, John Garbe, Jonathan P Badalamenti, Adam Herman, Hayley Mangelson, Ivan Liachko, Shawn Sullivan, Eli D Sone, Sergey Koren, Kevin A T Silverstein, Kenneth B Beckman, Daryl M Gohl
G3 Genes|Genomes|Genetics, doi:10.1093/g3journal/jkab423. 2021 Dec 13.
Multiscale, multi-perspective imaging assisted robotic microinjection of 3D biological structures
Amey S Joshi, Andrew D Alegria, Benjamin Auch, Kanav Khosla, Jorge Blanco Mendana, Kunpeng Liu, John Bischof, Daryl M Gohl, Suhasa B Kodandaramaiah
Annu Int Conf IEEE Eng Med Biol Soc., doi: 10.1109/EMBC46164.2021.9630858. 2021 Nov.
Genetic variants predictive of chemotherapy-induced peripheral neuropathy symptoms in gynecologic cancer survivors
Lauren Thomaier, Burcu F. Darst, Patricia Jewett, Cody Hoffmann, Katherine Brown, Aditi Makaram, Anne Blaes, Peter Argenta, Deanna Teoh, Rachel I.Vogel
Gynecologic Oncology, doi.org/10.1016/j.ygyno.2021.10.006. 2021 Oct18.
Effect of losartan on hospitalized patients with COVID-19-induced lung injury: A randomized clinical trial
Michael A. Puskarich, Nicholas E. Ingraham, Lisa H Merck, Brian E Driver, David A. Wacker, Lauren Page Black, Alan E. Jones, Courtney V. Fletcher, Andrew M. South, Andrew C. Nelson, Thomas A Murray, Christopher J. Tignanelli, Christopher Lewandowski, Joseph Farhat, Justin L. Benoit, Dana Byrne, Alex Hall, Ronald A. Reilkoff, Michelle H. Biros, Kartik Cherabuddi, Jeffrey G. Chipman, Timothy W. Schacker, Tyler Bold, Kenneth Beckman, Ryan Langlois, Matthew T. Aliota, Faheem W. Guirgis, James Galbriath, Margaret Beyer, Chas Salmen, Brian Roberts, David Wright, Helen T. Voelker, Joseph S. Koopmeiners
medRxiv doi:10.1101/2021.08.25.21262623. 2021 Aug 28.
CLAMP regulates Zygotic Genome Activation in Drosophila embryos
Megan M Colonnetta, Juan E Abrahante, Paul Schedl, Daryl M Gohl, Girish Deshpande
Genetics. iyab107. 2021 August 09.
Saliva testing is accurate for early-stage and presymptomatic COVID-19
Abigail J. Johnson, Shannon Zhou, Suzie L. Hoops, Benjamin Hillmann, Matthew Schomaker, Robyn Kincaid, Jerry Daniel, Kenneth Beckman, Daryl M. Gohl, Sophia Yohe, Dan Knights, Andrew C. Nelson
Microbiology Spectrum. 9(1) e00086-21. 2021 July 14.
Biological Aging Predicts Vulnerability to COVID-19 Severity in UK Biobank Participants
Kuo CL, Pilling LC, Atkins JL, Masoli JAH, Delgado J, Tignanelli C, Kuchel GA, Melzer D, Beckman KB, Levine ME
J Gerontol A Biol Sci Med Sci. 2021 Jul 13;76(8):e133-e141.
Development of a User-Friendly Pipeline for Mutational Analyses of HIV Using Ultra-Accurate Maximum-Depth Sequencing
Morgan E. Meissner, Emily J. Julik, Jonathan P. Badalamenti, William G. Arndt, Lauren J. Mills, Louis M. Mansky
Viruses. 13(7),1338. 2021 July 11.
Neither Donor nor Recipient Mitochondrial Haplotypes Are Associated with Unrelated Donor Transplant Outcomes: A Validation Study from the CIBMTR
Logan G. Spector, Stephen R. Spellman, Bharat Thyagarajan, Kenneth B. Beckman, Cody Hoffmann, John Garbe, Theresa Hahn, Lara Sucheston-Campbell, Michaela Richardson, Todd E. De For, Jakub Tolar, Michael R.Verneris
Transplantation and Cellular Therapy. doi: 10.1016/j.jtct.2021.06.019. 2021 June 23.
Dissecting and tuning primer editing by proofreading polymerases
Daryl M Gohl, Benjamin Auch, Amanda Certano, Brice LeFrançois, Anne Bouevitch, Evgueni Doukhanine, Christina Fragel, Jean Macklaim, Emily Hollister, John Garbe, Kenneth B Beckman
Nucleic Acids Research. 2021 14 June, gkab471.
Prediction of false positive SARS-CoV-2 molecular results in a high-throughput open platform system
Ryan John Martinez, Nathan Pankratz, Matthew Schomaker, Jerry Daniel, Kenneth Beckman, Amy BethKarger, Bharat Thyagarajan, Patricia Ferreri, Sophia Louise Yohe, Andrew Cook Nelson
The Journal of Molecular Diagnostics. Available online 8 June 2021.
Low frequency variants associated with leukocyte telomere length in the Singapore Chinese population
Xuling Chang, Resham L Gurung, Ling Wang, Aizhen Jin, Zheng Li, Renwei Wang, Kenneth B Beckman, Jennifer Adams-Haduch, Wee Yang Meah, Kar Seng Sim, Weng Khong Lim, Sonia Davila, Patrick Tan, Jing Xian Teo, Khung Keong Yeo, Yiamunaa M, Sylvia Liu, Su Chi Lim, Jianjun Liu, Rob M van Dam, Yechiel Friedlander, Woon-Puay Koh, Jian-Min Yuan, Chiea Chuen Khor, Chew-Kiat Heng, Rajkumar Dorajoo
Commun Biol. 2021 May 3;4(1):519.
Novel Microbial Groups Drive Productivity in an Archean Iron Formation
Cody S Sheik, Jonathan P Badalamenti, Jon Telling, David Hsu, Scott C Alexander, Daniel R Bond, Jeffrey A Gralnick, Barbara Sherwood Lollar, Brandy M Toner
Front Microbiol. 2021 Mar 30;12:627595. doi: 10.3389/fmicb.2021.627595.
Placentas delivered by pre-pregnant obese women have reduced abundance and diversity in the microbiome
Paula A. Benny, Fadhl M. Al-Akwaa, Corbin Dirkx, Ryan J. Schlueter, Thomas K. Wolfgruber, Ingrid Y. Chern, Suzie Hoops, Dan Knights, Lana X. Garmire
FASEB, doi.org/10.1096/fj.202002184RR. 2021 Mar 20.
Leukocyte telomere length, cancer incidence and all-cause mortality among Chinese adults: Singapore Chinese Health Study
Hamed Samavat, Hung N Luu, Kenneth B Beckman, Aizhen Jin, Renwei Wang, Woon-Puay Koh, Jian-Min Yuan
Int J Cancer. 2021 Jan 15;148(2):352-362.
2020
A rapid, cost-effective tailed amplicon method for sequencing SARS-CoV-2
Daryl M Gohl, John Garbe, Patrick Grady, Jerry Daniel, Ray H B Watson, Benjamin Auch, Andrew Nelson, Sophia Yohe, Kenneth B Beckman
Nucleic Acids Research. 2020 Dec 4;21(1):863.
Comparative analysis of genome-wide DNA methylation identifies patterns that associate with conserved transcriptional programs in osteosarcoma
Lauren J Mills, Milcah C Scott, Pankti Shah, Anne R Cunanan, Archana Deshpande, Benjamin Auch, Bridget Curtin, Kenneth B Beckman, Logan G Spector, Aaron L Sarver, Subbaya Subramanian, Todd A Richmond, Jaime F Modiano
Bone. 2020 Oct 27;115716. Online ahead of print.
Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium
Jessica K. Fiege, Joshua M. Thiede, Hezkiel Nanda, William E. Matchett, Patrick J. Moore, Noe Rico Montanari, Beth K. Thielen, Jerry Daniel, Emma Stanley, Ryan C. Hunter, Vineet D. Menachery, Steven S. Shen, Tyler D. Bold, Ryan A. Langlois
bioRxiv 343954. 2020 Oct 19.
Inhalation exposure to cigarette smoke and inflammatory agents induces epigenetic changes in the lung
Christopher L Seiler, J Ung Min Song, Delshanee Kotandeniya, Jianji Chen, Thomas J Y Kono, Qiyuan Han, Mathia Colwell, Benjamin Auch, Aaron L Sarver, Pramod Upadhyaya, Yanan Ren, Christopher Faulk, Silvio De Flora, Sebastiano La Maestra, Yue Chen, Fekadu Kassie, Natalia Y Tretyakova
Sci Rep. 2020 Jul 9;10(1):11290.
Diverse AR Gene Rearrangements Mediate Resistance to Androgen Receptor Inhibitors in Metastatic Prostate Cancer
Yingming Li, Rendong Yang, Christine M Henzler, Yeung Ho, Courtney Passow, Benjamin Auch, Suzanne Carreira, Daniel Nava Rodrigues, Claudia Bertan, Tae Hyun Hwang, David A Quigley, Ha X Dang, Colm Morrissey, Michael Frase, Stephen R Plymate, Christopher A Maher, Felix Y Feng, Johann S de Bono, Scott M Dehm
Clin Cancer Res. 2020 Apr 15;26(8):1965-1976.
Analytical Validation of a COVID-19 qRT-PCR Detection Assay Using a 384-well Format and Three Extraction Methods
Andrew C. Nelson, Benjamin Auch, Matthew Schomaker, Daryl M. Gohl, Patrick Grady, Darrell Johnson, Robyn Kincaid, Kylene E. Karnuth, Jerry Daniel, Jessica K. Fiege, Elizabeth J. Fay, Tyler Bold, Ryan A. Langlois, Kenneth B. Beckman, Sophia Yohe
bioRxiv. doi.org/10.1101/2020.04.02.022186. 2020 Apr 5.
2019
Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii
Nardini L, Holm I, Pain A, Bischoff E, Gohl DM, Zongo S, Guelbeogo W, Sagnon N, Vernick KD & Riehle MM.
Scientific Reports. 2019 Oct 24. 9(1):15275.
Association between mitochondrial genetic variation and breast cancer risk: The Multiethnic Cohort
Li Y, Giorgi E, Beckman KB, Caberto C, Kazma R, Lum-Jones A, Haiman C, Marchand L, Stram D, Saxena R, Cheng I.
PLos One. 2019 Oct 2. 14(10):e0222284.
Identification of Target Genes Mediated by Two-Component Regulators of Staphylococcus aureus Using RNA-Seq Technology
Lei T, Yang J, Becker AD, Ji Y.
Methods Mol Biol. 2019 Sept 16. 2020, 2069:125-138.
Genome projects in invasion biology
McCartney MA, Mallez S, Gohl DM.
Conservation Genetics. 2019 Sept 11. 20 (6):1201-1222.
Stress responses, M2 macrophages, and a distinct microbial signature in fatal intestinal acute graft-vesus-host disease
Holtan S, Shabaneh A, Betts B, Rashidi A, MacMillan M, Ustun C, Amin K, Vaughn B, Howard J, Khoruts A, Arora M, DeFor T, Johnson D, Blazar B, Weisdorf D, Wang J.
JCI Insight. 2019 Aug 8. 4(17):e129762.
Performance of gene expression analyses using de novo assembled transcripts in polyploid species.
Chen LY, Morales-Briones DF, Passow CN, Ya Y.
Bioinformatics. 2019 Aug 10. pii: btz620.
Long-term tolerance of islet allografts in nonhuman primates induced by apoptotic donor leukocytes.
Singh A, Ramachandran S, Graham ML, Daneshmandi S, Heller D, Suarez-Pinzon WL, Balamurugan AN, Ansite JD, Wilhelm JJ, Yang A, Zhang Y, Palani NP, Abrahante JE, Burlak C, Miller SD, Luo X, Hering BJ.
Nat Commun. 2019 Aug 2;10(1):3495.
The Genome of the Zebra Mussel, Dreissena polymorpha: A Resource for Invasive Species Research.
McCartney MA, Auch B, Kono T, Mallez S, Zhang Y, Obille A, Becker A, Abrahante JE, Garbe J, Badalamenti JP, Herman A, Mangelson H, Liachko I, Sullivan S, Sone ED, Koren S, Silverstein KAT, Beckman KB, Gohl DM.
bioRxiv 696732. 2019 July 9.
Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification.
Gohl DM, Magli A, Garbe J, Becker A, Johnson DM, Anderson S, Auch B, Billstein B, Froehling E, McDevitt SL, Beckman KB.
Genome Biol. 2019 Apr 29;20(1):85.
Loci for human leukocyte telomere length in the Singaporean Chinese population and transethnic genetic studies.
Dorajoo R, Chang X, Gurung RL, Li Z, Wang L, Wang R, Beckman KB, Adams-Haduch J, M Y, Liu S, Meah WY, Sim KS, Lim SC, Friedlander Y, Liu J, van Dam RM, Yuan JM, Koh WP, Khor CC, Heng CK.
Nat Commun. 2019 Jun 6;10(1):2491.
Next generation sequencing for clinical diagnostics: Five year experience of an academic laboratory.
Hartman P, Beckman K, Silverstein K, Yohe S, Schomaker M, Henzler C, Onsongo G, Lam HC, Munro S, Daniel J, Billstein B, Deshpande A, Hauge A, Mroz P, Lee W, Holle J, Wiens K, Karnuth K, Kemmer T, Leary M, Michel S, Pohlman L, Thayanithy V, Nelson A, Bower M, Thyagarajan B.
Mol Genet Metab Rep. 2019 Mar 1;19:100464.
Genomewide Assessment of Mycobacterium tuberculosis Conditionally Essential Metabolic Pathways.
Minato Y, Gohl DM, Thiede JM, Chacón JM, Harcombe WR, Maruyama F, Baughn AD.
mSystems. 2019 Jun 25;4(4). pii: e00070-19.
Resequencing Study Confirms Host Defense and Cell Senescence Gene Variants Contribute to the Risk of Idiopathic Pulmonary Fibrosis.
Moore C et al (including Beckman KB).
Am J Respir Crit Care Med. 2019 Apr 29.
2018
Evaluating the Information Content of Shallow Shotgun Metagenomics.
Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D.
mSystems. 2018 Nov 13;3(6). pii: e00069-18.
Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF.
Dale JL, Beckman KB, Willett JLE, Nilson JL, Palani NP, Baller JA, Hauge A, Gohl DM, Erickson R, Manias DA, Sadowsky MJ, Dunny GM.
mSystems. 2018 Sep 11;3(5). pii: e00062-18.
Optimization of a microfluidics-based next generation sequencing assay for clinical oncology diagnostics.
Henzler C, Schomaker M, Yang R, Lambert AP, LaRue R, Kincaid R, Beckman K, Kemmer T, Wilson J, Yohe S, Thyagarajan B, Nelson AC.
Ann Transl Med. 2018 May;6(9):162.
Leukocyte telomere length in relation to risk of lung adenocarcinoma incidence: Findings from the Singapore Chinese Health Study.
Yuan JM, Beckman KB, Wang R, Bull C, Adams-Haduch J, Huang JY, Jin A, Opresko P, Newman AB, Zheng YL, Fenech M, Koh WP.
Int J Cancer. 2018 Jun 1;142(11):2234-2243.
EditR: A Method to Quantify Base Editing from Sanger Sequencing.
Kluesner MG, Nedveck DA, Lahr WS, Garbe JR, Abrahante JE, Webber BR, Moriarity BS.
CRISPR J. 2018 Jun;1:239-250.
2017
The ecological landscape of microbiome science.
Gohl DM.
Nat Biotechnol. 2017 Nov;35(11):1047-1049.
Single-Strand Consensus Sequencing Reveals that HIV Type but not Subtype Significantly Impacts Viral Mutation Frequencies and Spectra.
Rawson JMO, Gohl DM, Landman SR, Roth ME, Meissner ME, Peterson TS, Hodges JS, Beckman KB, Mansky LM.
J Mol Biol. 2017 Jul 21;429(15):2290-2307.
Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells.
Winterhoff BJ, Maile M, Mitra AK, Sebe A, Bazzaro M, Geller MA, Abrahante JE, Klein M, Hellweg R, Mullany SA, Beckman K, Daniel J, Starr TK.
Gynecol Oncol. 2017 Mar;144(3):598-606.
Preferential suppression of Anopheles gambiae host sequences allows detection of the mosquito eukaryotic microbiome.
Belda E, Coulibaly B, Fofana A, Beavogui AH, Traore SF, Gohl DM, Vernick KD, Riehle MM.
Sci Rep. 2017 Jun 12;7(1):3241.
2016
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies.
Gohl DM, Vangay P, Garbe J, MacLean A, Hauge A, Becker A, Gould TJ, Clayton JB, Johnson TJ, Hunter R, Knights D, Beckman KB.
Nat Biotechnol. 2016 Sep;34(9):942-9.
Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia.
Fingerlin TE, Zhang W, Yang IV, Ainsworth HC, Russell PH, Blumhagen RZ, Schwarz MI, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch DA, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, du Bois RM, Garcia CK, Devine MS, Gudmundsson G, Isaksson HJ, Kaminski N, Zhang Y, Gibson KF, Lancaster LH, Maher TM, Molyneaux PL, Wells AU, Moffatt MF, Selman M, Pardo A, Kim DS, Crapo JD, Make BJ, Regan EA, Walek DS, Daniel JJ, Kamatani Y, Zelenika D, Murphy E, Smith K, McKean D, Pedersen BS, Talbert J, Powers J, Markin CR, Beckman KB, Lathrop M, Freed B, Langefeld CD, Schwartz DA.
BMC Genet. 2016 Jun 7;17(1):74.
No Association between the Mitochondrial Genome and Prostate Cancer Risk: The Multiethnic Cohort.
Giorgi EE, Li Y, Caberto CP, Beckman KB, Lum-Jones A, Haiman CA, Le Marchand L, Stram DO, Saxena R, Cheng I.
Cancer Epidemiol Biomarkers Prev. 2016 Jun;25(6):1001-3.
Toward clinical genomics in everyday medicine: perspectives and recommendations.
Delaney SK, Hultner ML, Jacob HJ, Ledbetter DH, McCarthy JJ, Ball M, Beckman KB, Belmont JW, Bloss CS, Christman MF, Cosgrove A, Damiani SA, Danis T, Delledonne M, Dougherty MJ, Dudley JT, Faucett WA, Friedman JR, Haase DH, Hays TS, Heilsberg S, Huber J, Kaminsky L, Ledbetter N, Lee WH, Levin E, Libiger O, Linderman M, Love RL, Magnus DC, Martland A, McClure SL, Megill SE, Messier H, Nussbaum RL, Palaniappan L, Patay BA, Popovich BW, Quackenbush J, Savant MJ, Su MM, Terry SF, Tucker S, Wong WT, Green RC.
Expert Rev Mol Diagn. 2016;16(5):521-32.
2015
Persistent microbial dysbiosis in preterm premature rupture of membranes from onset until delivery.
Baldwin EA, Walther-Antonio M, MacLean AM, Gohl DM, Beckman KB, Chen J, White B, Creedon DJ, Chia N.
PeerJ. 2015 Nov 26;3:e1398.
Association of Genes, Pathways, and Haplogroups of the Mitochondrial Genome with the Risk of Colorectal Cancer: The Multiethnic Cohort.
Li Y, Beckman KB, Caberto C, Kazma R, Lum-Jones A, Haiman CA, Le Marchand L, Stram DO, Saxena R, Cheng I.
PLoS One. 2015 Sep 4;10(9):e0136796.
mRNA 3‘-UTR shortening is a molecular signature of mTORC1 activation.
Chang JW, Zhang W, Yeh HS, de Jong EP, Jun S, Kim KH, Bae SS, Beckman K, Hwang TH, Kim KS, Kim DH, Griffin TJ, Kuang R, Yong J.
Nat Commun. 2015 Jun 15;6:7218.
Next generation sequencing in endocrine practice.
Forlenza GP, Calhoun A, Beckman KB, Halvorsen T, Hamdoun E, Zierhut H, Sarafoglou K, Polgreen LE, Miller BS, Nathan B, Petryk A.
Mol Genet Metab. 2015 Jun-Jul;115(2-3):61-71.
Clinical validation of targeted next-generation sequencing for inherited disorders.
Yohe S, Hauge A, Bunjer K, Kemmer T, Bower M, Schomaker M, Onsongo G, Wilson J, Erdmann J, Zhou Y, Deshpande A, Spears MD, Beckman K, Silverstein KA, Thyagarajan B.
Arch Pathol Lab Med. 2015 Feb;139(2):204-10.
2014
Genome-wide association study of breast cancer in Latinas identifies novel protective variants on 6q25.
Fejerman L, Ahmadiyeh N, Hu D, Huntsman S, Beckman KB, Caswell JL, Tsung K, John EM, Torres-Mejia G, Carvajal-Carmona L, Echeverry MM, Tuazon AM, Ramirez C; COLUMBUS Consortium, Gignoux CR, Eng C, Gonzalez-Burchard E, Henderson B, Le Marchand L, Kooperberg C, Hou L, Agalliu I, Kraft P, Lindström S, Perez-Stable EJ, Haiman CA, Ziv E.
Nat Commun. 2014 Oct 20;5:5260.
Implementation of Cloud based next generation sequencing data analysis in a clinical laboratory.
Onsongo G, Erdmann J, Spears MD, Chilton J, Beckman KB, Hauge A, Yohe S, Schomaker M, Bower M, Silverstein KA, Thyagarajan B.
BMC Res Notes. 2014 May 23;7:314.
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.
Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D.
Genome Res. 2014 Jan;24(1):14-24.
Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing.
Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, Shi J, Beckman K, Haudenschild C, McCormick C, Mei R, Gameroff MJ, Gindes H, Adams P, Goes FS, Mondimore FM, MacKinnon DF, Notes L, Schweizer B, Furman D, Montgomery SB, Urban AE, Koller D, Levinson DF.
Mol Psychiatry. 2014 Dec;19(12):1267-74.
Transcriptomic analysis of Staphylococcus aureus using microarray and advanced next-generation RNA-seq technologies.
Lei T, Becker A, Ji Y.
Methods Mol Biol. 2014;1085:213-29.
Identification of a new target of miR-16, Vacuolar Protein Sorting 4a.
Adhikari N, Guan W, Capaldo B, Mackey AJ, Carlson M, Ramakrishnan S, Walek D, Gupta M, Mitchell A, Eckman P, John R, Ashley E, Barton PJ, Hall JL.
PLoS One. 2014 Jul 17;9(7):e101509.
Vascular biomechanical properties in mice with smooth muscle specific deletion of Ndst1.
Adhikari N, Billaud M, Carlson M, Lake SP, Montaniel KR, Staggs R, Guan W, Walek D, Desir S, Isakson BE, Barocas VH, Hall JL.
Mol Cell Biochem. 2014 Jan;385(1-2):225-38.
Fed state prior to hemorrhagic shock and polytrauma in a porcine model results in altered liver transcriptomic response.
Determan C Jr, Anderson R, Becker A, Witowski N, Lusczek E, Mulier K, Beilman GJ.
PLoS One. 2014 Jun 17;9(6):e100088.
2013
Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis.
Fingerlin TE, Murphy E, Zhang W, Peljto AL, Brown KK, Steele MP, Loyd JE, Cosgrove GP, Lynch D, Groshong S, Collard HR, Wolters PJ, Bradford WZ, Kossen K, Seiwert SD, du Bois RM, Garcia CK, Devine MS, Gudmundsson G, Isaksson HJ, Kaminski N, Zhang Y, Gibson KF, Lancaster LH, Cogan JD, Mason WR, Maher TM, Molyneaux PL, Wells AU, Moffatt MF, Selman M, Pardo A, Kim DS, Crapo JD, Make BJ, Regan EA, Walek DS, Daniel JJ, Kamatani Y, Zelenika D, Smith K, McKean D, Pedersen BS, Talbert J, Kidd RN, Markin CR, Beckman KB, Lathrop M, Schwarz MI, Schwartz DA.
Nat Genet. 2013 Jun;45(6):613-20.
Genetic and environmental predictors of serum 25-hydroxyvitamin D concentrations among middle-aged and elderly Chinese in Singapore.
Robien K, Butler LM, Wang R, Beckman KB, Walek D, Koh WP, Yuan JM.
Br J Nutr. 2013 Feb 14;109(3):493-502.