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2. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B

Subjects
Microbiology, Biological Sciences, Developmental Biology, Biological sciences
Abstract

Following publication of the original article [1], it was reported that the article copyright was incorrect. The correct copyright statement is: © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. The original article [1] has been corrected.

Published
2021

3. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

Author

Olafson, Pia U, Aksoy, Serap, Attardo, Geoffrey M, Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J, Davis, Megan, Dykema, Justin, Emrich, Scott J, Friedrich, Markus, Holmes, Christopher J, Ioannidis, Panagiotis, Jansen, Evan N, Jennings, Emily C, Lawson, Daniel, Martinson, Ellen O, Maslen, Gareth L, Meisel, Richard P, Murphy, Terence D, Nayduch, Dana, Nelson, David R, Oyen, Kennan J, Raszick, Tyler J, Ribeiro, José MC, Robertson, Hugh M, Rosendale, Andrew J, Sackton, Timothy B, Saelao, Perot, Swiger, Sonja L, Sze, Sing-Hoi, Tarone, Aaron M, Taylor, David B, Warren, Wesley C, Waterhouse, Robert M, Weirauch, Matthew T, Werren, John H, Wilson, Richard K, Zdobnov, Evgeny M, and Benoit, Joshua B

Subjects
Chemoreceptor genes, Gene regulation, Insect adaptation, Insect immunity, Insect orthology, Metabolic detoxification genes, Muscid genomics, Opsin gene duplication, Stable fly genome, Biological Sciences, Developmental Biology
Abstract

BackgroundThe stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies.ResultsThis study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways.ConclusionsThe combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Published
2021

4. Bayesian Gamma-Negative Binomial Modeling of Single-Cell RNA Sequencing Data

Author

Dadaneh, Siamak Zamani, de Figueiredo, Paul, Sze, Sing-Hoi, Zhou, Mingyuan, and Qian, Xiaoning

Subjects
Statistics - Applications
Abstract

Background: Single-cell RNA sequencing (scRNA-seq) is a powerful profiling technique at the single-cell resolution. Appropriate analysis of scRNA-seq data can characterize molecular heterogeneity and shed light into the underlying cellular process to better understand development and disease mechanisms. The unique analytic challenge is to appropriately model highly over-dispersed scRNA-seq count data with prevalent dropouts (zero counts), making zero-inflated dimensionality reduction techniques popular for scRNA-seq data analyses. Employing zero-inflated distributions, however, may place extra emphasis on zero counts, leading to potential bias when identifying the latent structure of the data. Results: In this paper, we propose a fully generative hierarchical gamma-negative binomial (hGNB) model of scRNA-seq data, obviating the need for explicitly modeling zero inflation. At the same time, hGNB can naturally account for covariate effects at both the gene and cell levels to identify complex latent representations of scRNA-seq data, without the need for commonly adopted pre-processing steps such as normalization. Efficient Bayesian model inference is derived by exploiting conditional conjugacy via novel data augmentation techniques. Conclusion: Experimental results on both simulated data and several real-world scRNA-seq datasets suggest that hGNB is a powerful tool for cell cluster discovery as well as cell lineage inference.

Published
2019

5. Differential Expression Analysis of Dynamical Sequencing Count Data with a Gamma Markov Chain

Author

Hajiramezanali, Ehsan, Dadaneh, Siamak Zamani, de Figueiredo, Paul, Sze, Sing-Hoi, Zhou, Mingyuan, and Qian, Xiaoning

Subjects
Statistics - Applications, Quantitative Biology - Genomics, Statistics - Machine Learning
Abstract

Next-generation sequencing (NGS) to profile temporal changes in living systems is gaining more attention for deriving better insights into the underlying biological mechanisms compared to traditional static sequencing experiments. Nonetheless, the majority of existing statistical tools for analyzing NGS data lack the capability of exploiting the richer information embedded in temporal data. Several recent tools have been developed to analyze such data but they typically impose strict model assumptions, such as smoothness on gene expression dynamic changes. To capture a broader range of gene expression dynamic patterns, we develop the gamma Markov negative binomial (GMNB) model that integrates a gamma Markov chain into a negative binomial distribution model, allowing flexible temporal variation in NGS count data. Using Bayes factors, GMNB enables more powerful temporal gene differential expression analysis across different phenotypes or treatment conditions. In addition, it naturally handles the heterogeneity of sequencing depth in different samples, removing the need for ad-hoc normalization. Efficient Gibbs sampling inference of the GMNB model parameters is achieved by exploiting novel data augmentation techniques. Extensive experiments on both simulated and real-world RNA-seq data show that GMNB outperforms existing methods in both receiver operating characteristic (ROC) and precision-recall (PR) curves of differential expression analysis results., Comment: 30 pages, 7 figures

Published
2018

13. Global Reprogramming of Host Kinase Signaling in Response to Fungal Infection

Author

Pandey, Aseem, Ding, Sheng Li, Qin, Qing-Ming, Gupta, Rahul, Gomez, Gabriel, Lin, Furong, Feng, Xuehuan, Fachini da Costa, Luciana, Chaki, Sankar P., Katepalli, Madhu, Case, Elizabeth D., van Schaik, Erin J., Sidiq, Tabasum, Khalaf, Omar, Arenas, Angela, Kobayashi, Koichi S., Samuel, James E., Rivera, Gonzalo M., Alaniz, Robert C., Sze, Sing-Hoi, Qian, Xiaoning, Brown, William J., Rice-Ficht, Allison, Russell, William K., Ficht, Thomas A., and de Figueiredo, Paul

Published
2017
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20. Parameterized and Approximation Algorithms for the MAF Problem in Multifurcating Trees

Author

Chen, Jianer, Fan, Jia-Hao, Sze, Sing-Hoi, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Brandstädt, Andreas, editor, Jansen, Klaus, editor, and Reischuk, Rüdiger, editor

Published
2013
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24. Greedy Localization and Color-Coding: Improved Matching and Packing Algorithms

Author

Liu, Yang, Lu, Songjian, Chen, Jianer, Sze, Sing-Hoi, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Bodlaender, Hans L., editor, and Langston, Michael A., editor

Published
2006
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25. A Polynomial Time Solvable Formulation of Multiple Sequence Alignment

Author

Sze, Sing-Hoi, Lu, Yue, Yang, Qingwu, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Miyano, Satoru, editor, Mesirov, Jill, editor, Kasif, Simon, editor, and Pevzner, Pavel A., editor

Published
2005
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27. Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding

Author

Sze, Sing-Hoi, Lu, Songjian, Chen, Jianer, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Jonassen, Inge, editor, and Kim, Junhyong, editor

Published
2004
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29. Brucella activates the host RIDD pathway to subvert BLOS1-directed immune defense

Author

Wells, Kelsey Michelle, primary, He, Kai, additional, Pandey, Aseem, additional, Cabello, Ana, additional, Zhang, Dongmei, additional, Yang, Jing, additional, Gomez, Gabriel, additional, Liu, Yue, additional, Chang, Haowu, additional, Li, Xueqiang, additional, Zhang, Hao, additional, Feng, Xuehuang, additional, da Costa, Luciana Fachini, additional, Metz, Richard, additional, Johnson, Charles D, additional, Martin, Cameron Lee, additional, Skrobarczyk, Jill, additional, Berghman, Luc R, additional, Patrick, Kristin L, additional, Leibowitz, Julian, additional, Ficht, Allison, additional, Sze, Sing-Hoi, additional, Song, Jianxun, additional, Qian, Xiaoning, additional, Qin, Qing-Ming, additional, Ficht, Thomas A, additional, and de Figueiredo, Paul, additional

Published
2022
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33. Genome-Wide Identification of Genes Enabling Accurate Prediction of Hybrid Performance from Parents Across Environments and Populations for Gene-Based Breeding in Maize

Author

Zhang, Meiping, primary, Liu, Yun-Hua, additional, Wang, Yinglei, additional, Sze, Sing-Hoi, additional, Scheuring, Chantel F., additional, Qi, Xiaoli, additional, Ekinci, Ozge, additional, Pekar, Jacob, additional, Murray, Seth C., additional, and Zhang, Hong-Bin, additional

Published
2022
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34. Diverse pathogens activate the host RIDD pathway to subvert BLOS1-directed immune defense

Author

Wells, Kelsey, primary, He, Kai, additional, Pandey, Aseem, additional, Cabello, Ana, additional, Zhang, Dong-Mei, additional, Yang, Jing, additional, Gomez, Gabriel, additional, Liu, Yue, additional, Chang, Hao-Wu, additional, Li, Xue-Qing, additional, Zhang, Hao, additional, da Costa, Luciana Fachini, additional, Metz, Richard P., additional, Johnson, Charles D., additional, Martin, Cameron, additional, Skrobarczyk, Jill, additional, Berghman, Luc R., additional, Patrick, Kristin, additional, Leibowitz, Julian, additional, Rice-Ficht, Allison, additional, Sze, Sing-Hoi, additional, Qian, Xiaoning, additional, Qin, Qing-Ming, additional, Ficht, Thomas A., additional, and de Figueiredo, Paul, additional

Published
2021
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37. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control

Author

Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., Benoit, Joshua B., Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.

Abstract

Background: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. Results: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. Conclusions: The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Published
2021

38. Publisher Correction: The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control (BMC Biology, (2021), 19, 1, (41), 10.1186/s12915-021-00975-9)

Author

Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., Benoit, Joshua B., Olafson, Pia U., Aksoy, Serap, Attardo, Geoffrey M., Buckmeier, Greta, Chen, Xiaoting, Coates, Craig J., Davis, Megan, Dykema, Justin, Emrich, Scott J., Friedrich, Markus, Holmes, Christopher J., Ioannidis, Panagiotis, Jansen, Evan N., Jennings, Emily C., Lawson, Daniel, Martinson, Ellen O., Maslen, Gareth L., Meisel, Richard P., Murphy, Terence D., Nayduch, Dana, Nelson, David R., Oyen, Kennan J., Raszick, Tyler J., Ribeiro, José M.C., Robertson, Hugh M., Rosendale, Andrew J., Sackton, Timothy B., Saelao, Perot, Swiger, Sonja L., Sze, Sing Hoi, Tarone, Aaron M., Taylor, David B., Warren, Wesley C., Waterhouse, Robert M., Weirauch, Matthew T., Werren, John H., Wilson, Richard K., Zdobnov, Evgeny M., and Benoit, Joshua B.

Abstract

Following publication of the original article [1], it was reported that the article copyright was incorrect. The correct copyright statement is: © This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. The original article [1] has been corrected.

Published
2021

39. Identification of the syr-syp box in the promoter regions of genes dedicated to syringomycin and syringopeptin production by Pseudomonas syringae pv. syringae B301D

Author

Wang, Nian, Lu, Shi-En, Yang, Qingwu, Sze, Sing-Hoi, and Gross, Dennis C.

Subjects
Pseudomonas syringae -- Genetic aspects, Pseudomonas syringae -- Research, Gene expression -- Research, Genetic transcription -- Research, Biological sciences
Abstract

The phytotnxins syringopeptin and syringomycin are synthesized by nonribosomal peptide synthetases which are encoded by the syringomycin (syr) and syringopeptin (syp) genomic island of Pseudomonas syringae pv. syringae. Previous studies demonstrated that expression of the syr-syp genes was controlled by the salA-syrF regulator' pathway, which in turn was induced by plant signal molecules. In this study, the 132-kb syr-syp genomic island was found to be organized into five polycistronic operons along with eight individual genes based on reverse transcriptional PCR and bioinformatic analysis. The transcriptional start sites of the salA gene and operons III and IV were located 63, 75, and 104 bp upstream of the start codons of salA, syrP, and syrB1, respectively, using primer extension analysis. The predicted -10/ -35 promoter region of operon IV was confirmed based on deletion and site-directed mutagenesis analyses of the syrB1::uidA reporter with [beta]-glucuronidase assays. A 20-bp conserved sequence (TGtCccg[N.sub.6]cggGaCA, termed the syr-syp box) with dyad symmetry around the -35 region was identified via computer analysis for the syr-syp genes/operons responsible for biosynthesis and secretion of syringomycin and syringopeptin. Expression of the syrB1::uidA fusion was decreased 59% when 6 bp was deleted from the 5' end of the syr-syp box in the promoter region of operon IV. These results demonstrate that the conserved promoter sequences of the syr-syp genes contribute to the coregulation of syringomycin and syringopeptin production.

Published
2006

49. Promoter scanning during transcription initiation inSaccharomyces cerevisiae: Pol II in the “shooting gallery”

Author

Qiu, Chenxi, primary, Jin, Huiyan, additional, Vvedenskaya, Irina, additional, Llenas, Jordi Abante, additional, Zhao, Tingting, additional, Malik, Indranil, additional, Visbisky, Alex M., additional, Schwartz, Scott L., additional, Cui, Ping, additional, Čabart, Pavel, additional, Han, Kang Hoo, additional, Lai, William K. M., additional, Metz, Richard P., additional, Johnson, Charles D., additional, Sze, Sing-Hoi, additional, Pugh, B. Franklin, additional, Nickels, Bryce E., additional, and Kaplan, Craig D., additional

Published
2019
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