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1. Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing

Author

Gong, Binsheng, Li, Dan, Łabaj, Paweł P., Pan, Bohu, Novoradovskaya, Natalia, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Chen, Guangchun, Bergstrom Lucas, Anne, LoCoco, Jennifer S., Richmond, Todd A., Tseng, Elizabeth, Kusko, Rebecca, Happe, Scott, Mercer, Timothy R., Pabón-Peña, Carlos, Salmans, Michael, Tilgner, Hagen U., Xiao, Wenzhong, Johann, Jr, Donald J., Jones, Wendell, Tong, Weida, Mason, Christopher E., Kreil, David P., and Xu, Joshua

Published
2024
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3. Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project

Author

Gong, Binsheng, Li, Dan, Zhang, Yifan, Kusko, Rebecca, Lababidi, Samir, Cao, Zehui, Chen, Mingyang, Chen, Ning, Chen, Qiaochu, Chen, Qingwang, Dai, Jiacheng, Gan, Qiang, Gao, Yuechen, Guo, Mingkun, Hariani, Gunjan, He, Yujie, Hou, Wanwan, Jiang, He, Kushwaha, Garima, Li, Jian-Liang, Li, Jianying, Li, Yulan, Liu, Liang-Chun, Liu, Ruimei, Liu, Shiming, Meriaux, Edwin, Mo, Mengqing, Moore, Mathew, Moss, Tyler J., Niu, Quanne, Patel, Ananddeep, Ren, Luyao, Saremi, Nedda F., Shang, Erfei, Shang, Jun, Song, Ping, Sun, Siqi, Urban, Brent J., Wang, Danke, Wang, Shangzi, Wen, Zhining, Xiong, Xiangyi, Yang, Jingcheng, Yin, Lihui, Zhang, Chao, Zhang, Ruolan, Bhandari, Ambica, Cai, Wanshi, Eterovic, Agda Karina, Megherbi, Dalila B., Shi, Tieliu, Suo, Chen, Yu, Ying, Zheng, Yuanting, Novoradovskaya, Natalia, Sears, Renee L., Shi, Leming, Jones, Wendell, Tong, Weida, and Xu, Joshua

Published
2024
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4. Reporting guidelines for human microbiome research: the STORMS checklist

Author

Mirzayi, Chloe, Renson, Audrey, Zohra, Fatima, Elsafoury, Shaimaa, Geistlinger, Ludwig, Kasselman, Lora J, Eckenrode, Kelly, van de Wijgert, Janneke, Loughman, Amy, Marques, Francine Z, MacIntyre, David A, Arumugam, Manimozhiyan, Azhar, Rimsha, Beghini, Francesco, Bergstrom, Kirk, Bhatt, Ami, Bisanz, Jordan E, Braun, Jonathan, Bravo, Hector Corrada, Buck, Gregory A, Bushman, Frederic, Casero, David, Clarke, Gerard, Collado, Maria Carmen, Cotter, Paul D, Cryan, John F, Demmer, Ryan T, Devkota, Suzanne, Elinav, Eran, Escobar, Juan S, Fettweis, Jennifer, Finn, Robert D, Fodor, Anthony A, Forslund, Sofia, Franke, Andre, Furlanello, Cesare, Gilbert, Jack, Grice, Elizabeth, Haibe-Kains, Benjamin, Handley, Scott, Herd, Pamela, Holmes, Susan, Jacobs, Jonathan P, Karstens, Lisa, Knight, Rob, Knights, Dan, Koren, Omry, Kwon, Douglas S, Langille, Morgan, Lindsay, Brianna, McGovern, Dermot, McHardy, Alice C, McWeeney, Shannon, Mueller, Noel T, Nezi, Luigi, Olm, Matthew, Palm, Noah, Pasolli, Edoardo, Raes, Jeroen, Redinbo, Matthew R, Rühlemann, Malte, Balfour Sartor, R, Schloss, Patrick D, Schriml, Lynn, Segal, Eran, Shardell, Michelle, Sharpton, Thomas, Smirnova, Ekaterina, Sokol, Harry, Sonnenburg, Justin L, Srinivasan, Sujatha, Thingholm, Louise B, Turnbaugh, Peter J, Upadhyay, Vaibhav, Walls, Ramona L, Wilmes, Paul, Yamada, Takuji, Zeller, Georg, Zhang, Mingyu, Zhao, Ni, Zhao, Liping, Bao, Wenjun, Culhane, Aedin, Devanarayan, Viswanath, Dopazo, Joaquin, Fan, Xiaohui, Fischer, Matthias, Jones, Wendell, Kusko, Rebecca, Mason, Christopher E, Mercer, Tim R, Sansone, Susanna-Assunta, Scherer, Andreas, Shi, Leming, Thakkar, Shraddha, Tong, Weida, Wolfinger, Russ, Hunter, Christopher, Segata, Nicola, and Huttenhower, Curtis

Subjects
Human Genome, Genetics, Computational Biology, Dysbiosis, Humans, Microbiota, Observational Studies as Topic, Research Design, Translational Science, Biomedical, Genomic Standards Consortium, Massive Analysis and Quality Control Society, Medical and Health Sciences, Immunology
Abstract

The particularly interdisciplinary nature of human microbiome research makes the organization and reporting of results spanning epidemiology, biology, bioinformatics, translational medicine and statistics a challenge. Commonly used reporting guidelines for observational or genetic epidemiology studies lack key features specific to microbiome studies. Therefore, a multidisciplinary group of microbiome epidemiology researchers adapted guidelines for observational and genetic studies to culture-independent human microbiome studies, and also developed new reporting elements for laboratory, bioinformatics and statistical analyses tailored to microbiome studies. The resulting tool, called 'Strengthening The Organization and Reporting of Microbiome Studies' (STORMS), is composed of a 17-item checklist organized into six sections that correspond to the typical sections of a scientific publication, presented as an editable table for inclusion in supplementary materials. The STORMS checklist provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results.

Published
2021

5. Are Some Technologies Beyond Regulatory Regimes?

Author

Kusnezov, Dimitri and Jones, Wendell B.

Subjects
Physics - Physics and Society
Abstract

Regulatory frameworks are a common tool in governance to incent and coerce behaviors supporting national or strategic stability. This includes domestic regulations and international agreements. Though regulation is always a challenge, the domain of fast evolving threats, like cyber, are proving much more difficult to control. Many discussions are underway searching for approaches that can provide national security in these domains. We use game theoretic learning models to explore the question of strategic stability with respect to the democratization of certain technologies (such as cyber). We suggest that such many-player games could inherently be chaotic with no corresponding (Nash) equilibria. In the absence of such equilibria, traditional approaches, as measures to achieve levels of overall security, may not be suitable approaches to support strategic stability in these domains. Altogether new paradigms may be needed for these issues. At the very least, regulatory regimes that fail to address the basic nature of the technology domains should not be pursued as a default solution, regardless of success in other domains. In addition, the very chaotic nature of these domains may hold the promise of novel approaches to regulation., Comment: 9 pages

Published
2017

6. The Biomechanics of Fibrillin Microfibrils: Lessons from the Ciliary Zonule.

Author

Rathaur, Pooja, Rodriguez, Juan, Kuchtey, John, Insignares, Samuel, Jones, Wendell B., Kuchtey, Rachel W., and Bassnett, Steven

Subjects
CELL receptors, FIBRILLIN, MARFAN syndrome, EXTRACELLULAR matrix, CONNECTIVE tissues
Abstract

Marfan syndrome is an inherited connective tissue disorder that affects the cardiovascular, musculoskeletal, and ocular systems. It is caused by pathogenic variants in the fibrillin-1 gene (FBN1). Fibrillin is a primary component of microfibrils, which are found throughout the extracellular matrix (ECM) and provide elasticity and resilience to connective tissue. Microfibrils also play a role in signaling by sequestering growth factors and interacting with cell surface receptors. In many tissues, microfibrils are interwoven with elastin, collagens, and other elements of the ECM. However, uniquely in the ciliary zonule of the eye, microfibrils exist in cell-free bundles largely devoid of other components. This structure offers a rare opportunity to study a pure population of fibrillin microfibrils in a relatively native state. Here, we briefly review the organization of the zonule and describe recent experiments in which we measure zonular biomechanics, providing insights into microfibril dynamics that would be challenging to obtain in other contexts. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Author

Zhang, Yifan, Blomquist, Thomas M., Kusko, Rebecca, Stetson, Daniel, Zhang, Zhihong, Yin, Lihui, Sebra, Robert, Gong, Binsheng, Lococo, Jennifer S., Mittal, Vinay K., Novoradovskaya, Natalia, Yeo, Ji-Youn, Dominiak, Nicole, Hipp, Jennifer, Raymond, Amelia, Qiu, Fujun, Arib, Hanane, Smith, Melissa L., Brock, Jay E., Farkas, Daniel H., Craig, Daniel J., Crawford, Erin L., Li, Dan, Morrison, Tom, Tom, Nikola, Xiao, Wenzhong, Yang, Mary, Mason, Christopher E., Richmond, Todd A., Jones, Wendell, Johann, Jr, Donald J., Shi, Leming, Tong, Weida, Willey, James C., and Xu, Joshua

Published
2022
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10. Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA

Author

Willey, James C., Morrison, Tom B., Austermiller, Bradley, Crawford, Erin L., Craig, Daniel J., Blomquist, Thomas M., Jones, Wendell D., Wali, Aminah, Lococo, Jennifer S., Haseley, Nathan, Richmond, Todd A., Novoradovskaya, Natalia, Kusko, Rebecca, Chen, Guangchun, Li, Quan-Zhen, Johann, Donald J., Jr., Deveson, Ira W., Mercer, Timothy R., Wu, Leihong, and Xu, Joshua

Published
2021
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12. A B-Cell Gene Signature Correlates With the Extent of Gluten-Induced Intestinal Injury in Celiac Disease.

Author

Garber, Mitchell, Saldanha, Alok, Parker, Joel, Jones, Wendell, Kaukinen, Katri, Laurila, Kaija, Lähdeaho, Marja-Leena, Khatri, Purvesh, Khosla, Chaitan, Adelman, Daniel, and Mäki, Markku

Subjects
Autoimmunity, Cd, crypt depth, CeD, celiac disease, Mucosal Immunity, Oral Tolerance, Regulatory B Cell, TG2, transglutaminase 2, TR, T-cell receptor, Vh, villus height, Vh:Cd, ratio of villus height to crypt depth, cRNA, complementary RNA
Abstract

BACKGROUND & AIMS: Celiac disease (CeD) provides an opportunity to study autoimmunity and the transition in immune cells as dietary gluten induces small intestinal lesions. METHODS: Seventy-three celiac disease patients on a long-term, gluten-free diet ingested a known amount of gluten daily for 6 weeks. A peripheral blood sample and intestinal biopsy specimens were taken before and 6 weeks after initiating the gluten challenge. Biopsy results were reported on a continuous numeric scale that measured the villus-height-to-crypt-depth ratio to quantify gluten-induced intestinal injury. Pooled B and T cells were isolated from whole blood, and RNA was analyzed by DNA microarray looking for changes in peripheral B- and T-cell gene expression that correlated with changes in villus height to crypt depth, as patients maintained a relatively healthy intestinal mucosa or deteriorated in the face of a gluten challenge. RESULTS: Gluten-dependent intestinal damage from baseline to 6 weeks varied widely across all patients, ranging from no change to extensive damage. Genes differentially expressed in B cells correlated strongly with the extent of intestinal damage. A relative increase in B-cell gene expression correlated with a lack of sensitivity to gluten whereas their relative decrease correlated with gluten-induced mucosal injury. A core B-cell gene module, representing a subset of B-cell genes analyzed, accounted for the correlation with intestinal injury. CONCLUSIONS: Genes comprising the core B-cell module showed a net increase in expression from baseline to 6 weeks in patients with little to no intestinal damage, suggesting that these individuals may have mounted a B-cell immune response to maintain mucosal homeostasis and circumvent inflammation. DNA microarray data were deposited at the GEO repository (accession number: GSE87629; available: https://www.ncbi.nlm.nih.gov/geo/).

Published
2017

13. Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

Author

Xiao, Wenming, Ren, Luyao, Chen, Zhong, Fang, Li Tai, Zhao, Yongmei, Lack, Justin, Guan, Meijian, Zhu, Bin, Jaeger, Erich, Kerrigan, Liz, Blomquist, Thomas M., Hung, Tiffany, Sultan, Marc, Idler, Kenneth, Lu, Charles, Scherer, Andreas, Kusko, Rebecca, Moos, Malcolm, Xiao, Chunlin, Sherry, Stephen T., Abaan, Ogan D., Chen, Wanqiu, Chen, Xin, Nordlund, Jessica, Liljedahl, Ulrika, Maestro, Roberta, Polano, Maurizio, Drabek, Jiri, Vojta, Petr, Kõks, Sulev, Reimann, Ene, Madala, Bindu Swapna, Mercer, Timothy, Miller, Chris, Jacob, Howard, Truong, Tiffany, Moshrefi, Ali, Natarajan, Aparna, Granat, Ana, Schroth, Gary P., Kalamegham, Rasika, Peters, Eric, Petitjean, Virginie, Walton, Ashley, Shen, Tsai-Wei, Talsania, Keyur, Vera, Cristobal Juan, Langenbach, Kurt, de Mars, Maryellen, Hipp, Jennifer A., Willey, James C., Wang, Jing, Shetty, Jyoti, Kriga, Yuliya, Raziuddin, Arati, Tran, Bao, Zheng, Yuanting, Yu, Ying, Cam, Margaret, Jailwala, Parthav, Nguyen, Cu, Meerzaman, Daoud, Chen, Qingrong, Yan, Chunhua, Ernest, Ben, Mehra, Urvashi, Jensen, Roderick V., Jones, Wendell, Li, Jian-Liang, Papas, Brian N., Pirooznia, Mehdi, Chen, Yun-Ching, Seifuddin, Fayaz, Li, Zhipan, Liu, Xuelu, Resch, Wolfgang, Wang, Jingya, Wu, Leihong, Yavas, Gokhan, Miles, Corey, Ning, Baitang, Tong, Weida, Mason, Christopher E., Donaldson, Eric, Lababidi, Samir, Staudt, Louis M., Tezak, Zivana, Hong, Huixiao, Wang, Charles, and Shi, Leming

Published
2021
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15. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

Author

Gong, Binsheng, Li, Dan, Kusko, Rebecca, Novoradovskaya, Natalia, Zhang, Yifan, Wang, Shangzi, Pabón-Peña, Carlos, Zhang, Zhihong, Lai, Kevin, Cai, Wanshi, LoCoco, Jennifer S., Lader, Eric, Richmond, Todd A., Mittal, Vinay K., Liu, Liang-Chun, Johann, Jr, Donald J., Willey, James C., Bushel, Pierre R., Yu, Ying, Xu, Chang, Chen, Guangchun, Burgess, Daniel, Cawley, Simon, Giorda, Kristina, Haseley, Nathan, Qiu, Fujun, Wilkins, Katherine, Arib, Hanane, Attwooll, Claire, Babson, Kevin, Bao, Longlong, Bao, Wenjun, Lucas, Anne Bergstrom, Best, Hunter, Bhandari, Ambica, Bisgin, Halil, Blackburn, James, Blomquist, Thomas M., Boardman, Lisa, Burgher, Blake, Butler, Daniel J., Chang, Chia-Jung, Chaubey, Alka, Chen, Tao, Chierici, Marco, Chin, Christopher R., Close, Devin, Conroy, Jeffrey, Cooley Coleman, Jessica, Craig, Daniel J., Crawford, Erin, del Pozo, Angela, Deveson, Ira W., Duncan, Daniel, Eterovic, Agda Karina, Fan, Xiaohui, Foox, Jonathan, Furlanello, Cesare, Ghosal, Abhisek, Glenn, Sean, Guan, Meijian, Haag, Christine, Hang, Xinyi, Happe, Scott, Hennigan, Brittany, Hipp, Jennifer, Hong, Huixiao, Horvath, Kyle, Hu, Jianhong, Hung, Li-Yuan, Jarosz, Mirna, Kerkhof, Jennifer, Kipp, Benjamin, Kreil, David Philip, Łabaj, Paweł, Lapunzina, Pablo, Li, Peng, Li, Quan-Zhen, Li, Weihua, Li, Zhiguang, Liang, Yu, Liu, Shaoqing, Liu, Zhichao, Ma, Charles, Marella, Narasimha, Martín-Arenas, Rubén, Megherbi, Dalila B., Meng, Qingchang, Mieczkowski, Piotr A., Morrison, Tom, Muzny, Donna, Ning, Baitang, Parsons, Barbara L., Paweletz, Cloud P., Pirooznia, Mehdi, Qu, Wubin, Raymond, Amelia, Rindler, Paul, Ringler, Rebecca, Sadikovic, Bekim, Scherer, Andreas, Schulze, Egbert, Sebra, Robert, Shaknovich, Rita, Shi, Qiang, Shi, Tieliu, Silla-Castro, Juan Carlos, Smith, Melissa, López, Mario Solís, Song, Ping, Stetson, Daniel, Strahl, Maya, Stuart, Alan, Supplee, Julianna, Szankasi, Philippe, Tan, Haowen, Tang, Lin-ya, Tao, Yonghui, Thakkar, Shraddha, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Thodima, Venkat J., Thomas, David, Tichý, Boris, Tom, Nikola, Garcia, Elena Vallespin, Verma, Suman, Walker, Kimbley, Wang, Charles, Wang, Junwen, Wang, Yexun, Wen, Zhining, Wirta, Valtteri, Wu, Leihong, Xiao, Chunlin, Xiao, Wenzhong, Xu, Shibei, Yang, Mary, Ying, Jianming, Yip, Shun H., Zhang, Guangliang, Zhang, Sa, Zhao, Meiru, Zheng, Yuanting, Zhou, Xiaoyan, Mason, Christopher E., Mercer, Timothy, Tong, Weida, Shi, Leming, Jones, Wendell, and Xu, Joshua

Published
2021
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16. A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

Author

Jones, Wendell, Gong, Binsheng, Novoradovskaya, Natalia, Li, Dan, Kusko, Rebecca, Richmond, Todd A., Johann, Jr, Donald J., Bisgin, Halil, Sahraeian, Sayed Mohammad Ebrahim, Bushel, Pierre R., Pirooznia, Mehdi, Wilkins, Katherine, Chierici, Marco, Bao, Wenjun, Basehore, Lee Scott, Lucas, Anne Bergstrom, Burgess, Daniel, Butler, Daniel J., Cawley, Simon, Chang, Chia-Jung, Chen, Guangchun, Chen, Tao, Chen, Yun-Ching, Craig, Daniel J., del Pozo, Angela, Foox, Jonathan, Francescatto, Margherita, Fu, Yutao, Furlanello, Cesare, Giorda, Kristina, Grist, Kira P., Guan, Meijian, Hao, Yingyi, Happe, Scott, Hariani, Gunjan, Haseley, Nathan, Jasper, Jeff, Jurman, Giuseppe, Kreil, David Philip, Łabaj, Paweł, Lai, Kevin, Li, Jianying, Li, Quan-Zhen, Li, Yulong, Li, Zhiguang, Liu, Zhichao, López, Mario Solís, Miclaus, Kelci, Miller, Raymond, Mittal, Vinay K., Mohiyuddin, Marghoob, Pabón-Peña, Carlos, Parsons, Barbara L., Qiu, Fujun, Scherer, Andreas, Shi, Tieliu, Stiegelmeyer, Suzy, Suo, Chen, Tom, Nikola, Wang, Dong, Wen, Zhining, Wu, Leihong, Xiao, Wenzhong, Xu, Chang, Yu, Ying, Zhang, Jiyang, Zhang, Yifan, Zhang, Zhihong, Zheng, Yuanting, Mason, Christopher E., Willey, James C., Tong, Weida, Shi, Leming, and Xu, Joshua

Published
2021
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17. HOXA4/HOXB3 gene expression signature as a biomarker of recurrence in patients with high-grade serous ovarian cancer following primary cytoreductive surgery and first-line adjuvant chemotherapy

Author

Miller, Katherine R., Patel, Jai N., Zhang, Qing, Norris, Eric J., Symanowski, James, Michener, Chad, Sehouli, Jalid, Braicu, Ioana, Destephanis, Darla D., Sutker, Ashley P., Jones, Wendell, Livasy, Chad A., Biscotti, Charles, Ganapathi, Ram N., Tait, David L., and Ganapathi, Mahrukh K.

Published
2018
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21. Figure S6 from CBP/p300 Drives the Differentiation of Regulatory T Cells through Transcriptional and Non-Transcriptional Mechanisms

Author

Castillo, Joseph, primary, Wu, Esther, primary, Lowe, Christopher, primary, Srinivasan, Shrividhya, primary, McCord, Ron, primary, Wagle, Marie-Claire, primary, Jayakar, Sangeeta, primary, Edick, Melissa Gonzalez, primary, Eastham-Anderson, Jeffrey, primary, Liu, Bonnie, primary, Hutchinson, Katherine E., primary, Jones, Wendell, primary, Stokes, Matthew P., primary, Tarighat, Somayeh S., primary, Holcomb, Thomas, primary, Glibicky, Andrew, primary, Romero, F. Anthony, primary, Magnuson, Steven, primary, Huang, Shih-Min A., primary, Plaks, Vicki, primary, Giltnane, Jennifer M., primary, Lackner, Mark R., primary, and Mounir, Zineb, primary

Published
2023
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22. Table S1 to S5 from CBP/p300 Drives the Differentiation of Regulatory T Cells through Transcriptional and Non-Transcriptional Mechanisms

Author

Castillo, Joseph, primary, Wu, Esther, primary, Lowe, Christopher, primary, Srinivasan, Shrividhya, primary, McCord, Ron, primary, Wagle, Marie-Claire, primary, Jayakar, Sangeeta, primary, Edick, Melissa Gonzalez, primary, Eastham-Anderson, Jeffrey, primary, Liu, Bonnie, primary, Hutchinson, Katherine E., primary, Jones, Wendell, primary, Stokes, Matthew P., primary, Tarighat, Somayeh S., primary, Holcomb, Thomas, primary, Glibicky, Andrew, primary, Romero, F. Anthony, primary, Magnuson, Steven, primary, Huang, Shih-Min A., primary, Plaks, Vicki, primary, Giltnane, Jennifer M., primary, Lackner, Mark R., primary, and Mounir, Zineb, primary

Published
2023
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23. Data from CBP/p300 Drives the Differentiation of Regulatory T Cells through Transcriptional and Non-Transcriptional Mechanisms

Author

Castillo, Joseph, primary, Wu, Esther, primary, Lowe, Christopher, primary, Srinivasan, Shrividhya, primary, McCord, Ron, primary, Wagle, Marie-Claire, primary, Jayakar, Sangeeta, primary, Edick, Melissa Gonzalez, primary, Eastham-Anderson, Jeffrey, primary, Liu, Bonnie, primary, Hutchinson, Katherine E., primary, Jones, Wendell, primary, Stokes, Matthew P., primary, Tarighat, Somayeh S., primary, Holcomb, Thomas, primary, Glibicky, Andrew, primary, Romero, F. Anthony, primary, Magnuson, Steven, primary, Huang, Shih-Min A., primary, Plaks, Vicki, primary, Giltnane, Jennifer M., primary, Lackner, Mark R., primary, and Mounir, Zineb, primary

Published
2023
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24. AntiVEGF therapy vs Ozurdex for the treatment of Diabetic Macular Edema

Author

Jones, Wendell

Subjects
endocrine system diseases, genetic structures, eye diseases
Abstract

Diabetic Macular Edema (DME) is the leading cause of vision loss in patients with diabetes due to accumulation of fluid in the retina. The accumulation of fluid in the retina is beleived to be caused by upregulation of VEGF in retina. AntiVEGF therapy is the gold standard for the treatment of DME. Although effective, approximately two thirds of patients treated DME do not respond to antiVEGF therapy and continue to loss vision, suggesting an underlying mechanism. Recent studies suggest that inflammation plays a key role in development of DME. Ozurdex is a multi-potent corticosteroid that inhibits VEGF and inflammatory cytokines but, the use of Ozurdex for the treatment of DME has yet to be investigated. To determine whether Ozurdex is an effective treatment for DME, 100 randomized patients will receive monthly injections of Ozurdex or antiVEGF therapy for 12 months. The data collected in this study will serve as a pivotal dataset for future investigators to determine the appropriate course of treatment for the management of DME.

Published
2023
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31. Additional file 1 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Author

Zhang, Yifan, Blomquist, Thomas M., Kusko, Rebecca, Stetson, Daniel, Zhang, Zhihong, Yin, Lihui, Sebra, Robert, Gong, Binsheng, Lococo, Jennifer S., Mittal, Vinay K., Novoradovskaya, Natalia, Yeo, Ji-Youn, Dominiak, Nicole, Hipp, Jennifer, Raymond, Amelia, Qiu, Fujun, Arib, Hanane, Smith, Melissa L., Brock, Jay E., Farkas, Daniel H., Craig, Daniel J., Crawford, Erin L., Li, Dan, Morrison, Tom, Tom, Nikola, Xiao, Wenzhong, Yang, Mary, Mason, Christopher E., Richmond, Todd A., Jones, Wendell, Johann, Donald J., Shi, Leming, Tong, Weida, Willey, James C., and Xu, Joshua

Abstract

Additional file 1: Fig. S1. Detection and confirmation of sample contamination. Fig. S2. Violin plots of the false positive rate for fresh DNA samples versus QC passed inner FFPE samples in three panel regions (whole panel, within the CTR, or outside of the CTR). Fig. S3. Impact of additional VAF cutoffs on the FPR and sensitivity for each FFPE sample type.

Published
2022
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32. Additional file 4 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Author

Zhang, Yifan, Blomquist, Thomas M., Kusko, Rebecca, Stetson, Daniel, Zhang, Zhihong, Yin, Lihui, Sebra, Robert, Gong, Binsheng, Lococo, Jennifer S., Mittal, Vinay K., Novoradovskaya, Natalia, Yeo, Ji-Youn, Dominiak, Nicole, Hipp, Jennifer, Raymond, Amelia, Qiu, Fujun, Arib, Hanane, Smith, Melissa L., Brock, Jay E., Farkas, Daniel H., Craig, Daniel J., Crawford, Erin L., Li, Dan, Morrison, Tom, Tom, Nikola, Xiao, Wenzhong, Yang, Mary, Mason, Christopher E., Richmond, Todd A., Jones, Wendell, Johann, Donald J., Shi, Leming, Tong, Weida, Willey, James C., and Xu, Joshua

Abstract

Additional file 4. Visual Summary for FFPE materials preparation.

Published
2022
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33. Additional file 5 of Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples

Author

Zhang, Yifan, Blomquist, Thomas M., Kusko, Rebecca, Stetson, Daniel, Zhang, Zhihong, Yin, Lihui, Sebra, Robert, Gong, Binsheng, Lococo, Jennifer S., Mittal, Vinay K., Novoradovskaya, Natalia, Yeo, Ji-Youn, Dominiak, Nicole, Hipp, Jennifer, Raymond, Amelia, Qiu, Fujun, Arib, Hanane, Smith, Melissa L., Brock, Jay E., Farkas, Daniel H., Craig, Daniel J., Crawford, Erin L., Li, Dan, Morrison, Tom, Tom, Nikola, Xiao, Wenzhong, Yang, Mary, Mason, Christopher E., Richmond, Todd A., Jones, Wendell, Johann, Donald J., Shi, Leming, Tong, Weida, Willey, James C., and Xu, Joshua

Abstract

Additional file 5: Table S1. List of detailed information for four participating oncology panels.

Published
2022
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35. Baby Steps.

Author

Jones, Wendell H.

Abstract

A harried school counselor describes a tangled web of domestic discord and agency miscoordination (complicated by an unintelligible restraining order and a birth certificate mix-up) that try his patience and leave a young girl bereft of family. Dakota Stages's gutsiness and resiliency impress this counselor immensely. (MLH)

Published
1997

37. Transparency and reproducibility in artificial intelligence

Author

Haibe-Kains, Benjamin, Adam, George Alexandru, Hosny, Ahmed, Khodakarami, Farnoosh, Shraddha, Thakkar, Kusko, Rebecca, Sansone, Susanna-Assunta, Tong, Weida, Wolfinger, Russ D., Mason, Christopher E., Jones, Wendell, Dopazo, Joaquin, Furlanello, Cesare, Waldron, Levi, Wang, Bo, McIntosh, Chris, Goldenberg, Anna, Kundaje, Anshul, Greene, Casey S., Broderick, Tamara, Hoffman, Michael M., Leek, Jeffrey T., Korthauer, Keegan, Huber, Wolfgang, Brazma, Alvis, Pineau, Joelle, Tibshirani, Robert, Hastie, Trevor, Ioannidis, John P. A., Quackenbush, John, Aerts, Hugo J. W. L., RS: Carim - B06 Imaging, Beeldvorming, and MUMC+: DA BV Research (9)

Subjects
Reproducibility, Multidisciplinary, Computer science, Reproducibility of Results, Breast Neoplasms, Transparency (behavior), Data science, Article, United Kingdom, United States, Artificial Intelligence, AI, Humans, Female, Early Detection of Cancer, Algorithms, Mammography
Abstract

Breakthroughs in artificial intelligence (AI) hold enormous potential as it can automate complex tasks and go even beyond human performance. In their study, McKinney et al. showed the high potential of AI for breast cancer screening. However, the lack of methods’ details and algorithm code undermines its scientific value. Here, we identify obstacles hindering transparent and reproducible AI research as faced by McKinney et al., and provide solutions to these obstacles with implications for the broader field.

Published
2020
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39. Sandia National Laboratories Strategic Context Workshop Series 2017: National Security Futures for Strategic Thinking.

Author

Keller, Elizabeth, primary, Roll, Elizabeth, additional, Aamir, Munaf, additional, Bull, Diana, additional, Deland, Sharon, additional, Haddal, Chad, additional, Passell, Howard, additional, Foley, John, additional, Harwell, Amber, additional, Otis, Monique, additional, Backus, George, additional, Jones, Wendell, additional, Bawden, Michael, additional, Craft, Richard, additional, Kistin, David, additional, Martin, Jeffrey, additional, McNicol, Bradley, additional, Vannoni, Michael, additional, Trost, Lawrence, additional, Tsao, Jeffrey, additional, and Weaver, Karla, additional

Published
2018
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42. Views of Our Readers

Author

Bloch, Charles J., Randall, Claude, Clark, Edward J., Williams, John R., Freund, Arthur J., Jackson, Percival E., Angerstein, George W., Jones, Wendell R., Gutman, Paul, Buchanan, Lloyd, and Smith, John W. Brabner

Published
1962

44. Using RNA sample titrations to assess microarray platform performance and normalization techniques

Author

Shippy, Richard, Fulmer-Smentek, Stephanie, Jensen, Roderick V, Jones, Wendell D, Wolber, Paul K, Johnson, Charles D, Pine, P Scott, Boysen, Cecilie, Guo, Xu, Chudin, Eugene, Sun, Yongming Andrew, Willey, James C, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Setterquist, Robert A, Wilson, Mike, Lucas, Anne Bergstrom, Novoradovskaya, Natalia, Papallo, Adam, Turpaz, Yaron, Baker, Shawn C, Warrington, Janet A, Shi, Leming, and Herman, Damir

Published
2006
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45. Advancing quality-control for NGS measurement of actionable mutations in circulating tumor DNA

Author

Willey, James C., primary, Morrison, Tom, additional, Austermiller, Brad, additional, Crawford, Erin L., additional, Craig, Daniel J., additional, Blomquist, Thomas M., additional, Jones, Wendell D., additional, Wali, Aminah, additional, Lococo, Jennifer S., additional, Haseley, Nathan, additional, Richmond, Todd A., additional, Novoradovskaya, Natalia, additional, Kusko, Rebecca, additional, Chen, Guangchun, additional, Li, Quan-Zhen, additional, Johann, Don, additional, Deveson, Ira W., additional, Mercer, Tim, additional, Wu, Leihong, additional, and Xu, Joshua, additional

Published
2021
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46. Footprint of Sandia's August 15 2016 Informal Idea Exploration Session on "Towards an Engineering and Applied Science of Research".

Author

Tsao, Jeffrey, primary, Fleming Lindsley, Elizabeth, additional, Heffelfinger, Grant, additional, Narayanamurti, Venkatesh, additional, Schneider, Rick, additional, Starkweather, Lynne, additional, Ting, Christina, additional, Yajima, Rieko, additional, Bauer, Travis, additional, Coltrin, Michael, additional, Guy, Donald, additional, Jones, Wendell, additional, Mareda, John, additional, Nenoff, Tina, additional, and Turnley, Jessica, additional

Published
2017
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48. The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

Author

Su Zhenqiang, Shippy Richard, Puri Raj K, Peterson Ron L, Mei Nan, Ma Yunqing, Luo Yuling, Li Quan-Zhen, Kawasaki Ernest S, Hong Huixiao, Herman Damir, Han Jing, Guo Xu, Fuscoe James C, Frueh Felix W, Fan Xiao-hui, Collins Patrick J, Chu Tzu-Ming, Bertholet Vincent, Cao Xiaoxi, Bao Wenjun, Barbacioru Catalin C, Amur Shashi, Qian Feng, Fang Hong, Boysen Cecilie, Croner Lisa J, Guo Lei, Goodsaid Federico M, Perkins Roger G, Harris Stephen C, Jensen Roderick V, Jones Wendell D, Shi Leming, Sun Yongming, Sun Hongmei, Thorn Brett, Turpaz Yaron, Wang Charles, Wang Sue, Warrington Janet A, Willey James C, Wu Jie, Xie Qian, Zhang Liang, Zhang Lu, Zhong Sheng, Wolfinger Russell D, and Tong Weida

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists. Results Using the data sets generated by the MicroArray Quality Control (MAQC) project, we investigated the impact on the reproducibility of DEG lists of a few widely used gene selection procedures. We present comprehensive results from inter-site comparisons using the same microarray platform, cross-platform comparisons using multiple microarray platforms, and comparisons between microarray results and those from TaqMan – the widely regarded "standard" gene expression platform. Our results demonstrate that (1) previously reported discordance between DEG lists could simply result from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion with a non-stringent P-value cutoff filtering, the DEG lists become much more reproducible, especially when fewer genes are selected as differentially expressed, as is the case in most microarray studies; and (3) the instability of short DEG lists solely based on P-value ranking is an expected mathematical consequence of the high variability of the t-values; the more stringent the P-value threshold, the less reproducible the DEG list is. These observations are also consistent with results from extensive simulation calculations. Conclusion We recommend the use of FC-ranking plus a non-stringent P cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists. Specifically, the P-value cutoff should not be stringent (too small) and FC should be as large as possible. Our results provide practical guidance to choose the appropriate FC and P-value cutoffs when selecting a given number of DEGs. The FC criterion enhances reproducibility, whereas the P criterion balances sensitivity and specificity.

Published
2008
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