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3. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

Author

Nattestad, Maria, Goodwin, Sara, Ng, Karen, Baslan, Timour, Sedlazeck, Fritz J, Rescheneder, Philipp, Garvin, Tyler, Fang, Han, Gurtowski, James, Hutton, Elizabeth, Tseng, Elizabeth, Chin, Chen-Shan, Beck, Timothy, Sundaravadanam, Yogi, Kramer, Melissa, Antoniou, Eric, McPherson, John D, Hicks, James, McCombie, W Richard, and Schatz, Michael C

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Breast Cancer, Cancer, Biotechnology, 2.1 Biological and endogenous factors, Aetiology, Breast Neoplasms, Female, Gene Amplification, Gene Rearrangement, Genome, Human, Genomic Structural Variation, High-Throughput Nucleotide Sequencing, Humans, MCF-7 Cells, Oncogenes, Receptor, ErbB-2, Repetitive Sequences, Nucleic Acid, Transcriptome, Receptor, erbB-2, Medical and Health Sciences, Bioinformatics
Abstract

The SK-BR-3 cell line is one of the most important models for HER2+ breast cancers, which affect one in five breast cancer patients. SK-BR-3 is known to be highly rearranged, although much of the variation is in complex and repetitive regions that may be underreported. Addressing this, we sequenced SK-BR-3 using long-read single molecule sequencing from Pacific Biosciences and develop one of the most detailed maps of structural variations (SVs) in a cancer genome available, with nearly 20,000 variants present, most of which were missed by short-read sequencing. Surrounding the important ERBB2 oncogene (also known as HER2), we discover a complex sequence of nested duplications and translocations, suggesting a punctuated progression. Full-length transcriptome sequencing further revealed several novel gene fusions within the nested genomic variants. Combining long-read genome and transcriptome sequencing enables an in-depth analysis of how SVs disrupt the genome and sheds new light on the complex mechanisms involved in cancer genome evolution.

Published
2018

4. MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication

Author

Cahn, Jonathan, primary, Regulski, Michael, additional, Lynn, Jason, additional, Ernst, Evan, additional, Alves, Cristiane de Santis, additional, Ramakrishnan, Srividya, additional, Chougule, Kapeel, additional, Wei, Sharon, additional, Lu, Zhenyuan, additional, Xu, Xiaosa, additional, Drenkow, Jorg, additional, Kramer, Melissa, additional, Seetharam, Arun, additional, Hufford, Matthew B., additional, McCombie, W. Richard, additional, Ware, Doreen, additional, Jackson, David, additional, Schatz, Michael C., additional, Gingeras, Thomas R., additional, and Martienssen, Robert A., additional

Published
2024
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5. Design and Synthesis of Clinical Candidate PF-06852231 (CVL-231): A Brain Penetrant, Selective, Positive Allosteric Modulator of the M4 Muscarinic Acetylcholine Receptor.

Author

Butler, Christopher R., Popiolek, Michael, McAllister, Laura A., LaChapelle, Erik A., Kramer, Melissa, Beck, Elizabeth M., Mente, Scot, Brodney, Michael A., Brown, Matthew, Gilbert, Adam, Helal, Chris, Ogilvie, Kevin, Starr, Jeremy, Uccello, Daniel, Grimwood, Sarah, Edgerton, Jeremy, Garst-Orozco, Jonathan, Kozak, Rouba, Lotarski, Susan, and Rossi, Amie

Published
2024
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6. Design and Synthesis of Clinical Candidate PF-06852231 (CVL-231): A Brain Penetrant, Selective, Positive Allosteric Modulator of the M4Muscarinic Acetylcholine Receptor

Author

Butler, Christopher R., Popiolek, Michael, McAllister, Laura A., LaChapelle, Erik A., Kramer, Melissa, Beck, Elizabeth M., Mente, Scot, Brodney, Michael A., Brown, Matthew, Gilbert, Adam, Helal, Chris, Ogilvie, Kevin, Starr, Jeremy, Uccello, Daniel, Grimwood, Sarah, Edgerton, Jeremy, Garst-Orozco, Jonathan, Kozak, Rouba, Lotarski, Susan, Rossi, Amie, Smith, Deborah, O’Connor, Rebecca, Lazzaro, John, Steppan, Claire, and Steyn, Stefanus J.

Abstract

Selective activation of the M4muscarinic acetylcholine receptor subtype offers a novel strategy for the treatment of psychosis in multiple neurological disorders. Although the development of traditional muscarinic activators has been stymied due to pan-receptor activation, muscarinic receptor subtype selectivity can be achieved through the utilization of a subtype of a unique allosteric site. A major challenge in capitalizing on this allosteric site to date has been achieving a balance of suitable potency and brain penetration. Herein, we describe the design of a brain penetrant series of M4selective positive allosteric modulators (PAMs), ultimately culminating in the identification of 21 (PF-06852231, now CVL-231/emraclidine), which is under active clinical development as a novel mechanism and approach for the treatment of schizophrenia.

Published
2024
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7. Evaluating the quality of life impact of recurrent urinary tract infection: Validation and refinement of the Recurrent UTI Impact Questionnaire (RUTIIQ).

Author

Newlands, Abigail F., Kramer, Melissa, Roberts, Lindsey, Maxwell, Kayleigh, Price, Jessica L., and Finlay, Katherine A.

Subjects
URINARY tract infections, QUALITY of life, PATIENT experience, PATIENT reported outcome measures, PSYCHOMETRICS
Abstract

Background and Aims: Recurrent urinary tract infection (rUTI) has significant negative consequences for a wide variety of quality of life (QoL) domains. Without adequate validation and assessment of the unique insights of people living with rUTI, clinical results cannot be fully understood. The Recurrent UTI Impact Questionnaire (RUTIIQ), a novel patient‐reported outcome measure of rUTI psychosocial impact, has been robustly developed with extensive patient and clinician input to facilitate enhanced rUTI management and research. This study aimed to confirm the structural validity of the RUTIIQ, assessing its strength and bifactor model fit. Methods: A sample of 389 adults experiencing rUTI (96.9% female, aged 18–87 years) completed an online cross‐sectional survey comprising a demographic questionnaire and the RUTIIQ. A bifactor graded response model was fitted to the data, optimizing the questionnaire structure based on item fit, discrimination capability, local dependence, and differential item functioning. Results: The final RUTIIQ demonstrated excellent bifactor model fit (RMSEA = 0.054, CFI = 0.99, SRMSR = 0.052), and mean‐square fit indices indicated that all included items were productive for measurement (MNSQ = 0.52–1.41). The final questionnaire comprised an 18‐item general "rUTI QoL impact" factor, and five subfactor domains measuring "personal wellbeing" (three items), "social wellbeing" (four items), "work and activity interference" (four items), "patient satisfaction" (four items), and "sexual wellbeing" (three items). Together, the general factor and five subfactors explained 81.6% of the common model variance. All factor loadings were greater than 0.30 and communalities greater than 0.60, indicating good model fit and structural validity. Conclusions: The 18‐item RUTIIQ is a robust, patient‐tested questionnaire with excellent psychometric properties, which capably assesses the patient experience of rUTI‐related impact to QoL and healthcare satisfaction. Facilitating standardized patient monitoring and improved shared decision‐making, the RUTIIQ delivers the unique opportunity to improve patient‐centered care. [ABSTRACT FROM AUTHOR]

Published
2024
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12. The genome of the Wollemi pine, a critically endangered “living fossil” unchanged since the Cretaceous, reveals extensive ancient transposon activity

Author

Stevenson, Dennis Wm., primary, Ramakrishnan, Srividya, additional, Alves, Cristiane de Santis, additional, Coelho, Laís Araujo, additional, Kramer, Melissa, additional, Goodwin, Sara, additional, Ramos, Olivia Mendevil, additional, Eshel, Gil, additional, Sondervan, Veronica M., additional, Frangos, Samantha, additional, Zumajo-Cardona, Cecilia, additional, Jenike, Katherine, additional, Ou, Shujun, additional, Wang, Xiaojin, additional, Lee, Yin Peng, additional, Loke, Stella, additional, Rossetto, Maurizio, additional, McPherson, Hannah, additional, Nigris, Sebastiano, additional, Moschin, Silvia, additional, Little, Damon P., additional, Katari, Manpreet S., additional, Varala, Kranthi, additional, Kolokotronis, Sergios-Orestis, additional, Ambrose, Barbara, additional, Croft, Larry J., additional, Coruzzi, Gloria M., additional, Schatz, Michael, additional, McCombie, W. Richard, additional, and Martienssen, Robert A., additional

Published
2023
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13. Mutations in the pancreatic secretory enzymes CPA1 and CPB1 are associated with pancreatic cancer

Author

Tamura, Koji, Yu, Jun, Hata, Tatsuo, Suenaga, Masaya, Shindo, Koji, Abe, Toshiya, MacGregor-Das, Anne, Borges, Michael, Wolfgang, Christopher L., Weiss, Matthew J., He, Jin, Canto, Marcia Irene, Petersen, Gloria M., Gallinger, Steven, Syngal, Sapna, Brand, Randall E., Rustgi, Anil, Olson, Sara H., Stoffel, Elena, Cote, Michele L., Zogopoulos, George, Potash, James B., Goes, Fernando S., McCombie, Richard W., Zandi, Peter P., Pirooznia, Mehdi, Kramer, Melissa, Parla, Jennifer, Eshleman, James R., Roberts, Nicholas J., Hruban, Ralph H., Klein, Alison Patricia, and Goggins, Michael

Published
2018

17. Detailed analysis of a contiguous 22-Mb region of the maize genome.

Author

Wei, Fusheng, Stein, Joshua C, Liang, Chengzhi, Zhang, Jianwei, Fulton, Robert S, Baucom, Regina S, De Paoli, Emanuele, Zhou, Shiguo, Yang, Lixing, Han, Yujun, Pasternak, Shiran, Narechania, Apurva, Zhang, Lifang, Yeh, Cheng-Ting, Ying, Kai, Nagel, Dawn H, Collura, Kristi, Kudrna, David, Currie, Jennifer, Lin, Jinke, Kim, Hyeran, Angelova, Angelina, Scara, Gabriel, Wissotski, Marina, Golser, Wolfgang, Courtney, Laura, Kruchowski, Scott, Graves, Tina A, Rock, Susan M, Adams, Stephanie, Fulton, Lucinda A, Fronick, Catrina, Courtney, William, Kramer, Melissa, Spiegel, Lori, Nascimento, Lydia, Kalyanaraman, Ananth, Chaparro, Cristian, Deragon, Jean-Marc, Miguel, Phillip San, Jiang, Ning, Wessler, Susan R, Green, Pamela J, Yu, Yeisoo, Schwartz, David C, Meyers, Blake C, Bennetzen, Jeffrey L, Martienssen, Robert A, McCombie, W Richard, Aluru, Srinivas, Clifton, Sandra W, Schnable, Patrick S, Ware, Doreen, Wilson, Richard K, and Wing, Rod A

Subjects
Chromosomes, Plant, Sorghum, Zea mays, DNA Transposable Elements, RNA, Plant, Physical Chromosome Mapping, Evolution, Molecular, Gene Rearrangement, Gene Duplication, Base Sequence, Base Pairing, Sequence Homology, Nucleic Acid, Synteny, Mutation, Genes, Plant, Genome, Plant, Open Reading Frames, Molecular Sequence Data, Genetic Loci, Oryza, Chromosomes, Plant, Evolution, Molecular, Genes, Genome, RNA, Sequence Homology, Nucleic Acid, Genetics, Developmental Biology
Abstract

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.

Published
2009

18. The real-time fMRI neurofeedback based stratification of Default Network Regulation Neuroimaging data repository

Author

McDonald, Amalia R., Muraskin, Jordan, Dam, Nicholas T.Van, Froehlich, Caroline, Puccio, Benjamin, Pellman, John, Bauer, Clemens C.C., Akeyson, Alexis, Breland, Melissa M., Calhoun, Vince D., Carter, Steven, Chang, Tiffany P., Gessner, Chelsea, Gianonne, Alyssa, Giavasis, Steven, Glass, Jamie, Homann, Steven, King, Margaret, Kramer, Melissa, Landis, Drew, Lieval, Alexis, Lisinski, Jonathan, Mackay-Brandt, Anna, Miller, Brittny, Panek, Laura, Reed, Hayley, Santiago, Christine, Schoell, Eszter, Sinnig, Richard, Sital, Melissa, Taverna, Elise, Tobe, Russell, Trautman, Kristin, Varghese, Betty, Walden, Lauren, Wang, Runtang, Waters, Abigail B., Wood, Dylan C., Castellanos, F.Xavier, Leventhal, Bennett, Colcombe, Stanley J., LaConte, Stephen, Milham, Michael P., and Craddock, R.Cameron

Published
2017
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20. Supplementary Material from Transcriptional Silencing of ALDH2 Confers a Dependency on Fanconi Anemia Proteins in Acute Myeloid Leukemia

Author

Yang, Zhaolin, primary, Wu, Xiaoli S., primary, Wei, Yiliang, primary, Polyanskaya, Sofya A., primary, Iyer, Shruti V., primary, Jung, Moonjung, primary, Lach, Francis P., primary, Adelman, Emmalee R., primary, Klingbeil, Olaf, primary, Milazzo, Joseph P., primary, Kramer, Melissa, primary, Demerdash, Osama E., primary, Chang, Kenneth, primary, Goodwin, Sara, primary, Hodges, Emily, primary, McCombie, W. Richard, primary, Figueroa, Maria E., primary, Smogorzewska, Agata, primary, and Vakoc, Christopher R., primary

Published
2023
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21. Supplementary Table S1 from Transcriptional Silencing of ALDH2 Confers a Dependency on Fanconi Anemia Proteins in Acute Myeloid Leukemia

Author

Yang, Zhaolin, primary, Wu, Xiaoli S., primary, Wei, Yiliang, primary, Polyanskaya, Sofya A., primary, Iyer, Shruti V., primary, Jung, Moonjung, primary, Lach, Francis P., primary, Adelman, Emmalee R., primary, Klingbeil, Olaf, primary, Milazzo, Joseph P., primary, Kramer, Melissa, primary, Demerdash, Osama E., primary, Chang, Kenneth, primary, Goodwin, Sara, primary, Hodges, Emily, primary, McCombie, W. Richard, primary, Figueroa, Maria E., primary, Smogorzewska, Agata, primary, and Vakoc, Christopher R., primary

Published
2023
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22. Supplementary Table 1 from SLC5A3-Dependent Myo-inositol Auxotrophy in Acute Myeloid Leukemia

Author

Wei, Yiliang, primary, Huang, Yu-Han, primary, Skopelitis, Damianos S., primary, Iyer, Shruti V., primary, Costa, Ana S.H., primary, Yang, Zhaolin, primary, Kramer, Melissa, primary, Adelman, Emmalee R., primary, Klingbeil, Olaf, primary, Demerdash, Osama E., primary, Polyanskaya, Sofya A., primary, Chang, Kenneth, primary, Goodwin, Sara, primary, Hodges, Emily, primary, McCombie, W. Richard, primary, Figueroa, Maria E., primary, and Vakoc, Christopher R., primary

Published
2023
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23. Data from Whole Genome Sequencing Defines the Genetic Heterogeneity of Familial Pancreatic Cancer

Author

Roberts, Nicholas J., primary, Norris, Alexis L., primary, Petersen, Gloria M., primary, Bondy, Melissa L., primary, Brand, Randall, primary, Gallinger, Steven, primary, Kurtz, Robert C., primary, Olson, Sara H., primary, Rustgi, Anil K., primary, Schwartz, Ann G., primary, Stoffel, Elena, primary, Syngal, Sapna, primary, Zogopoulos, George, primary, Ali, Syed Z., primary, Axilbund, Jennifer, primary, Chaffee, Kari G., primary, Chen, Yun-Ching, primary, Cote, Michele L., primary, Childs, Erica J., primary, Douville, Christopher, primary, Goes, Fernando S., primary, Herman, Joseph M., primary, Iacobuzio-Donahue, Christine, primary, Kramer, Melissa, primary, Makohon-Moore, Alvin, primary, McCombie, Richard W., primary, McMahon, K. Wyatt, primary, Niknafs, Noushin, primary, Parla, Jennifer, primary, Pirooznia, Mehdi, primary, Potash, James B., primary, Rhim, Andrew D., primary, Smith, Alyssa L., primary, Wang, Yuxuan, primary, Wolfgang, Christopher L., primary, Wood, Laura D., primary, Zandi, Peter P., primary, Goggins, Michael, primary, Karchin, Rachel, primary, Eshleman, James R., primary, Papadopoulos, Nickolas, primary, Kinzler, Kenneth W., primary, Vogelstein, Bert, primary, Hruban, Ralph H., primary, and Klein, Alison P., primary

Published
2023
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24. Supplementary Tables S1 - S12 from Whole Genome Sequencing Defines the Genetic Heterogeneity of Familial Pancreatic Cancer

Author

Roberts, Nicholas J., primary, Norris, Alexis L., primary, Petersen, Gloria M., primary, Bondy, Melissa L., primary, Brand, Randall, primary, Gallinger, Steven, primary, Kurtz, Robert C., primary, Olson, Sara H., primary, Rustgi, Anil K., primary, Schwartz, Ann G., primary, Stoffel, Elena, primary, Syngal, Sapna, primary, Zogopoulos, George, primary, Ali, Syed Z., primary, Axilbund, Jennifer, primary, Chaffee, Kari G., primary, Chen, Yun-Ching, primary, Cote, Michele L., primary, Childs, Erica J., primary, Douville, Christopher, primary, Goes, Fernando S., primary, Herman, Joseph M., primary, Iacobuzio-Donahue, Christine, primary, Kramer, Melissa, primary, Makohon-Moore, Alvin, primary, McCombie, Richard W., primary, McMahon, K. Wyatt, primary, Niknafs, Noushin, primary, Parla, Jennifer, primary, Pirooznia, Mehdi, primary, Potash, James B., primary, Rhim, Andrew D., primary, Smith, Alyssa L., primary, Wang, Yuxuan, primary, Wolfgang, Christopher L., primary, Wood, Laura D., primary, Zandi, Peter P., primary, Goggins, Michael, primary, Karchin, Rachel, primary, Eshleman, James R., primary, Papadopoulos, Nickolas, primary, Kinzler, Kenneth W., primary, Vogelstein, Bert, primary, Hruban, Ralph H., primary, and Klein, Alison P., primary

Published
2023
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25. Supplementary Figures S1-S17 from SLC5A3-Dependent Myo-inositol Auxotrophy in Acute Myeloid Leukemia

Author

Wei, Yiliang, primary, Huang, Yu-Han, primary, Skopelitis, Damianos S., primary, Iyer, Shruti V., primary, Costa, Ana S.H., primary, Yang, Zhaolin, primary, Kramer, Melissa, primary, Adelman, Emmalee R., primary, Klingbeil, Olaf, primary, Demerdash, Osama E., primary, Polyanskaya, Sofya A., primary, Chang, Kenneth, primary, Goodwin, Sara, primary, Hodges, Emily, primary, McCombie, W. Richard, primary, Figueroa, Maria E., primary, and Vakoc, Christopher R., primary

Published
2023
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26. Data from Transcriptional Silencing of ALDH2 Confers a Dependency on Fanconi Anemia Proteins in Acute Myeloid Leukemia

Author

Yang, Zhaolin, primary, Wu, Xiaoli S., primary, Wei, Yiliang, primary, Polyanskaya, Sofya A., primary, Iyer, Shruti V., primary, Jung, Moonjung, primary, Lach, Francis P., primary, Adelman, Emmalee R., primary, Klingbeil, Olaf, primary, Milazzo, Joseph P., primary, Kramer, Melissa, primary, Demerdash, Osama E., primary, Chang, Kenneth, primary, Goodwin, Sara, primary, Hodges, Emily, primary, McCombie, W. Richard, primary, Figueroa, Maria E., primary, Smogorzewska, Agata, primary, and Vakoc, Christopher R., primary

Published
2023
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27. Data from SLC5A3-Dependent Myo-inositol Auxotrophy in Acute Myeloid Leukemia

Author

Wei, Yiliang, primary, Huang, Yu-Han, primary, Skopelitis, Damianos S., primary, Iyer, Shruti V., primary, Costa, Ana S.H., primary, Yang, Zhaolin, primary, Kramer, Melissa, primary, Adelman, Emmalee R., primary, Klingbeil, Olaf, primary, Demerdash, Osama E., primary, Polyanskaya, Sofya A., primary, Chang, Kenneth, primary, Goodwin, Sara, primary, Hodges, Emily, primary, McCombie, W. Richard, primary, Figueroa, Maria E., primary, and Vakoc, Christopher R., primary

Published
2023
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28. Supplementary Table 2 from SLC5A3-Dependent Myo-inositol Auxotrophy in Acute Myeloid Leukemia

Author

Wei, Yiliang, primary, Huang, Yu-Han, primary, Skopelitis, Damianos S., primary, Iyer, Shruti V., primary, Costa, Ana S.H., primary, Yang, Zhaolin, primary, Kramer, Melissa, primary, Adelman, Emmalee R., primary, Klingbeil, Olaf, primary, Demerdash, Osama E., primary, Polyanskaya, Sofya A., primary, Chang, Kenneth, primary, Goodwin, Sara, primary, Hodges, Emily, primary, McCombie, W. Richard, primary, Figueroa, Maria E., primary, and Vakoc, Christopher R., primary

Published
2023
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30. Data from Patient-Derived Triple-Negative Breast Cancer Organoids Provide Robust Model Systems That Recapitulate Tumor Intrinsic Characteristics

Author

Bhatia, Sonam, primary, Kramer, Melissa, primary, Russo, Suzanne, primary, Naik, Payal, primary, Arun, Gayatri, primary, Brophy, Kyle, primary, Andrews, Peter, primary, Fan, Cheng, primary, Perou, Charles M., primary, Preall, Jonathan, primary, Ha, Taehoon, primary, Plenker, Dennis, primary, Tuveson, David A., primary, Rishi, Arvind, primary, Wilkinson, John E., primary, McCombie, W. Richard, primary, Kostroff, Karen, primary, and Spector, David L., primary

Published
2023
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31. Supplementary Data from Patient-Derived Triple-Negative Breast Cancer Organoids Provide Robust Model Systems That Recapitulate Tumor Intrinsic Characteristics

Author

Bhatia, Sonam, primary, Kramer, Melissa, primary, Russo, Suzanne, primary, Naik, Payal, primary, Arun, Gayatri, primary, Brophy, Kyle, primary, Andrews, Peter, primary, Fan, Cheng, primary, Perou, Charles M., primary, Preall, Jonathan, primary, Ha, Taehoon, primary, Plenker, Dennis, primary, Tuveson, David A., primary, Rishi, Arvind, primary, Wilkinson, John E., primary, McCombie, W. Richard, primary, Kostroff, Karen, primary, and Spector, David L., primary

Published
2023
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32. Creating a value-driven Digital Identity Future: Engaging multiple stakeholders in strategic dialogues to balance values in the emergent ecosystem of digital identity in Europe

Author

Kramer, Melissa (author) and Kramer, Melissa (author)

Abstract

We live in an increasingly complex world in which policy regulations and system development must balance technology, existing regulations and all the people participating in the system. Currently, digital identities facilitate multiple verification processes in multiple contexts. For example, to give the ability to prove their own identity to buy alcohol or verify within the work environment, for as a healthcare practitioner. Experts and the EU Commission see unmet needs and problems within the digital identity field, which led to the revision process of eIDAS 2.0 to include the missed objectives of the present regulation on electronic identification and trust services, creating the rules for electronic transactions in the internal market. For example, identity theft rises, privacy concerns towards big tech grow, and there is little to no interoperability between sectors and borders (European Commission, 2021). This thesis explored the ongoing development process through a systemic approach and the lens of Value Sensitive Design (VSD) (Van Den Hoven et.al., 2015). A research-by-design approach uncovers the values and uniqueness of multiple stakeholders and provides new perspectives on the emergent system dynamics of digital identity. The EU Commission Vision on the EUDI Wallet was used as starting point to explore stakeholder values (Users¹, Relying Parties², Experts / Oversight Perspective³) and engage them in the future by still acting as the experts of their own experiences. Value tensions and risks are mapped to showcase the future implications of wrongly managed decisions in the process from a system perspective. Based on the systemic approach, a vision for all coming verification processes is created as the development is just a starting process for what is coming next within the wallet development field. The vision aims to help facilitate a way to include the values and mental models of different parties in the creation process of digital i, Strategic Product Design

Published
2023

34. Resensitizing daclatasvir-resistant hepatitis C variants by allosteric modulation of NS5A

Author

Sun, Jin-Hua, O'Boyle, II, Donald R., Fridell, Robert A., Langley, David R., Wang, Chunfu, Roberts, Susan B., Nower, Peter, Johnson, Benjamin M., Moulin, Frederic, Nophsker, Michelle J., Wang, Ying-Kai, Liu, Mengping, Rigat, Karen, Tu, Yong, Hewawasam, Piyasena, Kadow, John, Meanwell, Nicholas A., Cockett, Mark, Lemm, Julie A., Kramer, Melissa, and Belema, Makonen

Subjects
Phosphoproteins -- Health aspects, Hepatitis C -- Drug therapy, Drug sensitization -- Methods, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

It is estimated that more than 170 million people are infected with hepatitis C virus (HCV) worldwide (1,2). Clinical trials have demonstrated that, for the first time in human history, [...]

Published
2015

35. Development of BET Inhibitors as Potential Treatments for Cancer: Optimization of Pharmacokinetic Properties

Author

Hill, Matthew D., primary, Fang, Haiquan, additional, Norris, Derek, additional, Delucca, George V., additional, Huang, Hong, additional, DeBenedetto, Mikkel, additional, Quesnelle, Claude, additional, Schmitz, William D., additional, Tokarski, John S., additional, Sheriff, Steven, additional, Yan, Chunhong, additional, Fanslau, Caroline, additional, Haarhoff, Zuzana, additional, Huang, Christine, additional, Kramer, Melissa, additional, Madari, Shilpa, additional, Menard, Krista, additional, Monereau, Laura, additional, Morrison, John, additional, Raghavan, Nirmala, additional, Shields, Eric E., additional, Simmermacher-Mayer, Jean, additional, Sinz, Michael, additional, Tye, Ching Kim, additional, Westhouse, Richard, additional, Xie, Chunshan, additional, Zhang, Haiying, additional, Zhang, Lisa, additional, Zvyaga, Tatyana, additional, Lee, Francis, additional, Gavai, Ashvinikumar V., additional, and Degnan, Andrew P., additional

Published
2022
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37. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

Author

Luo, Ming-Cheng, Gu, Yong Q., You, Frank M., Deal, Karin R., Ma, Yaqin, Hu, Yuqin, Huo, Naxin, Wang, Yi, Wang, Jirui, Chen, Shiyong, Jorgensen, Chad M., Zhang, Yong, McGuire, Patrick E., Pasternak, Shiran, Stein, Joshua C., Ware, Doreen, Kramer, Melissa, McCombie, W. Richard, Kianian, Shahryar F., Martis, Mihaela M., Mayer, Klaus F. X., Sehgal, Sunish K., Li, Wanlong, Gill, Bikram S., Bevan, Michael W., Šimková, Hana, Doležel, Jaroslav, Weining, Song, Lazo, Gerard R., Anderson, Olin D., and Dvorak, Jan

Published
2013

38. Familial long-read sequencing increases yield of de novo mutations

Author

Noyes, Michelle D., primary, Harvey, William T., additional, Porubsky, David, additional, Sulovari, Arvis, additional, Li, Ruiyang, additional, Rose, Nicholas R., additional, Audano, Peter A., additional, Munson, Katherine M., additional, Lewis, Alexandra P., additional, Hoekzema, Kendra, additional, Mantere, Tuomo, additional, Graves-Lindsay, Tina A., additional, Sanders, Ashley D., additional, Goodwin, Sara, additional, Kramer, Melissa, additional, Mokrab, Younes, additional, Zody, Michael C., additional, Hoischen, Alexander, additional, Korbel, Jan O., additional, McCombie, W. Richard, additional, and Eichler, Evan E., additional

Published
2022
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39. Patient-Derived Triple-Negative Breast Cancer Organoids Provide Robust Model Systems That Recapitulate Tumor Intrinsic Characteristics

Author

Bhatia, Sonam, primary, Kramer, Melissa, additional, Russo, Suzanne, additional, Naik, Payal, additional, Arun, Gayatri, additional, Brophy, Kyle, additional, Andrews, Peter, additional, Fan, Cheng, additional, Perou, Charles M., additional, Preall, Jonathan, additional, Ha, Taehoon, additional, Plenker, Dennis, additional, Tuveson, David A., additional, Rishi, Arvind, additional, Wilkinson, John E., additional, McCombie, W. Richard, additional, Kostroff, Karen, additional, and Spector, David L., additional

Published
2022
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41. The B73 Maize Genome: Complexity, Diversity, and Dynamics

Author

Schnable, Patrick S., Ware, Doreen, Fulton, Robert S., Stein, Joshua C., Wei, Fusheng, Pasternak, Shiran, Liang, Chengzhi, Zhang, Jianwei, Fulton, Lucinda, Graves, Tina A., Minx, Patrick, Reily, Amy Denise, Courtney, Laura, Kruchowski, Scott S., Tomlinson, Chad, Strong, Cindy, Delehaunty, Kim, Fronick, Catrina, Courtney, Bill, Rock, Susan M., Belter, Eddie, Du, Feiyu, Kim, Kyung, Abbott, Rachel M., Cotton, Marc, Levy, Andy, Marchetto, Pamela, Ochoa, Kerri, Jackson, Stephanie M., Gillam, Barbara, Chen, Weizu, Yan, Le, Higginbotham, Jamey, Cardenas, Marco, Waligorski, Jason, Applebaum, Elizabeth, Phelps, Lindsey, Falcone, Jason, Kanchi, Krishna, Thane, Thynn, Scimone, Adam, Thane, Nay, Henke, Jessica, Wang, Tom, Ruppert, Jessica, Shah, Neha, Rotter, Kelsi, Hodges, Jennifer, Ingenthron, Elizabeth, Cordes, Matt, Kohlberg, Sara, Sgro, Jennifer, Delgado, Brandon, Mead, Kelly, Chinwalla, Asif, Leonard, Shawn, Crouse, Kevin, Collura, Kristi, Kudrna, Dave, Currie, Jennifer, He, Ruifeng, Angelova, Angelina, Rajasekar, Shanmugam, Mueller, Teri, Lomeli, Rene, Scara, Gabriel, Ko, Ara, Delaney, Krista, Wissotski, Marina, Lopez, Georgina, Campos, David, Braidotti, Michele, Ashley, Elizabeth, Golser, Wolfgang, Kim, HyeRan, Lee, Seunghee, Lin, Jinke, Dujmic, Zeljko, Kim, Woojin, Talag, Jayson, Zuccolo, Andrea, Fan, Chuanzhu, Sebastian, Aswathy, Kramer, Melissa, Spiegel, Lori, Nascimento, Lidia, Zutavern, Theresa, Miller, Beth, Ambroise, Claude, Muller, Stephanie, Spooner, Will, Narechania, Apurva, Ren, Liya, Wei, Sharon, Kumari, Sunita, Faga, Ben, Levy, Michael J., McMahan, Linda, Van Buren, Peter, Vaughn, Matthew W., Ying, Kai, Yeh, Cheng-Ting, Emrich, Scott J., Jia, Yi, Kalyanaraman, Ananth, Hsia, An-Ping, Barbazuk, W. Brad, Baucom, Regina S., Brutnell, Thomas P., Carpita, Nicholas C., Chaparro, Cristian, Chia, Jer-Ming, Deragon, Jean-Marc, Estill, James C., Fu, Yan, Jeddeloh, Jeffrey A., Han, Yujun, Lee, Hyeran, Li, Pinghua, Lisch, Damon R., Liu, Sanzhen, Liu, Zhijie, Nagel, Dawn Holligan, McCann, Maureen C., SanMiguel, Phillip, Myers, Alan M., Nettleton, Dan, Nguyen, John, Penning, Bryan W., Ponnala, Lalit, Schneider, Kevin L., Schwartz, David C., Sharma, Anupma, Soderlund, Carol, Springer, Nathan M., Sun, Qi, Wang, Hao, Waterman, Michael, Westerman, Richard, Wolfgruber, Thomas K., Yang, Lixing, Yu, Yeisoo, Zhang, Lifang, Zhou, Shiguo, Zhu, Qihui, Bennetzen, Jeffrey L., Dawe, R. Kelly, Jiang, Jiming, Jiang, Ning, Presting, Gernot G., Wessler, Susan R., Aluru, Srinivas, Martienssen, Robert A., Clifton, Sandra W., McCombie, W. Richard, Wing, Rod A., and Wilson, Richard K.

Published
2009
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43. Development of BET inhibitors as potential treatments for cancer: A new carboline chemotype

Author

Hill, Matthew D., Quesnelle, Claude, Tokarski, John, Fang, Haiquan, Fanslau, Carolynn, Haarhoff, Zuzana, Kramer, Melissa, Madari, Shilpa, Wiebesiek, Amy, Morrison, John, Simmermacher-Mayer, Jean, Sinz, Michael, Westhouse, Richard, Xie, Chunshan, Zhao, Jiuqiao, Huang, Lisa, Sheriff, Steven, Yan, Chunhong, Marsilio, Frank, Everlof, Gerry, Zvyaga, Tatyana, Lee, Francis, Gavai, Ashvinikumar V., and Degnan, Andrew P.

Published
2021
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44. Exome Sequencing of Familial Bipolar Disorder

Author

Goes, Fernando S., Pirooznia, Mehdi, Parla, Jennifer S., Kramer, Melissa, Ghiban, Elena, Mavruk, Senem, Chen, Yun-Ching, Monson, Eric T., Willour, Virginia L., Karchin, Rachel, Flickinger, Matthew, Locke, Adam E., Levy, Shawn E., Scott, Laura J., Boehnke, Michael, Stahl, Eli, Moran, Jennifer L., Hultman, Christina M., Landén, Mikael, Purcell, Shaun M., Sklar, Pamela, Zandi, Peter P., McCombie, W. Richard, and Potash, James B.

Published
2016
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45. Development of BET inhibitors as potential treatments for cancer: A search for structural diversity

Author

Hill, Matthew D., Fang, Haiquan, Tokarski, John, Fanslau, Carolynn, Haarhoff, Zuzana, Huang, Christine, Kramer, Melissa, Menard, Krista, Monereau, Laura, Morrison, John, Ranasinghe, Asoka, Shields, Eric E., Tye, Ching Kim, Westhouse, Richard, Everlof, Gerry, Sheriff, Steven, Yan, Chunhong, Marsilio, Frank, Zhang, Lisa, Zvyaga, Tatyana, Lee, Francis, Gavai, Ashvinikumar V., and Degnan, Andrew P.

Published
2021
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46. SLC5A3-Dependent Myo-inositol Auxotrophy in Acute Myeloid Leukemia

Author

Wei, Yiliang, primary, Huang, Yu-Han, additional, Skopelitis, Damianos S., additional, Iyer, Shruti V., additional, Costa, Ana S.H., additional, Yang, Zhaolin, additional, Kramer, Melissa, additional, Adelman, Emmalee R., additional, Klingbeil, Olaf, additional, Demerdash, Osama E., additional, Polyanskaya, Sofya A., additional, Chang, Kenneth, additional, Goodwin, Sara, additional, Hodges, Emily, additional, McCombie, W. Richard, additional, Figueroa, Maria E., additional, and Vakoc, Christopher R., additional

Published
2021
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47. Patient-derived triple negative breast cancer organoids provide robust model systems that recapitulate tumor intrinsic characteristics

Author

Bhatia, Sonam, primary, Kramer, Melissa, additional, Russo, Suzanne, additional, Naik, Payal, additional, Arun, Gayatri, additional, Brophy, Kyle, additional, Andrews, Peter, additional, Fan, Cheng, additional, Perou, Charles M., additional, Preall, Jonathan, additional, Ha, Taehoon, additional, Rishi, Arvind, additional, Wilkinson, J Erby, additional, McCombie, W. Richard, additional, Kostroff, Karen, additional, and Spector, David L., additional

Published
2021
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49. Analysis of the bread wheat genome using whole-genome shotgun sequencing

Author

Brenchley, Rachel, Spannagl, Manuel, Pfeifer, Matthias, Barker, Gary L.A., D'Amore, Rosalinda, Allen, Alexandra M., McKenzie, Neil, Kramer, Melissa, Kerhornou, Arnaud, Bolser, Dan, Kay, Suzanne, Waite, Darren, Trick, Martin, Bancroft, Ian, Gu, Yong, Huo, Naxin, Luo, Ming-Cheng, Sehgal, Sunish, Gill, Bikram, Kianian, Sharyar, Anderson, Olin, Kersey, Paul, Dvorak, Jan, McCombie, W. Richard, Hall, Anthony, Mayer, Klaus F.X., Edwards, Keith J., Bevan, Michael W., and Hall, Neil

Subjects
Plant genetics -- Research -- Physiological aspects -- Genetic aspects, Wheat -- Physiological aspects -- Genetic aspects -- Research, Genomics -- Research -- Physiological aspects -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop., With a global output of 681 million tonnes in 2011 (1), bread wheat accounts for 20% of the calories consumed by humans (2) and is an important source of protein, [...]

Published
2012
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