Search Results - "Krusche, Peter"

Strelka2: fast and accurate calling of germline and somatic variants by Kim, Sangtae, Scheffler, Konrad, Halpern, Aaron L., Bekritsky, Mitchell A., Noh, Eunho, Källberg, Morten, Chen, Xiaoyu, Kim, Yeonbin, Beyter, Doruk, Krusche, Peter, Saunders, Christopher T.

“…We describe Strelka2 ( https://github.com/Illumina/strelka ), an open-source small-variant-calling method for research and clinical germline and somatic…”
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A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree by Eberle, Michael A, Fritzilas, Epameinondas, Krusche, Peter, Källberg, Morten, Moore, Benjamin L, Bekritsky, Mitchell A, Iqbal, Zamin, Chuang, Han-Yu, Humphray, Sean J, Halpern, Aaron L, Kruglyak, Semyon, Margulies, Elliott H, McVean, Gil, Bentley, David R

“…Improvement of variant calling in next-generation sequence data requires a comprehensive, genome-wide catalog of high-confidence variants called in a set of…”
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Paragraph: a graph-based structural variant genotyper for short-read sequence data by Chen, Sai, Krusche, Peter, Dolzhenko, Egor, Sherman, Rachel M, Petrovski, Roman, Schlesinger, Felix, Kirsche, Melanie, Bentley, David R, Schatz, Michael C, Sedlazeck, Fritz J, Eberle, Michael A

“…Accurate detection and genotyping of structural variations (SVs) from short-read data is a long-standing area of development in genomics research and clinical…”
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ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions by Dolzhenko, Egor, Deshpande, Viraj, Schlesinger, Felix, Krusche, Peter, Petrovski, Roman, Chen, Sai, Emig-Agius, Dorothea, Gross, Andrew, Narzisi, Giuseppe, Bowman, Brett, Scheffler, Konrad, van Vugt, Joke J F A, French, Courtney, Sanchis-Juan, Alba, Ibáñez, Kristina, Tucci, Arianna, Lajoie, Bryan R, Veldink, Jan H, Raymond, F Lucy, Taft, Ryan J, Bentley, David R, Eberle, Michael A

“…Abstract Summary We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to…”
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Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle by Feillet, Céline, Krusche, Peter, Tamanini, Filippo, Janssens, Roel C., Downey, Mike J., Martin, Patrick, Teboul, Michèle, Saito, Shoko, Lévi, Francis A., Bretschneider, Till, van der Horst, Gijsbertus T. J., Delaunay, Franck, Rand, David A.

“…Daily synchronous rhythms of cell division at the tissue or organism level are observed in many species and suggest that the circadian clock and cell cycle…”
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Cyclin-dependent kinase inhibitor p20 controls circadian cell-cycle timing by Laranjeiro, Ricardo, Tamai, T. Katherine, Peyric, Elodie, Krusche, Peter, Ott, Sascha, Whitmore, David

“…Specific stages of the cell cycle are often restricted to particular times of day because of regulation by the circadian clock. In zebrafish, both mitosis (M…”
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Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants by Baxter, Laura, Jironkin, Aleksey, Hickman, Richard, Moore, Jay, Barrington, Christopher, Krusche, Peter, Dyer, Nigel P., Buchanan-Wollaston, Vicky, Tiskin, Alexander, Beynon, Jim, Denby, Katherine, Ott, Sascha

“…Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach…”
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Advancing data science in drug development through an innovative computational framework for data sharing and statistical analysis by Mallon, Ann-Marie, Häring, Dieter A, Dahlke, Frank, Aarden, Piet, Afyouni, Soroosh, Delbarre, Daniel, El Emam, Khaled, Ganjgahi, Habib, Gardiner, Stephen, Kwok, Chun Hei, West, Dominique M, Straiton, Ewan, Haemmerle, Sibylle, Huffman, Adam, Hofmann, Tom, Kelly, Luke J, Krusche, Peter, Laramee, Marie-Claude, Lheritier, Karine, Ligozio, Greg, Readie, Aimee, Santos, Luis, Nichols, Thomas E, Branson, Janice, Holmes, Chris

“…Abstract Background Novartis and the University of Oxford’s Big Data Institute (BDI) have established a research alliance with the aim to improve health care…”
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Peter Krusches and Frank Bretz's contribution to the Discussion of ‘Gaussian Differential Privacy’ by Dong et al by Krusche, Peter, Bretz, Frank

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Peter Krusche and Frank Bretz's Contribution to the Discussion of ‘Gaussian Differential Privacy’ by Dong et al by Krusche, Peter, Bretz, Frank

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Best practices for benchmarking germline small-variant calls in human genomes by Krusche, Peter, Trigg, Len, Boutros, Paul C., Mason, Christopher E., De La Vega, Francisco M., Moore, Benjamin L., Gonzalez-Porta, Mar, Eberle, Michael A., Tezak, Zivana, Lababidi, Samir, Truty, Rebecca, Asimenos, George, Funke, Birgit, Fleharty, Mark, Chapman, Brad A., Salit, Marc, Zook, Justin M.

“…Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Although variant-calling tools and the metrics…”
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Methodology for Good Machine Learning with Multi‐Omics Data by Coroller, Thibaud, Sahiner, Berkman, Amatya, Anup, Gossmann, Alexej, Karagiannis, Konstantinos, Moloney, Conor, Samala, Ravi K., Santana‐Quintero, Luis, Solovieff, Nadia, Wang, Craig, Amiri‐Kordestani, Laleh, Cao, Qian, Cha, Kenny H., Charlab, Rosane, Cross, Frank H., Hu, Tingting, Huang, Ruihao, Kraft, Jeffrey, Krusche, Peter, Li, Yutong, Li, Zheng, Mazo, Ilya, Paul, Rahul, Schnakenberg, Susan, Serra, Paolo, Smith, Sean, Song, Chi, Su, Fei, Tiwari, Mohit, Vechery, Colin, Xiong, Xin, Zarate, Juan Pablo, Zhu, Hao, Chakravartty, Arunava, Liu, Qi, Ohlssen, David, Petrick, Nicholas, Schneider, Julie A., Walderhaug, Mark, Zuber, Emmanuel

“…In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4‐year scientific collaboration to approach complex new…”
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Genomic plasticity and rapid host switching can promote the evolution of generalism: a case study in the zoonotic pathogen Campylobacter by Woodcock, Dan J., Krusche, Peter, Strachan, Norval J. C., Forbes, Ken J., Cohan, Frederick M., Méric, Guillaume, Sheppard, Samuel K.

“…Horizontal gene transfer accelerates bacterial adaptation to novel environments, allowing selection to act on genes that have evolved in multiple genetic…”
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Analysis of 5' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals by Davies, Nathaniel J, Krusche, Peter, Tauber, Eran, Ott, Sascha

“…Phylogenetic footprinting is a comparative method based on the principle that functional sequence elements will acquire fewer mutations over time than…”
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Evolutionary analysis of regulatory sequences (EARS) in plants by Picot, Emma, Krusche, Peter, Tiskin, Alexander, Carré, Isabelle, Ott, Sascha

“…Identification of regulatory sequences within non-coding regions of DNA is an essential step towards elucidation of gene networks. This approach constitutes a…”
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Author Correction: Best practices for benchmarking germline small-variant calls in human genomes by Krusche, Peter, Trigg, Len, Boutros, Paul C., Mason, Christopher E., De La Vega, Francisco M., Moore, Benjamin L., Gonzalez-Porta, Mar, Eberle, Michael A., Tezak, Zivana, Lababidi, Samir, Truty, Rebecca, Asimenos, George, Funke, Birgit, Fleharty, Mark, Chapman, Brad A., Salit, Marc, Zook, Justin M.

“…In the version of this article initially published online, two pairs of headings were switched with each other in Table 4: “Recall (PCR free)” was switched…”
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Evolutionary analysis of regulatory sequences (EARS) in plants: In silico detection of functional promoter elements by Picot, Emma, Krusche, Peter, Tiskin, Alexander, Carré, Isabelle, Ott, Sascha

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Using Large Language Models to Generate Clinical Trial Tables and Figures by Yang, Yumeng, Krusche, Peter, Pantoja, Kristyn, Shi, Cheng, Ludmir, Ethan, Roberts, Kirk, Zhu, Gen

“…Tables, figures, and listings (TFLs) are essential tools for summarizing clinical trial data. Creation of TFLs for reporting activities is often a…”
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TorchSurv: A Lightweight Package for Deep Survival Analysis by Monod, Mélodie, Krusche, Peter, Cao, Qian, Sahiner, Berkman, Petrick, Nicholas, Ohlssen, David, Coroller, Thibaud

“…TorchSurv is a Python package that serves as a companion tool to perform deep survival modeling within the PyTorch environment. Unlike existing libraries that…”
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Computing alignment plots efficiently by Krusche, Peter, Tiskin, Alexander

“…Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of…”
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