Article
Biochemistry & Molecular Biology
Marta Byrska-Bishop, Uday S. Evani, Xuefang Zhao, Anna O. Basile, Haley J. Abel, Allison A. Regier, Andre Corvelo, Wayne E. Clarke, Rajeeva Musunuri, Kshithija Nagulapalli, Susan Fairley, Alexi Runnels, Lara Winterkorn, Ernesto Lowy, Paul Flicek, Soren Germer, Harrison Brand, Ira M. Hall, Michael E. Talkowski, Giuseppe Narzisi, Michael C. Zody
Summary: The 1000 Genomes Project is the largest open resource of whole-genome sequencing data, and a new high-coverage WGS 1kGP resource has been released, improving the sensitivity and accuracy of variant calls and making it more valuable for association studies.
Editorial Material
Biochemistry & Molecular Biology
Neil A. Hanchard, Ananyo Choudhury
Summary: This article discusses the release of expanded high-depth sequencing data for the fourth phase of the 1000 Genomes Project. It explores how this dataset can serve as a more comprehensive and accurate resource for global genomics through extensive comparisons and benchmarks.
Article
Biotechnology & Applied Microbiology
Haoyu Cheng, Erich D. Jarvis, Olivier Fedrigo, Klaus-Peter Koepfli, Lara Urban, Neil J. Gemmell, Heng Li
Summary: This paper presents an algorithm that combines PacBio HiFi reads and Hi-C chromatin interaction data to achieve haplotype-resolved genome assembly from single samples without the need for parent sequencing. The algorithm outperforms existing single-sample assembly pipelines and produces assemblies of similar quality to the best pedigree-based assemblies when applied to human and other vertebrate samples.
NATURE BIOTECHNOLOGY
(2022)
Article
Computer Science, Software Engineering
Zezhong Wang, Hugo Romat, Fanny Chevalier, Nathalie Henry Riche, Dave Murray-Rust, Benjamin Bach
Summary: This paper investigates how to make data comics interactive and introduces a set of operations to support the narrative goals of data comics. Adding interactivity enables non-linear storytelling, personalization, and enriched user experiences. The authors propose a lightweight specification language, COMICSCRIPT, for designers to add interactivity to static comics. The viability of their approach is assessed through the creation of interactive comics by professional illustrators and designers.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2022)
Article
Multidisciplinary Sciences
Michael E. Deagen, Jamie P. McCusker, Tolulomo Fateye, Samuel Stouffer, L. Cate Brinson, Deborah L. McGuinness, Linda S. Schadler
Summary: This article presents the use of bespoke, interactive data graphics for visual exploration of a knowledge graph. By modeling charts as metadata that describe semantic and visual context, and utilizing SPARQL and Vega-Lite grammars, interactive data graphics synchronized to the knowledge graph can be concisely specified. Published charts populate a browsable gallery in the database.
Article
Computer Science, Software Engineering
Aditeya Pandey, Sehi L'Yi, Qianwen Wang, Michelle A. Borkin, Nils Gehlenborg
Summary: The interpretation of genomics data relies on visualization tools. However, the wide range of visualization techniques and tasks poses a challenge for analysts. Existing visualization recommendation systems are not designed to handle domain-specific problems. To address this, GenoREC is designed as a novel visualization recommendation system for genomics, enabling analysts to choose effective visualizations based on their data and tasks.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Clinical Neurology
Fulya Akcimen, Jay P. Ross, Calwing Liao, Dan Spiegelman, Patrick A. Dion, Guy A. Rouleau
Summary: The study identified HTT-positive, ATXN2-positive, ATXN3-positive, and possibly ATXN1-positive samples in 0.5% of these populations, indicating the presence of asymptomatic small expanded repeats. There was no correlation between repeat sizes of different genes and the distribution of CAG alleles varied by ethnicity.
MOVEMENT DISORDERS
(2021)
Article
Biochemical Research Methods
Kshitij Srivastava, Anne-Sophie Fratzscher, Bo Lan, Willy Albert Flegel
Summary: This study identified long reference sequences by analyzing homozygous genomic regions in the 1000 Genomes Project database. A total of 902 ACKR1 haplotypes of varying lengths were confirmed, with the longest being 80,584 nucleotides and the shortest being 1,901 nucleotides. The approach of using tracts of homozygosity for definitive reference sequences is scalable and can be applied to any gene.
BMC BIOINFORMATICS
(2021)
Article
Computer Science, Software Engineering
Benedikt Mayer, Nastasja Steinhauer, Bernhard Preim, Monique Meuschke
Summary: Large-scale issues such as the COVID-19 pandemic, the war against Ukraine, and climate change have brought attention to visual storytelling with data in online journalism, confirming its effectiveness and relevance. However, there is limited research on interactive visual data stories with a spatio-temporal context. This study proposes a design space and analyzes 130 collected web-based visual data stories to understand common techniques used in conveying complex information in a comprehensible way.
COMPUTER GRAPHICS FORUM
(2023)
Article
Biochemical Research Methods
Dibyajyoti Maity, Debnath Pal
Summary: MD DaVis is a python package developed to facilitate quick comparative analysis of MD trajectories of proteins, improving productivity and saving time by creating interactive visualizations with a few simple steps.
Article
Genetics & Heredity
Tamara Soledad Frontanilla, Guilherme Valle-Silva, Jesus Ayala, Celso Teixeira Mendes-Junior
Summary: By conducting a comprehensive genotyping analysis of STRs obtained from the 1000 Genome populations, we established a reliable open-access STR database and identified limitations of HipSTR in detecting longer alleles.
Article
Computer Science, Software Engineering
Sehi L'Yi, Qianwen Wang, Fritz Lekschas, Nils Gehlenborg
Summary: This article introduces an interactive and scalable grammar called Gosling for genomics data visualization, along with its accompanying JavaScript toolkit Gosling.js. The grammar balances expressiveness for comprehensive multi-scale genomics visualizations with accessibility for domain scientists, addressing the issue of limited customization in existing tools.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2022)
Article
Computer Science, Information Systems
Xiaojian Chen, Hailong Wang, Yu Zhu, Hansheng Wang, Mingjun Su, Shuyu Bao, Yiping Wu
Summary: This paper presents a new immersive visualization tool for better illustrating stratigraphic data, which is particularly useful for domain experts in petroleum information exploration. The tool allows for flexible interaction, enables experts to obtain desired underground flow path structures through surface queries, and supports different display modes and integration of geological information. Feedback from experts indicates that this tool contributes more to their scientific exploration of stratigraphic data compared to existing visualization tools in the field.
ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION
(2022)
Article
Computer Science, Software Engineering
Leilani Battle, Carlos Scheidegger
Summary: In the past 30 years, a systematic review was conducted on adjacent fields, highlighting techniques and principles that are underappreciated in visualization work. By categorizing 131 research papers, it was found that five notions in data management venues suit interactive visualization systems well.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Genetics & Heredity
Jeffrey K. Ng, Pankaj Vats, Elyn Fritz-Waters, Stephanie Sarkar, Eleanor I. Sams, Evin M. Padhi, Zachary L. Payne, Shawn Leonard, Marc A. West, Chandler Prince, Lee Trani, Marshall Jansen, George Vacek, Mehrzad Samadi, Timothy T. Harkins, Craig Pohl, Tychele N. Turner
Summary: In this study, a graphics processing units-based workflow was developed to accelerate the detection of de novo variants (DNVs). The workflow was applied to whole-genome sequencing data from different sources, revealing unexpected results in the DNV callsets and potential cell line artifacts. Additionally, mutation signature analysis identified associations with B-cell lymphoma and variants in DNA repair genes. These findings have important implications for reference building and disease-related projects.
Article
Microbiology
Natasha Arora, Verena J. Schuenemann, Guenter Jaeger, Alexander Peltzer, Alexander Seitz, Alexander Herbig, Michal Strouhal, Linda Grillova, Leonor Sanchez-Buso, Denise Kuhnert, Kirsten I. Bos, Leyla Rivero Davis, Lenka Mikalova, Sylvia Bruisten, Peter Komericki, Patrick French, Paul R. Grant, Maria A. Pando, Lucia Gallo Vaulet, Marcelo Rodriguez Fermepin, Antonio Martinez, Arturo Centurion Lara, Lorenzo Giacani, Steven J. Norris, David Smajs, Philipp P. Bosshard, Fernando Gonzalez-Candelas, Kay Nieselt, Johannes Krause, Homayoun C. Bagheri
NATURE MICROBIOLOGY
(2017)
Article
Multidisciplinary Sciences
Iosif Lazaridis, Alissa Mittnik, Nick Patterson, Swapan Mallick, Nadin Rohland, Saskia Pfrengle, Anja Furtweangler, Alexander Peltzer, Cosimo Posth, Andonis Vasilakis, P. J. P. McGeorge, Eleni Konsolaki-Yannopoulou, George Korres, Holley Martlew, Manolis Michalodimitrakis, Mehmet Ozsait, Nesrin Ozsait, Anastasia Papathanasiou, Michael Richards, Songul Alpaslan Roodenberg, Yannis Tzedakis, Robert Arnott, Daniel M. Fernandes, Jeffery R. Hughey, Dimitra M. Lotakis, Patrick A. Navas, Yannis Maniatis, John A. S. Tamatoyannopoulos, Kristin Stewardson, Philipp Stockhammer, Ron Pinhasi, David Reich, Johannes Krause, George Stamatoyannopoulos
Article
Multidisciplinary Sciences
Verena J. Schuenemann, Alexander Peltzer, Beatrix Welte W. Paul van Pelt, Martyna Molak, Chuan-Chao Wang, Anja Furtwaengler, Christian Urban, Ella Reiter, Kay Nieselt, Barbara Tessmann, Michael Francken, Katerina Harvati, Wolfgang Haak, Stephan Schiffels, Johannes Krause
NATURE COMMUNICATIONS
(2017)
Article
Multidisciplinary Sciences
Alexander Peltzer, Alissa Mittnik, Chuan-Chao Wang, Tristan Begg, Cosimo Posth, Kay Nieselt, Johannes Krause
SCIENTIFIC REPORTS
(2018)
Article
Biochemical Research Methods
Sven Fillinger, Luis de la Garza, Alexander Peltzer, Oliver Kohlbacher, Sven Nahnsen
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2019)
Article
Biochemical Research Methods
Leon Bichmann, Annika Nelde, Michael Ghosh, Lukas Heumos, Christopher Mohr, Alexander Peltzer, Leon Kuchenbecker, Timo Sachsenberg, Juliane S. Walz, Stefan Stevanovic, Hans-Georg Rammensee, Oliver Kohlbacher
JOURNAL OF PROTEOME RESEARCH
(2019)
Article
Oncology
Zulrahman Erlangga, Katharina Wolff, Tanja Poth, Alexander Peltzer, Sven Nahnsen, Steffi Spielberg, Kai Timrott, Norman Woller, Florian Kuehnel, Michael P. Manns, Anna Saborowski, Arndt Vogel, Michael Saborowski
Letter
Biotechnology & Applied Microbiology
Philip A. Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso, Sven Nahnsen
NATURE BIOTECHNOLOGY
(2020)
Editorial Material
Biochemical Research Methods
Judit Kumuthini, Michael Chimenti, Sven Nahnsen, Alexander Peltzer, Rebone Meraba, Ross McFadyen, Gordon Wells, Deanne Taylor, Mark Maienschein-Cline, Jian-Liang Li, Jyothi Thimmapuram, Radha Murthy-Karuturi, Lyndon Zass
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Microbiology
Daniel Straub, Nia Blackwell, Adrian Langarica-Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
James A. Fellows Yates, Thiseas C. Lamnidis, Maxime Borry, Aida Andrades Valtuena, Zandra Fagernaes, Stephen Clayton, Maxime U. Garcia, Judith Neukamm, Alexander Peltzer
Summary: The advancement of ancient DNA applications has led to the development of a redesigned and extended version of the EAGER pipeline, aiming to ensure accessibility, reproducibility, and alignment with the latest practices. Developed within the nf-core initiative, nfcore/eager provides high-quality software development and maintenance support to facilitate a wider range of ancient DNA analyses across diverse research groups and fields.
Article
Multidisciplinary Sciences
Cosimo Posth, Valentina Zaro, Maria A. Spyrou, Stefania Vai, Guido A. Gnecchi-Ruscone, Alessandra Modi, Alexander Peltzer, Angela Motsch, Kathrin Nagele, Ashild J. Vagene, Elizabeth A. Nelson, Rita Radzeviciute, Cacilia Freund, Lorenzo M. Bondioli, Luca Cappuccini, Hannah Frenzel, Elsa Pacciani, Francesco Boschin, Giulia Capecchi, Ivan Martini, Adriana Moroni, Stefano Ricci, Alessandra Sperduti, Maria Angela Turchetti, Alessandro Riga, Monica Zavattaro, Andrea Zifferero, Henrike O. Heyne, Eva Fernandez-Dominguez, Guus J. Kroonen, Michael McCormick, Wolfgang Haak, Martina Lari, Guido Barbujani, Luca Bondioli, Kirsten Bos, David Caramelli, Johannes Krause
Summary: The study found that during the Iron Age, the Etruscans had a component of Indo-European-associated steppe ancestry, but lacked recent Anatolian-related admixture. However, during the Roman Imperial period, there was an abrupt population-wide shift to eastern Mediterranean ancestry. Northern European components appeared in central Italy during the Early Middle Ages, shaping the genetic landscape of present-day Italian populations.
Meeting Abstract
Biochemistry & Molecular Biology
J. Alneberg, M. U. Garcia, A. Peltzer, T. Koch, M. Proks, A. Wilm, P. A. Ewels
EUROPEAN JOURNAL OF HUMAN GENETICS
(2019)
Meeting Abstract
Anthropology
Verena J. Schuenemann, Alexander Peltzer, Wolfgang Haak, Stephan Schiffels, Johannes Krause
AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Pontus Skoglund, Jessica C. Thompson, Mary E. Prendergast, Alissa Mittnik, Kendra Sirak, Mateja Hajdinjak, Tasneem Salie, Nadin Rohland, Swapan Mallick, Alexander Peltzer, Anja Heinze, Inigo Olalde, Matthew Ferry, Eadaoin Harney, Megan Michel, Kristin Stewardson, Jessica I. Cerezo-Romam, Chrissy Chiumia, Alison Crowther, Elizabeth Gomani-Chindebvu, Agness O. Gidna, Katherine M. Grillo, I. Taneli Helenius, Garrett Hellenthal, Richard Helm, Mark Horton, Saioa Lopez, Audax Z. P. Mabulla, John Parkington, Ceri Shipton, Mark G. Thomas, Ruth Tibesasa, Menno Welling, Vanessa M. Hayes, Douglas J. Kennett, Raj Ramesar, Matthias Meyer, Svante Paeaebo, Nick Patterson, Alan G. Morris, Nicole Boivin, Ron Pinhasi, Johannes Krause, David Reich