Article
Genetics & Heredity
Karen H. Miga, Evan E. Eichler
Summary: Advances in long-read sequencing and assembly allow labs to generate phased genomes that are more accurate and contiguous than the original human reference genome. Complete genome assemblies will become standard in human genetics, even in clinical settings, due to advancements in technology and computational processing.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Multidisciplinary Sciences
Jason Pugh, Lisbeth Guethlein, Peter Parham
Summary: KIR3DL2 is an inhibitory NK cell receptor that recognizes a common epitope of human and pathogen DNA, allowing NK cells to differentiate between self and pathogen DNA and respond accordingly to activate immune responses.
Article
Biochemistry & Molecular Biology
Abhinav Jain, Rahul C. Bhoyar, Kavita Pandhare, Anushree Mishra, Disha Sharma, Mohamed Imran, Vigneshwar Senthivel, Mohit Kumar Divakar, Mercy Rophina, Bani Jolly, Arushi Batra, Sumit Sharma, Sanjay Siwach, Arun G. Jadhao, Nikhil Palande, Ganga Nath Jha, Nishat Ashrafi, Prashant Kumar Mishra, A. K. Vidhya, Suman Jain, Debasis Dash, Nachimuthu Senthil Kumar, Andrew Vanlallawma, Ranjan Jyoti Sarma, Lalchhandama Chhakchhuak, Shantaraman Kalyanaraman, Radha Mahadevan, Sunitha Kandasamy, B. M. Pabitha, Raskin Erusan Rajagopal, Ezhil J. Ramya, Nirmala P. Devi, Anjali Bajaj, Vishu Gupta, Samatha Mathew, Sangam Goswami, Mohit Mangla, Savinitha Prakash, Kandarp Joshi, S. Sreedevi, Devarshi Gajjar, Ronibala Soraisham, Rohit Yadav, Yumnam Silla Devi, Aayush Gupta, Mitali Mukerji, Sivaprakash Ramalingam, B. K. Binukumar, Vinod Scaria, Sridhar Sivasubbu
Summary: With the advent of next-generation sequencing, a pilot phase of the 'IndiGen' program performed whole genome sequencing of 1029 healthy Indian individuals to create the IndiGenomes database, which is now freely accessible. This comprehensive genetic variant resource for the Indian population has been extensively accessed by the worldwide community.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Simon Roux, David Paez-Espino, I-Min A. Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, T. B. K. Reddy, Stephen Nayfach, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides
Summary: Viruses play a crucial role in shaping microbial community structures and driving global nutrient cycles by infecting cellular hosts. The IMG/VR database offers access to a vast collection of viral sequences, providing insights into viral genome diversity.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Antonio Pedro Camargo, Stephen Nayfach, I-Min A. Chen, Krishnaveni Palaniappan, Anna Ratner, Ken Chu, Stephan J. Ritter, T. B. K. Reddy, Supratim Mukherjee, Frederik Schulz, Lee Call, Russell Y. Neches, Tanja Woyke, Natalia N. Ivanova, Emiley A. Eloe-Fadrosh, Nikos C. Kyrpides, Simon Roux
Summary: Viruses play critical roles in all microbiomes and their genomic diversity and impacts on biological processes are extensively explored through metagenomics. IMG/VR is a platform providing access to a large collection of viral sequences along with functional annotation and metadata. The latest version, IMG/VR v4, contains over 15 million virus genomes and genome fragments.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Supriya Khedkar, Georgy Smyshlyaev, Ivica Letunic, Oleksandr M. Maistrenko, Luis Pedro Coelho, Askarbek Orakov, Sofia K. Forslund, Falk Hildebrand, Mechthild Luetge, Thomas S. B. Schmidt, Orsolya Barabas, Peer Bork
Summary: Prokaryotic Mobile Genetic Elements (MGEs) play important roles in evolution and the spread of antibiotic resistance. However, current understanding of their global dispersal is limited. In this study, a computational framework was developed to capture different MGE types and their cargos, allowing for a better understanding of MGE dispersal. The findings were integrated into a resource, providing a valuable tool for future research on the mobile part of genomes and its horizontal dispersal.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Health Care Sciences & Services
Andrew Wen, Huan He, Sunyang Fu, Sijia Liu, Kurt Miller, Liwei Wang, Kirk E. Roberts, Steven D. Bedrick, William R. Hersh, Hongfang Liu
Summary: Clinical phenotyping is essential for developing digital health applications, but the traditional manual abstraction method is time-consuming and costly. Therefore, there is significant interest in using in-silico methods to accomplish this task. However, current in-silico phenotyping development lacks reusable tools for cross-task generalization and is inaccessible for many potential users. This article highlights the barriers to using in-silico phenotyping and proposes a framework with potential solutions. An example implementation of this framework is introduced as a software application, focusing on ease of adoption, cross-task reusability, and facilitating clinical phenotyping algorithm development.
NPJ DIGITAL MEDICINE
(2023)
Article
Ecology
Maravillas Ruiz Minano, Geoffrey M. While, Weizhao Yang, Christopher P. Burridge, Daniele Salvi, Tobias Uller
Summary: In this study, researchers found that climate can cause genetic differentiation among populations of common wall lizards, despite high levels of gene flow. They identified specific genetic loci associated with thermal tolerance, temperature-dependent metabolism, reproductive activity, and body colouration. These findings provide evidence for the significant role of climate in shaping genetic variation in lizards.
Article
Genetics & Heredity
Chao Ning, Hong-Xiang Zheng, Fan Zhang, Sihao Wu, Chunxiang Li, Yongbin Zhao, Yang Xu, Dong Wei, Yong Wu, Shizhu Gao, Li Jin, Yinqiu Cui
Summary: Ancient DNA studies in Xinjiang suggest that the population in the region since the early Bronze Age was a mixture of West Eurasian migrants and indigenous Central Asian people. Genetic links indicate an early presence of Indo-Iranian languages and suggest that the Andronovo culture in western Xinjiang involved both the spread of ideas and population movement.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Bonnita Werner, Nicole Yuwono, Jennifer Duggan, Dongli Liu, Catherine David, Sivatharsny Srirangan, Pamela Provan, Anna DeFazio, Vivek Arora, Rhonda Farrell, Yeh Chen Lee, Kristina Warton, Caroline Ford
Summary: Malignant ascites is a common clinical feature of ovarian cancer, providing a rich source of cell-free tumor DNA (cftDNA). This study characterized the cfDNA in ascites by size, stability, and cftDNA content, revealing stable levels of cfDNA over 72 hours and inter-patient variability in ovarian cancer ascites.
GYNECOLOGIC ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Diamantis Sellis, Frederic Guerin, Olivier Arnaiz, Walker Pett, Emmanuelle Lerat, Nicole Boggetto, Sascha Krenek, Thomas Berendonk, Arnaud Couloux, Jean-Marc Aury, Karine Labadie, Sophie Malinsky, Simran Bhullar, Eric Meyer, Linda Sperling, Laurent Duret, Sandra Duharcourt
Summary: Ciliates are unicellular eukaryotes with a complex genomic architecture including internal eliminated sequences (IESs) that have undergone multiple waves of gains, some of which are under strong purifying selection. The evolution of IESs in Paramecium highlights the important role of selfish genetic elements in shaping genome complexity and gene expression, similar to the evolution of introns in eukaryotes.
Article
Multidisciplinary Sciences
Chi-Chun Liu, David Witonsky, Anna Gosling, Ju Hyeon Lee, Harald Ringbauer, Richard Hagan, Nisha Patel, Raphaela Stahl, John Novembre, Mark Aldenderfer, Christina Warinner, Anna Di Rienzo, Choongwon Jeong
Summary: Present-day Tibetans have genetically and culturally adapted to the high altitude environment of the Tibetan Plateau, with recent research suggesting an early population entering the area within the past 40 thousand years and subsequent groups arriving within the past 10 thousand years. Ancient individuals from high elevation sites in Nepal are most closely related to present-day Tibetans, deriving their ancestry from Late Neolithic populations at the northeastern edge of the Plateau with a minor genetic component from a distinct Paleolithic Eurasian ancestry. Compared to Tibetans, non-Tibetan Tibeto-Burman speakers living at mid-elevations along the Plateau form a distinct genetic cline, and ongoing positive selection of high altitude adaptive alleles is confirmed through a comparison of ancient and present-day highlanders.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Selim Ben Chehida, Denis Filloux, Emmanuel Fernandez, Oumaima Moubset, Murielle Hoareau, Charlotte Julian, Laurence Blondin, Jean-Michel Lett, Philippe Roumagnac, Pierre Lefeuvre
Summary: Next-generation sequencing (NGS) has led to the discovery of numerous new viruses, but the current metagenomic protocols are still laborious and costly. In the study of CRESS DNA viruses, alternative long-read NGS protocols showed promise in detecting and characterizing viral genomes, although there are accuracy issues with homopolymeric tracks that need to be addressed. The use of bench-top sequencers could offer new possibilities for CRESS DNA virus research.
Article
Multidisciplinary Sciences
Ariel Antonio Moran-Reyes
Summary: The main ethical challenges in Information Sciences are related to the concept of moral responsibility, particularly from a metaethical perspective. The reflection on the implementation of technology in relation to human autonomy goes beyond individual responsibility and requires a group ethics approach. These challenges need to be addressed using theoretical postulates from various disciplines, such as metaethics, normative ethics, digital hermeneutics, and the philosophy of technology.
Article
Environmental Studies
Zhongping Zeng, Siqi Li, Jiunn-Woei Lian, Jiang Li, Tao Chen, Yujia Li
Summary: This study examines why users switch from traditional paper-based work patterns to land information system (LIS) applications using a push-pull-mooring framework. Results show that push factors, pulling factors, and mooring factors all play a role in influencing switching intentions among users. Based on these findings, behavior interventions and land information usage policy suggestions are put forward to promote digital transformation in land sectors.
Article
Plant Sciences
Habte Nida, Shula Blum, Dina Zielinski, Dhruv A. Srivastava, Rivka Elbaum, Zhanguo Xin, Yaniv Erlich, Eyal Fridman, Noam Shental
Article
Biochemical Research Methods
Thomas Willems, Dina Zielinski, Jie Yuan, Assaf Gordon, Melissa Gymrek, Yaniv Erlich
Article
Multidisciplinary Sciences
Yaniv Erlich, Dina Zielinski
Letter
Biochemical Research Methods
Dina Zielinski, Assaf Gordon, Benjamin L. Zaks, Yaniv Erlich
Article
Multidisciplinary Sciences
Dina Zielinski, Barak Markus, Mona Sheikh, Melissa Gymrek, Clement Chu, Marta Zaks, Balaji Srinivasan, Jodi D. Hoffman, Dror Aizenbud, Yaniv Erlich
Editorial Material
Genetics & Heredity
Dina Zielinski, Melissa Gymrek, Yaniv Erlich
Article
Multidisciplinary Sciences
Antoine Campagne, Ming-Kang Lee, Dina Zielinski, Audrey Michaud, Stephanie Le Corre, Florent Dingli, Hong Chen, Lara Z. Shahidian, Ivaylo Vassilev, Nicolas Servant, Damarys Loew, Eric Pasmant, Sophie Postel-Vinay, Michel Wassef, Raphael Margueron
NATURE COMMUNICATIONS
(2019)
Article
Multidisciplinary Sciences
Michel Wassef, Armelle Luscan, Setareh Aflaki, Dina Zielinski, Pascal W. T. C. Jansen, H. Irem Baymaz, Aude Battistella, Carole Kersouani, Nicolas Servant, Margaret R. Wallace, Pierre Romero, Olivier Kosmider, Pierre-Alexandre Just, Mikael Hivelin, Sebastien Jacques, Anne Vincent-Salomon, Michiel Vermeulen, Michel Vidaud, Eric Pasmant, Raphael Margueron
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Genetics & Heredity
Jie Yuan, Henry Xing, Alexandre Louis Lamy, Todd Lencz, Itsik Pe'er
Editorial Material
Multidisciplinary Sciences
Brad Wible
Article
Multidisciplinary Sciences
Lucile Marion-Poll, Benjamin Foret, Dina Zielinski, Florian Massip, Mikael Attia, Ava C. Carter, Laurene Syx, Howard Y. Chang, Anne-Valerie Gendrel, Edith Heard
Summary: Researchers have identified robust monoallelic expression in cell lines and mice, with some genes displaying various modalities of allelic expression and different degrees of allelic imbalance. Non-canonical allelic regulation has been found to have important implications for development and disease, including autosomal dominant disorders.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Daniel Holoch, Michel Wassef, Cecilia Lovkvist, Dina Zielinski, Setareh Aflaki, Berangere Lombard, Tiphaine Hery, Damarys Loew, Martin Howard, Raphael Margueron
Summary: Epigenetic inheritance plays a role in maintaining cellular identities and transcriptional memory, particularly at Polycomb targets, depends on both histone modifications and the gene-regulatory network, varying with cellular context. Polycomb proteins are involved in regulating this type of epigenetic transcriptional memory during cell differentiation.
Article
Public, Environmental & Occupational Health
Olivier Aubert, Daniel Yoo, Dina Zielinski, Emanuele Cozzi, Massimo Cardillo, Michael Durr, Beatriz Dominguez-Gil, Elisabeth Coll, Margarida Ivo Da Silva, Ville Sallinen, Karl Lemstrom, Karsten Midtvedt, Camilo Ulloa, Franz Immer, Annemarie Weissenbacher, Natalie Vallant, Nikolina Basic-Jukic, Kazunari Tanabe, Georgios Papatheodoridis, Georgia Menoudakou, Martin Torres, Carlos Soratti, Daniela Hansen Krogh, Carmen Lefaucheur, Gustavo Ferreira, Helio Tedesco Silva, David Hartell, John Forsythe, Lisa Mumford, Peter P. Reese, Francois Kerbaul, Christian Jacquelinet, Serge Vogelaar, Vassilios Papalois, Alexandre Loupy
Summary: The study evaluated the impact of the COVID-19 pandemic on worldwide organ transplantation activities and found an overall decrease in transplant activity in all countries studied. Kidney transplantation was most affected, followed by lung, liver, and heart transplants. There was a marked reduction in transplant activity during the first 3 months of the pandemic, with losses stabilizing after June 2020 but decreasing again from October to December 2020.
LANCET PUBLIC HEALTH
(2021)
