Article
Biochemical Research Methods
Jinzhuang Dou, Degang Wu, Lin Ding, Kai Wang, Minghui Jiang, Xiaoran Chai, Dermot F. Reilly, E. Shyong Tai, Jianjun Liu, Xueling Sim, Shanshan Cheng, Chaolong Wang
Summary: WEScall is a genotype calling pipeline that reduces genotype discordance rates in WES analyses and performs well in off-target data. By analyzing WES data using WEScall, significant loci related to metabolic traits can be identified and multi-gene risk prediction accuracy can be improved.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Critical Care Medicine
Sipeng Shen, Zaiming Li, Yunke Jiang, Weiwei Duan, Hongru Li, Sha Du, Manel Esteller, Hongbing Shen, Zhibin Hu, Yang Zhao, David C. Christiani, Feng Chen
Summary: This study aimed to evaluate the contribution of rare exome-wide variants to lung cancer. Their findings demonstrated that loss-of-function variants in the exome had the most notable effects on lung cancer risk. They also identified four novel variants and found associations between these variants and intermediate exposures. These findings provide important insights into the role of exome genetics in lung cancer predisposition.
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2023)
Article
Behavioral Sciences
Leejee Choi, Joon-Yong An
Summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic component. Advances in genomic technologies have enabled researchers to identify genetic variations associated with ASD and to understand the genetic architecture of the disorder. Large-scale genetic analyses, including microarray and next-generation sequencing (NGS), have resulted in successful gene discovery and provided new insights into the neurobiology of ASD.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2021)
Article
Computer Science, Information Systems
Lena Oden
Summary: The use of Deep Learning methods is seen as a key opportunity for processing large-scale scientific datasets, but efficient processing requires hierarchical storage architectures for faster access to frequently used data. Different staging techniques are evaluated for Deep Learning usecases, with DRAM staging or usecase specific staging techniques showing the best performance, while a technique called split staging provides improved performance compared to non-staged usecases and comparable performance to specialized solutions. Performance often depends more on data layout and transformations used than on storage layer bandwidth.
IEEE TRANSACTIONS ON EMERGING TOPICS IN COMPUTING
(2021)
Article
Mathematical & Computational Biology
Kelley Paskov, Jae-Yoon Jung, Brianna Chrisman, Nate T. Stockham, Peter Washington, Maya Varma, Min Woo Sun, Dennis P. Wall
Summary: Family data can be used to estimate sequencing error rates and produce genome-wide error estimates for each sample by observing Mendelian errors as part of the family. A new method utilizes Mendelian errors in sequencing data to make highly granular per-sample estimates of precision and recall for any set of variant calls.
Article
Biotechnology & Applied Microbiology
Hongchun Xiong, Huijun Guo, Meiyu Fu, Yongdun Xie, Linshu Zhao, Jiayu Gu, Shirong Zhao, Yuping Ding, Qidi Du, Jiazi Zhang, Lin Qiu, Xiaomei Xie, Libin Zhou, Zhongxu Chen, Luxiang Liu
Summary: To overcome the challenge posed by the large genome of hexaploid wheat, researchers generated a wheat mutant database through whole-exome sequencing. The database contains a diverse array of genetic variations induced by different mutagenesis methods, providing a valuable resource for functional genomics studies in wheat.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Green & Sustainable Science & Technology
Anna Trendl, Anne Owen, Lara Vomfell, Lena Kilian, John Gathergood, Neil Stewart, David Leake
Summary: Financial transactions are increasingly used to estimate carbon emissions. This approach offers a low-resource and scalable way to measure emissions at different levels of policy intervention. We provide a step-by-step description of our approach, compare it with standard data sources, and highlight the advantages of using transaction data.
JOURNAL OF INDUSTRIAL ECOLOGY
(2023)
Article
Multidisciplinary Sciences
Susan Athey, Billy Ferguson, Matthew Gentzkow, Tobias Schmidt
Summary: The study estimates a measure of segregation called experienced isolation, which captures individuals' exposure to diverse others in the places they visit over the course of their days. Using GPS data collected from smartphones, the study finds that experienced isolation is substantially lower than standard residential isolation measures suggest, but that experienced isolation is highly correlated with residential isolation across cities. Experienced isolation is lower relative to residential isolation in denser, wealthier, more educated cities with high levels of public transit use, and is negatively correlated with income mobility.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Kaja Wasik, Tomaz Berisa, Joseph K. Pickrell, Jeremiah H. Li, Dana J. Fraser, Karen King, Charles Cox
Summary: The study found that low-pass sequencing to a depth above 0.4x coverage achieves higher power for association studies in pharmacogenetics compared to genotyping arrays.
Article
Humanities, Multidisciplinary
Sarah Morrison-Smith, Christina Boucher, Aleksandra Sarcevic, Noelle Noyes, Catherine O'Brien, Nazaret Cuadros, Jaime Ruiz
Summary: Biological and biomedical research conducted in large, interdisciplinary collaborations faces challenges in communication and collaboration. Multiple disciplines and work culture differences influence collaboration in life science. Solutions and training programs are needed to better support collaborative tasks and workflows in life science research.
HUMANITIES & SOCIAL SCIENCES COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Gokalp Celik, Timur Tuncali
Summary: A new strategy was developed in this study to detect Runs of long homozygous (ROH) by examining the X chromosome non-pseudoautosomal region, utilizing genotype probabilities and the hidden Markov model algorithm. Testing on simulated and real population data demonstrated that this method, named ROHMM, performed robustly and with high accuracy, surpassing its natural competitors.
Letter
Neurosciences
Wei Zhou, Luan Chen, Bixuan Jiang, Yidan Sun, Mo Li, Hao Wu, Na Zhang, Xiaofang Sun, Shengying Qin
Summary: In this study, a wide-ranging investigation of rare disease-causing variants for major depressive disorder (MDD) was conducted using samples from the UK Biobank. The gene-based analysis highlighted FOXH1 as significantly associated with MDD, while the sphingolipid metabolism pathway was found to be less enriched with rare disease-causing variants in the MDD group, suggesting its involvement in the pathophysiology of MDD.
CNS NEUROSCIENCE & THERAPEUTICS
(2021)
Article
Transportation Science & Technology
Elham Saffari, Mehmet Yildirimoglu, Mark Hickman
Summary: This study aims to estimate the MFD for a large-scale urban network by combining probe vehicle data with an unknown penetration rate and full-scale approximate traffic data based on loop detector data. The Bayesian fusion method outperforms the baseline method in average flow and density estimations, especially showing significant improvement in average density estimations.
TRANSPORTATION RESEARCH PART C-EMERGING TECHNOLOGIES
(2022)
Article
Endocrinology & Metabolism
Bushra Gorsi, Edgar Hernandez, Marvin Barry Moore, Mika Moriwaki, Clement Y. Chow, Emily Coelho, Elaine Taylor, Claire Lu, Amanda Walker, Philippe Touraine, Lawrence M. Nelson, Amber R. Cooper, Elaine R. Mardis, Aleksander Rajkovic, Mark Yandell, Corrine K. Welt
Summary: The study identified candidate causative variants in women with POI through whole exome sequencing (WES) and found gene sets with increased burden of deleterious variants. Seven new risk genes for POI were discovered with functional evidence, expanding the genetic architecture of heterozygous rare gene variants causing risk for POI.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2022)
Article
Environmental Studies
Xilei Zhao, Yiming Xu, Ruggiero Lovreglio, Erica Kuligowski, Daniel Nilsson, Thomas J. Cova, Alex Wu, Xiang Yan
Summary: This study proposes a new methodology to analyze wildfire evacuation using a largescale GPS dataset, and found that self-evacuees and shadow evacuees accounted for a large proportion of evacuees during the wildfire evacuation. These findings can help emergency managers and transportation planners better prepare WUI communities for future wildfire events.
TRANSPORTATION RESEARCH PART D-TRANSPORT AND ENVIRONMENT
(2022)
Article
Mathematical & Computational Biology
Vladimir Vutov, Thorsten Dickhaus
Summary: Large-scale hypothesis testing is a common problem in high-dimensional statistical inference, and has broad applications in various scientific disciplines. This paper introduces a multiple marginal models inference procedure using the correlation matrix in imaging mass spectrometry association studies, and applies it to oncological data.
BIOMETRICAL JOURNAL
(2023)
Review
Genetics & Heredity
Benjamin D. Solomon, Margaret P. Adam, Chin-To Fong, Katta M. Girisha, Judith G. Hall, Anna C. E. Hurst, Peter M. Krawitz, Shahida Moosa, Shubha R. Phadke, Cedrik Tekendo-Ngongang, Tara L. Wenger
Summary: The field of clinical genetics and genomics is evolving with milestones like the sequencing of the human genome, advances in sequencing technologies, and the introduction of artificial intelligence. The practice of dysmorphology, the study of abnormal development of tissue form, has also been influenced by technological advances and trends in biomedicine. To explore the future of dysmorphology, a group of clinical geneticists have provided insights about its development over the next few decades.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2023)
Article
Multidisciplinary Sciences
Justus Contzen, Thorsten Dickhaus, Gerrit Lohmann
Summary: We propose a new approach to model the future development of extreme temperatures globally and on a long timescale using non-stationary generalized extreme value distributions combined with logistic functions. Our statistical models are applied to daily temperature data from climate models from 1850 to 2300, allowing us to investigate changes in extremes in terms of both magnitude and timing across different geographic locations. Our findings show that changes in extremes are generally stronger and quicker over land masses than over oceans. We also find that the mean and variance change simultaneously in most regions, while the shape parameter remains constant.
Article
Genetics & Heredity
Hannah Klinkhammer, Christian Staerk, Carlo Maj, Peter Michael Krawitz, Andreas Mayr
Summary: Polygenic risk scores (PRS) evaluate individual genetic liability and are important in clinical risk stratification. This study develops an efficient algorithm, snpboost, for fitting multivariable models to genetic data for improved PRS predictive performance. By iteratively working on smaller batches of variants most correlated with residuals, snpboost increases computational efficiency without sacrificing prediction accuracy. Results show competitive prediction accuracy and efficiency compared to other commonly used methods, making snpboost a valuable tool for constructing PRS.
FRONTIERS IN GENETICS
(2023)
Article
Genetics & Heredity
Nina Ishorst, Leonie Henschel, Frederic Thieme, Dmitriy Drichel, Sugirthan Sivalingam, Sarah L. Mehrem, Ariane C. Fechtner, Julia Fazaal, Julia Welzenbach, Andre Heimbach, Carlo Maj, Oleg Borisov, Jonas Hausen, Ruth Raff, Alexander Hoischen, Michael Dixon, Alvaro Rada-Iglesias, Michaela Bartusel, Augusto Rojas-Martinez, Khalid Aldhorae, Bert Braumann, Teresa Kruse, Christian Kirschneck, Gerrit Spanier, Heiko Reutter, Stefanie Nowak, Lina Goelz, Michael Knapp, Andreas Buness, Peter Krawitz, Markus M. Noethen, Michael Nothnagel, Tim Becker, Kerstin U. Ludwig, Elisabeth Mangold
Summary: This study investigates the genetic mechanisms of nonsyndromic cleft lip with/without cleft palate (nsCL/P) and identifies new candidate genes through the detection of highly penetrant de novo variants (DNVs). By conducting a series of analyses and validations on a discovery sample of 50 nsCL/P patient/parent-trios, MDN1 and PAXIP1 were identified as top candidate genes.
MOLECULAR GENETICS & GENOMIC MEDICINE
(2023)
Article
Genetics & Heredity
Emadeldin Hassanin, Isabel Spier, Dheeraj R. Bobbili, Rana Aldisi, Hannah Klinkhammer, Friederike David, Nuria Duenas, Robert Hueneburg, Claudia Perne, Joan Brunet, Gabriel Capella, Markus M. Noethen, Andreas J. Forstner, Andreas Mayr, Peter Krawitz, Patrick May, Stefan Aretz, Carlo Maj
Summary: The effect of common genetic variants associated with colorectal cancer (CRC) can be assessed using polygenic risk scores (PRS), which can be used for risk stratification. The PRS, along with carrier status and family history, contribute to CRC risk prediction and can improve personalized risk stratification.
BMC MEDICAL GENOMICS
(2023)
Article
Biochemistry & Molecular Biology
Mio Aerden, Anne-Sophie Denomme-Pichon, Dominique Bonneau, Ange-Line Bruel, Julian Delanne, Benedicte Gerard, Benoit Mazel, Christophe Philippe, Lucile Pinson, Clement Prouteau, Audrey Putoux, Frederic Tran Mau-Them, Eleonore Viora-Dupont, Antonio Vitobello, Alban Ziegler, Amelie Piton, Bertrand Isidor, Christine Francannet, Pierre-Yves Maillard, Sophie Julia, Anais Philippe, Elise Schaefer, Saskia Koene, Claudia Ruivenkamp, Mariette Hoffer, Eric Legius, Miel Theunis, Boris Keren, Julien Buratti, Perrine Charles, Thomas Courtin, Mala Misra-Isrie, Mieke van Haelst, Quinten Waisfisz, Dagmar Wieczorek, Ariane Schmetz, Theresia Herget, Fanny Kortuem, Jasmin Lisfeld, Francois-Guillaume Debray, Nuria C. Bramswig, Isis Atallah, Heidi Fodstad, Guillaume Jouret, Berta Almoguera, Saoud Tahsin-Swafiri, Fernando Santos-Simarro, Maria Palomares-Bralo, Vanesa Lopez-Gonzalez, Maria Kibaek, Pernille M. Torring, Alessandra Renieri, Lucia Pia Bruno, Katrin Ounap, Monica Wojcik, Tzung-Chien Hsieh, Peter Krawitz, Hilde Van Esch
Summary: Haploinsufficiency of TRIP12 causes Clark-Baraitser syndrome, a neurodevelopmental disorder characterized by intellectual disability, epilepsy, autism spectrum disorder, and dysmorphic features. Through GestaltMatcher image analysis based on deep-learning algorithms, a distinct facial gestalt was established. The largest cohort to date of individuals with TRIP12 variants was studied, further defining the associated phenotype and introducing a facial gestalt.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Mathematical & Computational Biology
Vladimir Vutov, Thorsten Dickhaus
Summary: Modern high-throughput biomedical devices generate large-scale data, and analyzing high-dimensional datasets is common in biomedical studies. This article proposes a procedure to simultaneously evaluate the strength of associations between a categorical response variable and multiple features. The proposed approach involves multiple testing under arbitrary correlation dependency among test statistics. It offers a trade-off between the expected numbers of true and false findings. The practical application of the method on hyperspectral imaging data obtained through a MALDI instrument is demonstrated.
STATISTICS IN MEDICINE
(2023)
Article
Genetics & Heredity
Luis La Rocca, Julia Frank, Heidi Beate Bentzen, Jean Tori Pantel, Konrad Gerischer, Peter Krawitz, Anton Bovier
Summary: Population medical genetics aims to apply findings from large-scale studies to individual healthcare, but genetic counseling is still mainly based on family history. In a multi-ethnic society, healthcare professionals should also consider the influence of different mating schemes.
AMERICAN JOURNAL OF MEDICAL GENETICS PART A
(2023)
Article
Mathematical & Computational Biology
Daniel Ochieng, Anh-Tuan Hoang, Thorsten Dickhaus
Summary: In this study, two approaches utilizing randomized p-values are presented to deal with the conservativeness issue. The experiments conducted on binomial models show that the proposed randomized p-values are less conservative compared to nonrandomized p-values. The validity of the randomized p-values is also proved under various discrete statistical models.
BIOMETRICAL JOURNAL
(2023)
Article
Computer Science, Interdisciplinary Applications
Luca Cappelletti, Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr, Tiffany J. J. Callahan, Carlos Cano, Marcin P. P. Joachimiak, Christopher J. J. Mungall, Peter N. N. Robinson, Justin Reese, Giorgio Valentini
Summary: GRAPE is a software resource for graph processing and embedding that can scale with big graphs, showing substantial improvements in space and time complexity compared to existing resources. It offers efficient graph-processing utilities, node embedding methods, and inference models, making it a valuable tool for graph representation learning. GRAPE is capable of handling millions of nodes and billions of edges, enabling large-graph analysis in various real-world applications.
NATURE COMPUTATIONAL SCIENCE
(2023)
Article
Biochemical Research Methods
Guy Karlebach, Leigh Carmody, Jagadish Chandrabose Sundaramurthi, Elena Casiraghi, Peter Hansen, Justin Reese, Christopher J. Mungall, Giorgio Valentini, Peter N. Robinson
Summary: This article proposes a method called isoform interpretation to infer isoform-specific functions using expectation-maximization. It predicts specific functional annotations for 85,617 isoforms of 17,900 protein-coding genes and outperforms other methods in comparison to manually annotated results.
Article
Genetics & Heredity
Hanna K. Zieger, Leonie Weinhold, Axel Schmidt, Manuel Holtgrewe, Stefan A. Juranek, Anna Siewert, Annika B. Scheer, Frederic Thieme, Elisabeth Mangold, Nina Ishorst, Fabian U. Brand, Julia Welzenbach, Dieter Beule, Katrin Paeschke, Peter M. Krawitz, Kerstin U. Ludwig
Summary: In this study, whole-genome sequence data from 211 European individuals with non-syndromic cleft lip/palate were analyzed, and 13,522 de novo mutations were identified. These mutations were enriched at two genome-wide association study risk loci, suggesting a convergence of common and rare variants at these loci. Additionally, mutations in the binding region of the Musculin transcription factor were found to contribute to the etiology of cleft lip/palate.
HUMAN GENETICS AND GENOMICS ADVANCES
(2023)
Article
Biochemical Research Methods
Tudor Groza, Honghan Wu, Marcel E. Dinger, Daniel Danis, Coleman Hilton, Anita Bagley, Jon R. Davids, Ling Luo, Zhiyong Lu, Peter N. Robinson
Summary: Motivation methods for concept recognition in clinical texts are often tested on abstracts or articles, but texts from electronic health records (EHRs) often contain errors and nonstandard representations. This study presents a method inspired by the BLAST algorithm that screens texts for matches based on k-mer counts and scores candidates based on typical patterns of spelling errors. Experimental results show a significant enhancement in entity linking task performance, supporting the use of this method alongside existing approaches.
Article
Biochemistry & Molecular Biology
Tim E. Putman, Kevin Schaper, Nicolas Matentzoglu, Vincent P. Rubinetti, Faisal S. Alquaddoomi, Corey Cox, J. Harry Caufield, Glass Elsarboukh, Sarah Gehrke, Harshad Hegde, Justin T. Reese, Ian Braun, Richard M. Bruskiewich, Luca Cappelletti, Seth Carbon, Anita R. Caron, Lauren E. Chan, Christopher G. Chute, Katherina G. Cortes, Vinicius De Souza, Tommaso Fontana, Nomi L. Harris, Emily L. Hartley, Eric Hurwitz, Julius O. B. Jacobsen, Madan Krishnamurthy, Bryan J. Laraway, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Kathleen R. Mullen, Shawn T. O'Neil, Kent A. Shefchek, Ray Stefancsik, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Patricia L. Whetzel, David Osumi-Sutherland, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres
Summary: The Monarch Initiative aims to bridge the gap between genetic variations, environmental determinants, and phenotypic outcomes by developing an integrated platform with open ontologies, semantic data models, and knowledge graphs. It provides advanced analysis tools and curated datasets for clinical diagnosis and understanding disease mechanisms.
NUCLEIC ACIDS RESEARCH
(2023)
