Article
Genetics & Heredity
Luca A. Lotta, Maik Pietzner, Isobel D. Stewart, Laura B. L. Wittemans, Chen Li, Roberto Bonelli, Johannes Raffler, Emma K. Biggs, Clare Oliver-Williams, Victoria P. W. Auyeung, Jian'an Luan, Eleanor Wheeler, Ellie Paige, Praveen Surendran, Gregory A. Michelotti, Robert A. Scott, Stephen Burgess, Verena Zuber, Eleanor Sanderson, Albert Koulman, Fumiaki Imamura, Nita G. Forouhi, Kay-Tee Khaw, Julian L. Griffin, Angela M. Wood, Gabi Kastenmueller, John Danesh, Adam S. Butterworth, Fiona M. Gribble, Frank Reimann, Melanie Bahlo, Eric Fauman, Nicholas J. Wareham, Claudia Langenberg
Summary: By conducting a cross-platform analysis of metabolites, we identified various genetic regulators associated with metabolite levels, including their impact on diseases such as type 2 diabetes and macular telangiectasia type 2.
Article
Oncology
Heng Pan, Loic Renaud, Ronan Chaligne, Johannes Bloehdorn, Eugen Tausch, Daniel Mertens, Anna Maria Fink, Kirsten Fischer, Chao Zhang, Doron Betel, Andreas Gnirkell, Marcin Imielinski, Jerome Moreaux, Michael Hallek, Alexander Meissner, Stephan Stilgenbauer, Catherine J. Wu, Olivier Elemento, Dan A. Landau
Summary: MethSig is a novel statistical framework for analyzing DNA methylation changes in cancer, specifically identifying candidate DNA methylation driver genes of cancer progression and relapse, empowering the discovery of epigenetic mechanisms that enhance cancer cell fitness.
Article
Multidisciplinary Sciences
Fasil Tekola-Ayele, Xuehuo Zeng, Suvo Chatterjee, Marion Ouidir, Corina Lesseur, Ke Hao, Jia Chen, Markos Tesfaye, Carmen J. Marsit, Tsegaselassie Workalemahu, Ronald Wapner
Summary: Abnormal birthweight is associated with increased risk for cardiometabolic diseases in later life. This study integrated placental methylation and gene expression data with genetic loci associated with birthweight to identify functional genes involved in fetal growth regulation.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Ananya Roy, Sharadha Sakthikumar, Sergey V. Kozyrev, Jessika Nordin, Raphaela Pensch, Suvi Makelainen, Mats Pettersson, Elinor K. Karlsson, Kerstin Lindblad-Toh, Karin Forsberg-Nilsson
Summary: Current knowledge of cancer genomics is biased against noncoding mutations. This study assessed mutations in conserved positions in the genome to identify genes enriched in noncoding constraint mutations (NCCMs). The comparison of two types of tumors showed different frequencies of NCCMs. These newly identified NCCMs in different molecular pathways may aid in patient stratification and personalized treatment options.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Aiara Garitazelaia, Aintzane Rueda-Martinez, Rebeca Arauzo, Jokin de Miguel, Ariadna Cilleros-Portet, Sergi Mari, Jose Ramon Bilbao, Nora Fernandez-Jimenez, Iraia Garcia-Santisteban
Summary: Endometriosis is a complex disease characterized by the growth of endometrial-like tissue in extra-uterine locations, often appearing together with other phenotypes such as autoimmune diseases and anthropometric traits. Genetic analysis suggests potential common roots between endometriosis and female anthropometric and reproductive traits, with weight and BMI possibly mediating the genetic susceptibility to the disease. Furthermore, genetic variants related to more frequent menstruation exposure could also increase the risk of developing endometriosis.
Article
Horticulture
Siddharood Maragal, Eguru Sreenivasa Rao, D. C. Lakshmana Reddy
Summary: This study investigated the genes/QTLs governing important fruit quality traits in watermelon, particularly focusing on fruit shape and flesh color. Through QTL mapping and candidate gene analysis, several major QTLs and potential candidate genes were identified. The results provide valuable information for future functional validation and breeding of important fruit quality traits in watermelon.
SCIENTIA HORTICULTURAE
(2023)
Article
Multidisciplinary Sciences
Musalula Sinkala
Summary: This study analyzes the genomic sequences of 20,331 primary tumors, identifying driver mutations in 727 known cancer genes and revealing significant variations in mutation frequency and co-occurrence in different cancer types. The study also finds that patients with tumors displaying different combinations of gene mutation patterns have variable survival outcomes, providing new insights into the genetic landscape and mechanisms of cancer development.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Jan Fehmi Sayilgan, Turkan Haliloglu, Mehmet Gonen
Summary: Recent research has shown that cancer missense mutations tend to target the hinge residues in protein dynamics. By developing a computational pipeline to detect enriched clustering of missense mutations around hinge residues, new candidate mutations and genes were identified in addition to known ones. This study demonstrates the importance of considering clustering around hinge residues in understanding the functional role of mutations in cancer genes and discovering potential new genes.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2021)
Article
Medicine, General & Internal
Yanni Li, Kristina Sundquist, Naiqi Zhang, Xiao Wang, Jan Sundquist, Ashfaque A. Memon
Summary: This study used genetic instruments to investigate the causal relationship between mitochondrial dysfunction and multiple cancers. It identified potential candidate genes for cancer prevention and treatment.
Article
Plant Sciences
Michael F. Nagle, Jialin Yuan, Damanpreet Kaur, Cathleen Ma, Ekaterina Peremyslova, Yuan Jiang, Bahiya Zahl, Alexa Nino de Rivera, Wellington Muchero, Li Fuxin, Steven H. Strauss
Summary: Adventitious rooting (AR) plays a crucial role in tree propagation, breeding, and genetic engineering. However, the genetic basis of AR is not well-characterized. To identify genetic regulators of AR, a genome-wide association study (GWAS) was performed using 1148 Populus trichocarpa genotypes. A computer vision system was developed to measure various traits related to adventitious root development. GWAS analysis revealed 277 unique associations, indicating that genes involved in hormone signaling, cell division, and other root development processes play a role in AR. Numerous genes with unknown functions were also identified as candidates for further analysis.
HORTICULTURE RESEARCH
(2023)
Article
Genetics & Heredity
Sunil S. Gangurde, Janila Pasupuleti, Sejal Parmar, Murali T. Variath, Deekshitha Bomireddy, Surendra S. Manohar, Rajeev K. Varshney, Prashant Singam, Baozhu Guo, Manish K. Pandey
Summary: Seed size is a crucial factor determining the commercial value of groundnut in the international market. Genetic analysis identified several genomic regions associated with seed weight and shelling percentage, with potential candidate genes identified. These findings can be used to develop markers for improving cultivars with desired seed size and shelling percentage.
FRONTIERS IN GENETICS
(2023)
Article
Genetics & Heredity
Mitchell J. Feldmann, Giovanny Covarrubias-Pazaran, Hans-Peter Piepho
Summary: Large-effect loci discovered by genome-wide association studies or linkage mapping segregate with minor genetic effects in wild and domesticated plants and animals. Accurate attributing of mean differences and variance explained is important for selecting superior progeny and parents in breeding and genetics research. Marker-assisted prediction and genomic prediction have advantages for selecting superior individuals, but are less integrated in studying complex traits.
G3-GENES GENOMES GENETICS
(2023)
Article
Multidisciplinary Sciences
Walid K. Chatila, Henry Walch, Jaclyn F. Hechtman, Sydney M. Moyer, Valeria Sgambati, David M. Faleck, Amitabh Srivastava, Laura Tang, Jamal Benhamida, Dorina Ismailgeci, Carl Campos, Fan Wu, Qing Chang, Efsevia Vakiani, Elisa de Stanchina, Martin R. Weiser, Maria Widmar, Rhonda K. Yantiss, Manish A. Shah, Adam J. Bass, Zsofia K. Stadler, Lior H. Katz, Ingo K. Mellinghoff, Nilay S. Sethi, Nikolaus Schultz, Karuna Ganesh, David Kelsen, Rona Yaeger
Summary: Inflammation is recognized as a contributing factor to cancer development, particularly in the gastrointestinal tract. In this study, the clinical features, genomic landscape, and germline alterations of colitis-associated cancers were defined. TP53 alterations were a common event in colitis-associated cancers, occurring in half of dysplasia, while Wnt pathway alterations were infrequent. The sequencing results from multiple dysplasia/cancer lesions suggest that these lesions largely occur as genetically independent events with lineage plasticity away from Wnt activation.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Yang Liu, Congyang Yi, Qian Liu, Chunhui Wang, Wenpeng Wang, Fangpu Han, Xiaojun Hu
Summary: This study investigated the mechanisms regulating seed size in peanut by using a multi-omics approach. Two mutants with bigger seed size were isolated and analyzed through whole genome sequencing and RNA-Seq analysis, leading to the identification of candidate genes associated with seed size.
Article
Multidisciplinary Sciences
Tara N. Yankee, Sungryong Oh, Emma Wentworth Winchester, Andrea Wilderman, Kelsey Robinson, Tia Gordon, Jill A. Rosenfeld, Jennifer VanOudenhove, Daryl A. Scott, Elizabeth J. Leslie, Justin Cotney
Summary: Craniofacial disorders are one of the most common congenital defects that arise during early pregnancy. The authors utilized RNA-seq analysis to identify 239 genes that are highly expressed during craniofacial development. Gene co-expression analysis revealed that regulatory hubs containing these genes are associated with known disease causing genes and are less susceptible to mutation in the normal healthy population. By combining transcriptomic and epigenomic data, they identified 539 genes likely to contribute to craniofacial disorders, many of which have not been previously implicated in these disorders.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Isabel Romero-Calvo, Christopher R. Weber, Mohana Ray, Miguel Brown, Kori Kirby, Rajib K. Nandi, Tiha M. Long, Samantha M. Sparrow, Andrey Ugolkov, Wenan Qiang, Yilin Zhang, Tonya Brunetti, Hedy Kindler, Jeremy P. Segal, Andrey Rzhetsky, Andrew P. Mazar, Mary M. Buschmann, Ralph Weichselbaum, Kevin Roggin, Kevin P. White
MOLECULAR CANCER RESEARCH
(2019)
Article
Biochemical Research Methods
Rose Orenbuch, Ioan Filip, Devon Comito, Jeffrey Shaman, Itsik Pe'er, Raul Rabadan
Article
Statistics & Probability
Lorin Crawford, Anthea Monod, Andrew X. Chen, Sayan Mukherjee, Raul Rabadan
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2020)
Article
Biochemistry & Molecular Biology
Jian Zhang, Abdullah M. Ali, Yen K. Lieu, Zhaoqi Liu, Jianchao Gao, Raul Rabadan, Azra Raza, Siddhartha Mukherjee, James L. Manley
Article
Multidisciplinary Sciences
Floris P. Barthel, Kevin C. Johnson, Frederick S. Varn, Anzhela D. Moskalik, Georgette Tanner, Emre Kocakavuk, Kevin J. Anderson, Olajide Abiola, Kenneth Aldape, Kristin D. Alfaro, Donat Alpar, Samirkumar B. Amin, David M. Ashley, Pratiti Bandopadhayay, Jill S. Barnholtz-Sloan, Rameen Beroukhim, Christoph Bock, Priscilla K. Brastianos, Daniel J. Brat, Andrew R. Brodbelt, Alexander F. Bruns, Ketan R. Bulsara, Aruna Chakrabarty, Arnab Chakravarti, Jeffrey H. Chuang, Elizabeth B. Claus, Elizabeth J. Cochran, Jennifer Connelly, Joseph F. Costello, Gaetano Finocchiaro, Michael N. Fletcher, Pim J. French, Hui K. Gan, Mark R. Gilbert, Peter V. Gould, Matthew R. Grimmer, Antonio Iavarone, Azzam Ismail, Michael D. Jenkinson, Mustafa Khasraw, Hoon Kim, Mathilde C. M. Kouwenhoven, Peter S. LaViolette, Meihong Li, Peter Lichter, Keith L. Ligon, Allison K. Lowman, Tathiane M. Malta, Tali Mazor, Kerrie L. McDonald, Annette M. Molinaro, Do-Hyun Nam, Naema Nayyar, Ho Keung Ng, Chew Yee Ngan, Simone P. Niclou, Johanna M. Niers, Houtan Noushmehr, Javad Noorbakhsh, D. Ryan Ormond, Chul-Kee Park, Laila M. Poisson, Raul Rabadan, Bernhard Radlwimmer, Ganesh Rao, Guido Reifenberger, Jason K. Sa, Michael Schuster, Brian L. Shaw, Susan C. Short, Peter A. Sillevis Smitt, Andrew E. Sloan, Marion Smits, Hiromichi Suzuki, Ghazaleh Tabatabai, Erwin G. Van Meir, Colin Watts, Michael Weller, Pieter Wesseling, Bart A. Westerman, Georg Widhalm, Adelheid Woehrer, W. K. Alfred Yung, Gelareh Zadeh, Jason T. Huse, John F. De Groot, Lucy F. Stead, Roel G. W. Verhaak
Article
Multidisciplinary Sciences
Neil Vasan, Pedram Razavi, Jared L. Johnson, Hong Shao, Hardik Shah, Alesia Antoine, Erik Ladewig, Alexander Gorelick, Ting-Yu Lin, Eneda Toska, Guotai Xu, Abiha Kazmi, Matthew T. Chang, Barry S. Taylor, Maura N. Dickler, Komal Jhaveri, Sarat Chandarlapaty, Raul Rabadan, Ed Reznik, Melissa L. Smith, Robert Sebra, Frauke Schimmoller, Timothy R. Wilson, Lori S. Friedman, Lewis C. Cantley, Maurizio Scaltriti, Jose Baselga
Article
Biochemical Research Methods
Hanxin Zhang, Torsten Dahlen, Atif Khan, Gustaf Edgren, Andrey Rzhetsky
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Brooke Schuster, Michael Junkin, Sara Saheb Kashaf, Isabel Romero-Calvo, Kori Kirby, Jonathan Matthews, Christopher R. Weber, Andrey Rzhetsky, Kevin P. White, Savas Tay
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Hanxin Zhang, Atif Khan, Qi Chen, Henrik Larsson, Andrey Rzhetsky
Summary: This study examines the annual patterns of psychiatric disorders in the U.S. and Sweden using large datasets. The findings show remarkable similarities in annual patterns across studied diseases, with greater variation in Sweden for psychiatric disorders. Results varied for different age groups in terms of healthcare-seeking visit patterns. The study suggests that uncorrected results may capture real trends, while corrected results may reflect artifacts influenced by fluctuating health-seeking visits.
Article
Biochemical Research Methods
Yanan H. Long, Qi Chen, Henrik H. Larsson, Andrey Rzhetsky
Summary: The study investigates the association between the human sex ratio at birth and environmental factors using large datasets from the US and Sweden. While seasonal and temperature variations were not found to affect the sex ratio, various pollutants, including industrial and agricultural activities, were associated with lower sex ratios. Additionally, some environmental toxins were found to induce higher sex ratios.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Psychiatry
Hanxin Zhang, Atif Khan, Steven A. Kushner, Andrey Rzhetsky
Summary: Schizophrenia is a leading cause of disability worldwide, and its etiology involves genetic and environmental factors. This study utilized unique data sources and mathematical models to estimate the contributions of genetic and environmental factors to schizophrenia risk, finding that environmental factors are an important source of explanatory variance.
Article
Medicine, Research & Experimental
Mahmudur Rahman, Atqiya Munawara Mahi, Rachel Melamed, Mohammad Arif Ul Alam
Summary: Through large-scale observational data and statistical analysis, this study found that antidepressants may increase the risk of COVID-19 complications and uncovered a correlation between certain antidepressants and a lower risk of hospitalization. These findings can guide preventive care and provide suggestions for drug repurposing in COVID-19 treatment.
INTERACTIVE JOURNAL OF MEDICAL RESEARCH
(2023)
Article
Geriatrics & Gerontology
Chengjian Shi, Niser Babiker, Jacek K. Urbanek, Robert L. Grossman, Megan Huisingh-Scheetz, Andrey Rzhetsky
Summary: This study used accelerometer data to predict cognitive decline in older adults within 1 or 5 years, with high accuracy. The proposed models can be applied to clinical practices serving aging populations.
Article
Health Care Sciences & Services
Rachel D. Melamed
Article
Biotechnology & Applied Microbiology
Jason K. Sa, Jae Ryoung Hwang, Young-Jae Cho, Ji-Yoon Ryu, Jung-Joo Choi, Soo Young Jeong, Jihye Kim, Myeong Seon Kim, E. Sun Paik, Yoo-Young Lee, Chel Hun Choi, Tae-Joong Kim, Byoung-Gie Kim, Duk-Soo Bae, Yeri Lee, Nam-Gu Her, Yong Jae Shin, Hee Jin Cho, Ja Yeon Kim, Yun Jee Seo, Harim Koo, Jeong-Woo Oh, Taebum Lee, Hyun-Soo Kim, Sang Yong Song, Joon Seol, Woong-Yang Park, Hee Dong Han, Hyung Jun Ahn, Anil K. Sood, Raul Rabadan, Jin-Ku Lee, Do-Hyun Nam, Jeong-Won Lee