Article
Biochemical Research Methods
James Gooch, Sireethorn Tungsirisurp, Hayley Costanzo, Richard Napier, Nunzianda Frascione
Summary: The study selected ssDNA aptamers against human sperm cells using Cell-SELEX and massively parallel sequencing technologies, revealing promising aptamer candidates that selectively bind sperm cells. These aptamers have the potential to increase the efficiency of sexual offence investigations by facilitating sperm detection.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Genetics & Heredity
Lucinda Davenport, Laurence Devesse, Denise Syndercombe Court, David Ballard
Summary: The study focuses on the analysis of SNPs for identity or kinship applications in forensic genetics. It shows that including flanking region variation in the analysis can significantly reduce the match probability between different populations, improving the accuracy and reliability of identification.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Biology
Yan Zheng, Xuequn Shang, Wing-Kin Sung
Summary: Structural variations (SVs) are genomic rearrangements larger than 50bp, and they are important in genetic diseases and evolution mechanisms. Existing long-read SV callers often fail to detect true SVs or mistakenly detect false SVs in repetitive regions and regions with multi-allelic SVs, primarily due to messy alignments caused by high error rate in ONT long reads. To address this, we propose a novel method called SVsearcher, which greatly improves SV detection accuracy and is capable of identifying a high percentage of multi-allelic SVs.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Chemistry, Multidisciplinary
Yu-An Kuo, Cheulhee Jung, Yu-An Chen, Hung-Che Kuo, Oliver S. Zhao, Trung D. Nguyen, James R. Rybarski, Soonwoo Hong, Yuan- Chen, Dennis C. Wylie, John A. Hawkins, Jada N. Walker, Samuel W. J. Shields, Jennifer S. Brodbelt, Jeffrey T. Petty, Ilya J. Finkelstein, Hsin-Chih Yeh
Summary: The study revealed that the nucleobases at positions 7-12 of the 18-nucleotide-long activator are critical to creating bright NCBs, while positions 4-6 and 2-4 are hotspots to generate yellow-orange and red POTs.
ADVANCED MATERIALS
(2022)
Article
Nanoscience & Nanotechnology
Cong Wang, Shi-Jun Liang, Chen-Yu Wang, Zai-Zheng Yang, Yingmeng Ge, Chen Pan, Xi Shen, Wei Wei, Yichen Zhao, Zaichen Zhang, Bin Cheng, Chuan Zhang, Feng Miao
Summary: The growth of intelligent devices in the Internet of Things has created a need for real-time processing of large volumes of analogue data. Utilizing continuous data representation and frequency multiplexing in nanoscale crossbar arrays enables the implementation of a scalable massively parallel computing scheme for direct processing of analogue information.
NATURE NANOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Sihan Liu, Yuanyuan Zeng, Chao Wang, Qian Zhang, Meilin Chen, Xiaolu Wang, Lanchen Wang, Yu Lu, Hui Guo, Fengxiao Bu
Summary: This study validated a new gender-inference tool, seGMM, which accurately determines the gender of samples and identifies sex chromosomal abnormalities. The seGMM tool demonstrated high accuracy and outperformed other existing tools in gender inference on different gene panel datasets. Furthermore, seGMM accurately identified sex chromosomal abnormalities through the analysis of sex chromosome marker genes.
FRONTIERS IN GENETICS
(2022)
Review
Endocrinology & Metabolism
Aideen M. McInerney-Leo, Emma L. Duncan
Summary: There have been two major eras in gene discovery history, from linkage analysis to massively parallel sequencing (MPS). MPS has greatly accelerated the identification of disease genes, reducing the time needed to determine disease genes from years to weeks.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Review
Genetics & Heredity
Cordula Haas, Jacqueline Neubauer, Andrea Patrizia Salzmann, Erin Hanson, Jack Ballantyne
Summary: Transcriptome analyses have seen significant growth in forensic genetics in recent years, with applications such as body fluid and tissue identification, determining stain and donor age, estimating post-mortem interval, and conducting post mortem death investigations. The introduction of Massively Parallel Sequencing (MPS) has opened up new possibilities for this field, allowing for high-resolution analyses and whole transcriptome sequencing of forensically relevant materials.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2021)
Article
Genetics & Heredity
Ruiyang Tao, Qiannan Xu, Shouyu Wang, Ruocheng Xia, Qi Yang, Anqi Chen, Yiling Qu, Yehui Lv, Suhua Zhang, Chengtao Li
Summary: With the development of massively parallel sequencing (MPS), the kinship analysis has become more convenient. In this study, 243 Chinese Han individuals from 17 families were sequenced using the ForenSeq Signature Kit, and the analysis was conducted using likelihood ratio and identical by state methods. The results showed that the kit was effective in analyzing parent-child, full sibling, and most second-degree kinships.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2022)
Article
Genetics & Heredity
Athina Vidaki, Benjamin Planterose Jimenez, Brando Poggiali, Vivian Kalamara, Kristiaan J. van der Gaag, Silvana C. E. Maas, Mohsen BIOS Consortium, Mohsen Ghanbari, Titia Sijen, Manfred Kayser
Summary: Tobacco smoking is a widespread habit with significant health risks and mortality. This study aims to predict smoking habits using blood DNA methylation. The results show high reproducibility of methylation measurements and accurate prediction of smoking habits using corrected data.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Biochemical Research Methods
Yadong Liu, Tao Jiang, Junhao Su, Bo Liu, Tianyi Zang, Yadong Wang
Summary: The SKSV toolkit is proposed for detecting structural variations, which shows a significantly faster speed and higher F1 scores compared to state-of-the-art SV calling approaches.
Article
Geosciences, Multidisciplinary
Piyoosh Jaysaval, Glenn E. Hammond, Timothy C. Johnson
Summary: Electrical resistivity tomography (ERT) is a widely used geophysical method for subsurface investigations. This study presents a robust and scalable implementation of forward modeling and inversion algorithms for ERT data, developed within the framework of the open-source code PFLOTRAN. The implementation shows good agreement with analytical solutions and exhibits almost linear scalability for forward modeling and superlinear scalability for Jacobian computation on high-performance computing resources.
GEOSCIENTIFIC MODEL DEVELOPMENT
(2023)
Article
Biotechnology & Applied Microbiology
Alexander Schmitz, Fuzhong Zhang
Summary: Our study demonstrates that sequences with higher tRNA Adaptation Index (TAI) scores and Codon Adaptation Index (CAI) scores exhibit higher variation in green fluorescent protein (GFP) expression. This variation is not observed in sequences with high Normalized Translation Efficiency Index (nTE) scores or based on mRNA secondary structure folding energy. We found that noise in GFP expression scales with mean protein abundance for low-abundant proteins but remains constant for high-abundant proteins, suggesting that noise for high-abundance proteins is not primarily due to translation elongation. This indicates that codon optimization can be performed without worrying about gene expression noise in biotechnology applications.
Article
Energy & Fuels
Juraj Kardos, Timothy Holt, Vincenzo Fazio, Luca Fabietti, Filippo Spazzini, Olaf Schenk
Summary: This study analyzes the computational aspects in massively parallel simulations from the perspective of efficient hardware utilization, presenting a method for efficiently managing and processing computational tasks. A series of numerical experiments demonstrate that the optimized high-throughput computation strategy significantly reduces response times and prevents memory bottlenecks.
SUSTAINABLE ENERGY GRIDS & NETWORKS
(2022)
Article
Biochemical Research Methods
Wenyan Gu, Aizhong Zhou, Lusheng Wang, Shiwei Sun, Xuefeng Cui, Daming Zhu
Summary: Long-read sequencing technologies have enabled the detection of genome structural variants, with the SVLR method being able to detect new types of SVs and achieve high accuracy levels. Additionally, SVLR shows improvements in recall rates for classic SVs without compromising precision.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Claudia Calabrese, Natalie R. Davidson, Deniz Demircioglu, Nuno A. Fonseca, Yao He, Andre Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, Liliana Greger, Siliang Li, Dongbing Liu, Marc D. Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter Bailey, Serap Erkek, Katherine A. Hoadley, Yong Hou, Matthew R. Huska, Helena Kilpinen, Jan O. Korbel, Maximillian G. Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarstrom, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G. Stark, Hong Su, Patrick Tan, Sebastian M. Waszak, Christina Yung, Shida Zhu, Philip Awadalla, Chad J. Creighton, Matthew Meyerson, B. F. Francis Ouellette, Kui Wu, Huanming Yang, Alvis Brazma, Angela N. Brooks, Jonathan Goke, Gunnar Raetsch, Roland F. Schwarz, Oliver Stegle, Zemin Zhang
Article
Oncology
Zhouwei Zhang, Netta Makinen, Yosuke Kasai, Grace E. Kim, Begona Diosdado, Eric Nakakura, Matthew Meyerson
GENES CHROMOSOMES & CANCER
(2020)
Article
Multidisciplinary Sciences
Li C. Xia, Paul Van Hummelen, Matthew Kubit, HoJoon Lee, John M. Bell, Susan M. Grimes, Christina Wood-Bouwens, Stephanie U. Greer, Tyler Barker, Derrick S. Haslem, James M. Ford, Gail Fulde, Hanlee P. Ji, Lincoln D. Nadauld
SCIENTIFIC REPORTS
(2020)
Article
Oncology
Yusuke Koga, Hanbing Song, Zachary R. Chalmers, Justin Newberg, Eejung Kim, Jian Carrot-Zhang, Daphnee Piou, Paz Polak, Sarki A. Abdulkadir, Elad Ziv, Matthew Meyerson, Garrett M. Frampton, Joshua D. Campbell, Franklin W. Huang
CLINICAL CANCER RESEARCH
(2020)
Editorial Material
Biochemistry & Molecular Biology
Matthew Meyerson
Article
Biochemical Research Methods
Liam F. Spurr, Mehdi Touat, Alison M. Taylor, Adrian M. Dubuc, Juliann Shih, David M. Meredith, William Pisano, Matthew L. Meyerson, Keith L. Ligon, Andrew D. Cherniack, Yvonne Y. Li, Rameen Beroukhim
Summary: The expansion of targeted panel sequencing efforts has created opportunities for large-scale genomic analysis, but tools for copy-number quantification on panel data are lacking. We introduce ASCETS, a method for the efficient quantitation of arm and chromosome-level copy-number changes from targeted sequencing data.
Article
Oncology
Harshabad Singh, Yvonne Y. Li, Liam F. Spurr, Atul B. Shinagare, Ritika Abhyankar, Emma Reilly, Lauren K. Brais, Anwesha Nag, Matthew D. Ducar, Aaron R. Thorner, Geoffrey Shapiro, Rachel B. Keller, Cheta Siletti, Jeffrey W. Clark, Anna F. Farago, Jessica J. Lin, George D. Demetri, Rahul Gujrathi, Matthew H. Kulke, Laura E. MacConaill, Azra H. Ligon, Ewa Sicinska, Matthew L. Meyerson, Jeffrey A. Meyerhardt, Andrew D. Cherniack, Brian M. Wolpin, Kimmie Ng, Marios Giannakis, Jason L. Hornick, James M. Cleary
Summary: RTK fusions in colorectal cancer are rare but enrich in right-sided and MMR-D colorectal cancers. They occur in RAS and BRAF wild-type tumors, providing an important therapeutic target for MSS colorectal cancer.
CLINICAL CANCER RESEARCH
(2021)
Article
Oncology
Jian Carrot-Zhang, Giovanny Soca-Chafre, Nick Patterson, Aaron R. Thorner, Anwesha Nag, Jacqueline Watson, Giulio Genovese, July Rodriguez, Maya K. Gelbard, Luis Corrales-Rodriguez, Yoichiro Mitsuishi, Gavin Ha, Joshua D. Campbell, Geoffrey R. Oxnard, Oscar Arrieta, Andres F. Cardona, Alexander Gusev, Matthew Meyerson
Summary: This study found significant associations between Native American ancestry and somatic genomic landscape in lung cancer patients, suggesting that germline genetics may play a key role in tumor mutation burden and specific driver mutations. Further studies are needed to identify the genetic alleles underlying the variation in EGFR and KRAS mutation frequencies.
Article
Immunology
Mark N. Lee, Matthew Meyerson
Summary: This study introduces a high-throughput epitope identification system that combines T cell-secreted cytokines capture, cell sorting, and next-generation sequencing to identify new class I- and class II-restricted epitopes. The technology successfully validated known viral, neoepitope, and autoimmune epitope-specific TCR targets, as well as discovered new epitopes encoded by the human cytomegalovirus genome. This cytokine capture-based assay enables pooled screening of thousands of encoded peptides for epitope discovery and may lead to identification of HLA-epitope-TCR complexes relevant to disease control, etiology, or treatment.
SCIENCE IMMUNOLOGY
(2021)
Correction
Cell Biology
Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S. Damrauer, Tiago Chedraoui Silva, Christopher K. Wong, Hyo Young Choi, Ina Felau, A. Gordon Robertson, Mauro A. A. Castro, Lisui Bao, Esther Rheinbay, Eric Minwei Liu, Tuan Trieu, David Haan, Christina Yau, Toshinori Hinoue, Yuexin Liu, Ofer Shapira, Kiran Kumar, Karen L. Mungall, Hailei Zhang, Jake June-Koo Lee, Ashton Berger, Galen F. Gao, Binyamin Zhitomirsky, Wen-Wei Liang, Meng Zhou, Sitapriya Moorthi, Alice H. Berger, Eric A. Collisson, Michael C. Zody, Li Ding, Andrew D. Cherniack, Gad Getz, Olivier Elemento, Christopher C. Benz, Josh Stuart, J. C. Zenklusen, Rameen Beroukhim, Jason C. Chang, Joshua D. Campbell, D. Neil Hayes, Lixing Yang, Peter W. Laird, John N. Weinstein, David J. Kwiatkowski, Ming S. Tsao, William D. Travis, Ekta Khurana, Benjamin P. Berman, Katherine A. Hoadley, Nicolas Robine, Matthew Meyerson, Ramaswamy Govindan, Marcin Imielinski
Article
Oncology
Zhouwei Zhang, Lior Golomb, Matthew Meyerson
Summary: This study provides functional genomic insight into the sensitivity of cancer cells to CDK4 or CDK6 inhibition, and identifies unique cancer cell populations that might be sensitive to CDK4-selective or CDK6-selective inhibitors.
Article
Microbiology
Jason Nomburg, Wei Zou, Thomas C. Frost, Chandreyee Datta, Shobha Vasudevan, Gabriel J. Starrett, Michael J. Imperiale, Matthew Meyerson, James A. DeCaprio
Summary: The study compares the transcriptome of different polyomaviruses and identifies complex transcription patterns and novel transcripts that increase the coding capacity of the viruses. This research provides insights into the transcriptome architecture of polyomaviruses and their role in human diseases.
Article
Genetics & Heredity
Netta Makinen, Meng Zhou, Zhouwei Zhang, Yosuke Kasai, Elizabeth Perez, Grace E. Kim, Chrissie Thirlwell, Eric Nakakura, Matthew Meyerson
Summary: This study reveals the major genomic diversity among multifocal ileal NETs, showing that synchronous primary tumors within each patient develop independently with different somatic variations. Additionally, tumors from the same patient can gain or lose different parental alleles, emphasizing the need to identify and remove all primary tumors to prevent metastasis and to optimize targeted treatments.
Editorial Material
Oncology
Blake E. Sanders, Guanxi Qiao, Jodi Hirschman, Matthew Meyerson
Summary: The role of the microbiome in human cancer is a subject of intense research and debate. The physical association of Fusobacterium with colorectal cancer has been extensively studied, offering potential for diagnosis and treatment, but controversies remain regarding the impact of Fusobacterium species on colorectal cancer proliferation and the immune microenvironment.
Article
Biochemistry & Molecular Biology
Sooncheol Lee, Stephanie Hoyt, Xiaoyun Wu, Colin Garvie, Joseph McGaunn, Mrinal Shekhar, Marcus Totzl, Matthew G. Rees, Andrew D. Cherniack, Matthew Meyerson, Heidi Greulich
Summary: The study reveals that Velcrin compounds kill cancer cells by inducing complex formation between phosphodiesterase 3A (PDE3A) and Schlafen family member 12 (SLFN12). SLFN12 specifically digests tRNA(Leu)(TAA), and Velcrin treatment promotes the cleavage of tRNA(Leu)(TAA) by inducing PDE3A-SLFN12 complex formation. This leads to downregulation of tRNA(Leu)(TAA), ribosome pausing at Leu-TTA codons, and global inhibition of protein synthesis, defining a new mechanism of apoptosis initiation.
NATURE CHEMICAL BIOLOGY
(2023)