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24th Annual Conference on Research in Computational Molecular Biology, RECOMB 2020

作者： Johnson, Ruth Burch, Kathryn S. Hou, Kangcheng Paciuc, Mario Pasaniuc, Bogdan Sankararaman, Sriram Department of Computer Science University of California Los Angeles Los AngelesCA90095 United States Bioinformatics Interdepartmental Program University of California Los Angeles Los AngelesCA90095 United States Department of Statistics Rice University HoustonTX77005 United States Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA90095 United States Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los AngelesCA90095 United States Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA90095 United States

ISBN: (纸本)9783030452568

A key question in human genetics is understanding the proportion of SNPs modulating a particular phenotype or the proportion of susceptibility SNPs for a disease, termed polygenicity. Previous studies have observed that complex traits tend to be highly polygenic, opposing the previous belief that only a handful of SNPs contribute to a trait [1–4]. Beyond these genome-wide estimates, the distribution of polygenicity across genomic regions as well as the genomic factors that affect regional polygenicity remain poorly understood. © Springer Nature Switzerland AG 2020.

关键词： Genome

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Cyclic alternation of quiet and active sleep states in the octopus

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iscience 2021年第4期24卷 102223页

作者： Medeiros, Sylvia Lima de Souza Paiva, Mizziara Marlen Matias de Lopes, Paulo Henrique Blanco, Wilfredo Lima, Françoise Dantas de Oliveira, Jaime Bruno Cirne de Medeiros, Inácio Gomes Sequerra, Eduardo Bouth de Souza, Sandro Leite, Tatiana Silva Ribeiro, Sidarta Brain Institute Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Graduate Program in Psychobiology Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Graduate Program in Neuroscience Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Computer Science Department State University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Bioinformatics Multidisciplinary Environment Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil Department of Ecology and Zoology Federal University of Santa Catarina Florianópolis Santa Catarina Brazil Graduate Program in Bioinformatics Federal University of Rio Grande do Norte Natal Rio Grande do Norte Brazil

Previous observations suggest the existence of ‘Active sleep’ in cephalopods. To investigate in detail the behavioral structure of cephalopod sleep, we video-recorded four adult specimens of Octopus insularis and quantified their distinct states and transitions. Changes in skin color and texture and movements of eyes and mantle were assessed using automated image processing tools, and arousal threshold was measured using sensory stimulation. Two distinct states unresponsive to stimulation occurred in tandem. The first was a ‘Quiet sleep’ state with uniformly pale skin, closed pupils, and long episode durations (median 415.2 s). The second was an ‘Active sleep’ state with dynamic skin patterns of color and texture, rapid eye movements, and short episode durations (median 40.8 s). ‘Active sleep’ was periodic (60% of recurrences between 26 and 39 min) and occurred mostly after ‘Quiet sleep’ (82% of transitions). These results suggest that cephalopods have an ultradian sleep cycle analogous to that of amniotes. © 2021 The Authors

关键词： Biological sciences Ethology Zoology

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Author Correction: Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis

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Nature genetics 2024年第6期56卷 1319页

作者： Sneha Mitra Rohan Malik Wilfred Wong Afsana Rahman Alexander J Hartemink Yuri Pritykin Kushal K Dey Christina S Leslie Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York City NY USA. Rye Country Day School Rye NY USA. Tri-Institutional Training Program in Computational Biology and Medicine New York City NY USA. Hunter College City University of New York New York City NY USA. Department of Computer Science Duke University Durham NC USA. Program in Computational Biology and Bioinformatics Duke University Durham NC USA. Center for Genomic and Computational Biology Duke University Durham NC USA. Department of Computer Science Princeton University Princeton NJ USA. Lewis-Sigler Institute for Integrative Genomics Princeton University Princeton NJ USA. Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York City NY USA. deyk@***. Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York City NY USA. lesliec@***.

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Design and energy assessment of a new hybrid solar drying dome - Enabling Low-Cost, Independent and Smart Solar Dryer for Indonesia Agriculture 4.0

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IOP Conference Series: Earth and Environmental science 2022年第1期998卷

作者： F E Gunawan A S Budiman B Pardamean E Djuana S Romeli N Hananda C Harito D P B Aji D N N Putri Stevanus Industrial Engineering Department BINUS Graduate Program - Master of Industrial Engineering Bina Nusantara University Jakarta Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480 Electrical Engineering Department Faculty of Industrial Technology Universitas Trisakti Jakarta 11440 Indonesia PT. Impack Pratama Industri Jakarta Indonesia Industrial Engineering Department Faculty of Engineering Bina Nusantara University Jakarta 11480 Indonesia. Mechanical Engineering Department. Faculty of Industrial Technology Universitas Trisakti Jakarta 11440 Indonesia

Solar dryer is typically used for agricultural purposes in Indonesia. There are many economically important crops requiring storage or drying under particular environmental conditions such as temperature and humidity. High temperatures inside solar dryer prevents the growth of microorganism, and quickly reduce moisture content from the substance. A hybrid solar dryer is generally considered to provide the most optimum solution, however solar panels may be expensive and they still only provide heat or energy in the daytime. Hence, we propose here a new kind of hybrid solar dryer for 24/7 optimum conditions for crops - enabled by recent advances in energy technologies as well as Industry 4.0. This study aims to create an efficient, affordable and a self-sufficient intelligent energy system that will be applied to agriculture for storage or drying purposes by measuring the energy needs for the optimal drying system. Therefore, it is crucial to estimate and assess the critical energy needs for such new systems in order to optimize and design such smart solar dryer (SSD) system especially for Indonesia's agricultural needs. We use design experience of our industry partner (PT Impack Pratama Industri, Indonesia) who has been working extensively on such solar dryer dome (SDD) based on polycarbonate material (only solar irradiation, no other technologies) and theoretical framework based on first principles in thermodynamics to estimate and assess critical energy needs for such dome with all the smart technologies. The calculation was performed based on Mollier diagram and the result still a rough estimation of energy required.

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A meta-analysis of Boolean network models reveals design principles of gene regulatory networks

arXiv

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arXiv 2020年

作者： Kadelka, Claus Butrie, Taras-Michael Hilton, Evan Kinseth, Jack Schmidt, Addison Serdarevic, Haris Department of Mathematics Iowa State University AmesIA50011 United States Department of Aerospace Engineering Iowa State University AmesIA50011 United States Department of Computer Science Iowa State University AmesIA50011 United States Bioinformatics and Computational Biology Program Iowa State University AmesIA50011 United States

Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean networks, which are intuitive, simple to describe, and can yield qualitative results even when data is sparse. We assembled the largest repository of expert-curated Boolean GRN models. A meta-analysis of this diverse set of models reveals several design principles. GRNs exhibit more canalization, redundancy and stable dynamics than expected. Moreover, they are enriched for certain recurring network motifs. This raises the important question why evolution favors these design mechanisms. Copyright © 2020, The Authors. All rights reserved.

关键词： Decision making

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Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries (vol 55, pg 89, 2023)

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NATURE GENETICS 2023年第3期55卷 519-520页

作者： Fernandez-Rozadilla, Ceres Timofeeva, Maria Chen, Zhishan Law, Philip Thomas, Minta Schmit, Stephanie Diez-Obrero, Virginia Hsu, Li Fernandez-Tajes, Juan Palles, Claire Sherwood, Kitty Briggs, Sarah Svinti, Victoria Donnelly, Kevin Farrington, Susan Blackmur, James Vaughan-Shaw, Peter Shu, Xiao-ou Long, Jirong Cai, Qiuyin Guo, Xingyi Lu, Yingchang Broderick, Peter Studd, James Huyghe, Jeroen Harrison, Tabitha Conti, David Dampier, Christopher Devall, Mathew Schumacher, Fredrick Melas, Marilena Rennert, Gad Obon-Santacana, Mireia Martin-Sanchez, Vicente Moratalla-Navarro, Ferran Oh, Jae Hwan Kim, Jeongseon Jee, Sun Ha Jung, Keum Ji Kweon, Sun-Seog Shin, Min-Ho Shin, Aesun Ahn, Yoon-Ok Kim, Dong-Hyun Oze, Isao Wen, Wanqing Matsuo, Keitaro Matsuda, Koichi Tanikawa, Chizu Ren, Zefang Gao, Yu-Tang Jia, Wei-Hua Hopper, John Jenkins, Mark Win, Aung Ko Pai, Rish Figueiredo, Jane Haile, Robert Gallinger, Steven Woods, Michael Newcomb, Polly Duggan, David Cheadle, Jeremy Kaplan, Richard Maughan, Timothy Kerr, Rachel Kerr, David Kirac, Iva Bohm, Jan Mecklin, Lukka-Pekka Jousilahti, Pekka Knekt, Paul Aaltonen, Lauri Rissanen, Harri Pukkala, Eero Eriksson, Johan Cajuso, Tatiana Hanninen, Ulrika Kondelin, Johanna Palin, Kimmo Tanskanen, Tomas Renkonen-Sinisalo, Laura Zanke, Brent Mannisto, Satu Albanes, Demetrius Weinstein, Stephanie Ruiz-Narvaez, Edward Palmer, Julie Buchanan, Daniel Platz, Elizabeth Visvanathan, Kala Ulrich, Cornelia Siegel, Erin Brezina, Stefanie Gsur, Andrea Campbell, Peter Chang-Claude, Jenny Hoffmeister, Michael Brenner, Hermann Slattery, Martha Potter, John Tsilidis, Konstantinos Schulze, Matthias Gunter, Marc Murphy, Neil Castells, Antoni Castellvi-Bel, Sergi Moreira, Leticia Arndt, Volker Shcherbina, Anna Stern, Mariana Pardamean, Bens Bishop, Timothy Giles, Graham Southey, Melissa Idos, Gregory McDonnell, Kevin Abu-Ful, Zomoroda Greenson, Joel Shulman, Katerina Lejbkowicz, Flavio Offit, Kenneth Su, Yu-Ru Steinfelder, Robert Keku, Temitope van Guelpen, Bethany Hudson, Thomas Hampel, Heather Pearlman, Edinburgh Cancer Research Centre Institute of Genomics and Cancer University of Edinburgh Edinburgh UK Genomic Medicine Group Instituto de Investigacion Sanitaria de Santiago Santiago de Compostela Spain Colon Cancer Genetics Group Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK Danish Institute for Advanced Study Department of Public Health University of Southern Denmark Odense Denmark Division of Epidemiology Department of Medicine Vanderbilt-Ingram Cancer Center Vanderbilt Epidemiology Center Vanderbilt University Medical Center Nashville TN USA Division of Genetics and Epidemiology Institute of Cancer Research London UK Public Health Sciences Division Fred Hutchinson Cancer Research Center Seattle WA USA Genomic Medicine Institute Cleveland Clinic Cleveland OH USA Population and Cancer Prevention Program Case Comprehensive Cancer Center Cleveland OH USA Colorectal Cancer Group ONCOBELL Program Bellvitge Biomedical Research Institute Barcelona Spain Oncology Data Analytics Program Catalan Institute of Oncology Barcelona Spain Consortium for Biomedical Research in Epidemiology and Public Health Madrid Madrid Spain Department of Clinical Sciences Faculty of Medicine University of Barcelona Barcelona Spain Department of Biostatistics School of Public Health University of Washington Seattle WA USA Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Birmingham UK Department of Public Health Richard Doll Building University of Oxford Oxford UK Department of Biomedical Informatics Vanderbilt University School of Medicine Nashville TN USA Department of Preventive Medicine USC Norris Comprehensive Cancer Center Keck School of Medicine University of Southern California Los Angeles CA USA Center for Public Health Genomics Department of Public Health Sciences University of Virginia Charlottesville VA USA Department of Populat

Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.

关键词： Colorectal cancer Epigenomics Genome-wide association studies Transcriptomics

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The cell surface marker CD36 selectively identifies matured,mitochondria-rich hPSC-cardiomyocytes

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细胞研究（英文版） 2020年第7期30卷 626-629页

作者： Ellen Ngar-Yun Poon Xiao-ling Luo Sarah E.Webb Bin Yan Rui Zhao Stanley Chun Ming Wu Yong Yang Peng Zhang Huajun Bai Jiaofang Shao Ching Man Chan Godfrey Chi-Fung Chan Suk Ying Tsang Rebekah L.Gundry Huang-Tian Yang Kenneth R.Boheler Department of Medicine and Therapeutics and Centre for Cardiovascular Genomics and Medicine The Chinese University of Hong Kong (CUHK) HKSAR China CAS Key Laboratory of Tissue Microenvironment and Tumor Laboratory of Molecular CardiologyShanghai Institute of Nutrition and Health University of Chinese Academy of Sciences (CAS) CAS Shanghai China Division of Life Science and State Key Laboratory of Molecular Neuroscience The Hong Kong University of Science and Technology HKSAR China Department of Computer Science The University of Hong Kong (HKU) HKSAR China Intervention and Cell Therapy Center Peking University Shenzhen Hospital Shenzhen China School of Life Sciences CUHK HKSAR China Department of Paediatrics and Adolescent Medicine HKU HKSAR China School of Biomedical Sciences HKU HKSAR China SUSTech Academy for Advanced Interdisciplinary Studies Southern University of Science and Technology (SUSTech) Shenzhen China Department of Bioinformatics School of Biomedical Engineering and InformaticsNanjing Medical University Nanjing Jiangsu China State Key Laboratory of Agrobiotechnology CUHK HKSAR China Department of Biochemistry and Center for Biomedical Mass Spectrometry Research Medical College of Wisconsin Milwaukee WIUSA CardiOmics Program Center for Heart and Vascular Research Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology University of Nebraska Medical Center Omaha NE USA Institute for Stem Cell and Regeneration Medicine CASBeijing China Division of Cardiology Department of Medicineand Department of Biomedical Engineering The Johns Hopkins University Baltimore MD USA

Dear Editor,Human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) are of significant translational value to in vitro studies of human cardiac development, drug and cardiotoxicity testing and cardiac disease *** of hPSCs to CMs,however, yields mixed cultures of atrial-, ventricular-, and pacemaker-like cells as well as non-CMs in variable proportions.1

关键词： Stem-cell differentiation Stem cells

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SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest

SeqScreen: a biocuration platform for robust taxonomic and b...

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IEEE International Conference on bioinformatics and Biomedicine

作者： Dreycey Albin Dan Nasko R. A. Leo Elworth Jacob Lu Advait Balaji Christian Diaz Nidhi Shah Jeremy Selengut Chris Hulme-Lowe Pravin Muthu Gene Godbold Mikael Lindvall Madeline Diep Adam Porter Mihai Pop Krista Ternus Todd J. Treangen Program in Systems Synthetic and Physical Biology Rice University Center for Bioinformatics and Computational Biology University of Maryland Department of Computer Science Rice University Signature Science LLC Fraunhofer Center for Experimental Software Engineering Department of Computer Science University of Maryland

ISBN: (纸本)9781728118680

Rapid advancements in synthetic biology and nucleic acid synthesis, in particular concerns about its intentional or accidental misuse, call for more sophisticated screening tools to identify genes of interest within short sequence fragments. One major gap in predicting genes of concern is the inadequacy of current tools and ontologies to describe the specific biological processes of pathogenic proteins. The objective of this work is to design software that sensitively assigns taxonomic classifications, functional annotations, and biological processes of interest to short nucleotide sequences of unknown origin (50bp-1,000bp). The overarching goal is to perform sensitive characterization of short sequences and highlight specific pathogenic biological processes of interest (BPoIs). The SeqScreen software executes these tasks in analytical workflows with Nextflow and outputs results in a tab-delimited report. Local and global alignments differentiate hits to taxonomically-related sequences from similar but unrelated sequences, and an ensemble approach leverages multiple tools and databases to assign a variety of functional terms to each query sequence. Final biological process assessments are made from the predicted functional annotations, which leverage information in pre-existing databases, as well as new custom biocurations. Machine learning models predict each biological process of interest on large protein databases before incorporation into the SeqScreen framework to streamline computational efficiency, ensure reproducible results, allow for version control, and facilitate the review of the automated predictions by expert biocurators. The SeqScreen source code is available at .

关键词： Biological Process interest Base Sequence Nucleic acids Version control protein database Database synthetic biology ANNOTATIONS Leverage

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Rewriting regulatory DNA to dissect and reprogram gene expression

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Cell 2025年第12期188卷 3349-3366.e23,26页

作者： Martyn, Gabriella E. Montgomery, Michael T. Jones, Hank Guo, Katherine Doughty, Benjamin R. Linder, Johannes Bisht, Deepa Xia, Fan Cai, Xiangmeng S. Chen, Ziwei Cochran, Kelly Lawrence, Kathryn A. Munson, Glen Pampari, Anusri Fulco, Charles P. Sahni, Nidhi Kelley, David R. Lander, Eric S. Kundaje, Anshul Engreitz, Jesse M. Department of Genetics Stanford University School of Medicine Stanford 94305 CA United States Basic Science and Engineering Initiative Stanford Children's Health Betty Irene Moore Children's Heart Center Stanford 94305 CA United States Calico Life Sciences LLC South San Francisco 94080 CA United States Department of Genitourinary Medical Oncology Division of Cancer Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Genomic Medicine The University of Texas MD Anderson Cancer Center Houston 77030 TX United States Department of Epigenetics and Molecular Carcinogenesis The University of Texas MD Anderson Cancer Center Houston 77230 TX United States Department of Bioengineering Stanford University Stanford 94305 CA United States Department of Computer Science Stanford University Stanford 94305 CA United States Novo Nordisk Foundation Center for Genomic Mechanisms of Disease Broad Institute of MIT and Harvard Cambridge 02142 MA United States Gene Regulation Observatory Broad Institute of MIT and Harvard Cambridge 02142 MA United States Broad Institute of MIT and Harvard Cambridge 02142 MA United States Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston 77230 TX United States Quantitative and Computational Biosciences Program Baylor College of Medicine Houston 77030 TX United States Department of Biology MIT Cambridge 02139 MA United States Department of Systems Biology Harvard Medical School Boston 02115 MA United States Stanford Cardiovascular Institute Stanford University Stanford 94305 CA United States

Regulatory DNA provides a platform for transcription factor binding to encode cell-type-specific patterns of gene expression. However, the effects and programmability of regulatory DNA sequences remain difficult to map or predict. Here, we develop variant effects from flow-sorting experiments with CRISPR targeting screens (Variant-EFFECTS) to introduce hundreds of designed edits to endogenous regulatory DNA and quantify their effects on gene expression. We systematically dissect and reprogram 3 regulatory elements for 2 genes in 2 cell types. These data reveal endogenous binding sites with effects specific to genomic context, transcription factor motifs with cell-type-specific activities, and limitations of computational models for predicting the effect sizes of variants. We identify small edits that can tune gene expression over a large dynamic range, suggesting new possibilities for prime-editing-based therapeutics targeting regulatory DNA. Variant-EFFECTS provides a generalizable tool to dissect regulatory DNA and to identify genome editing reagents that tune gene expression in an endogenous context. © 2025 Elsevier Inc.

关键词： CRISPR enhancers gene regulation high-throughput screening non-coding variants predictive models prime editing RNA FlowFISH sequence design transcription factors

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Improvement of Jakarta's air quality during large scale social restriction

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IOP Conference Series: Earth and Environmental science 2021年第1期729卷

作者： R Rahutomo K Purwandari J W C Sigalingging B Pardamean Information System Department School of Information Systems Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480 Database Center Division of BMKG Meteorological Climatological and Geophysical Agency Jakarta Indonesia 10720 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480

After Large-Scale Social Restriction (PSBB) established in Jakarta, a change of air quality was indicated by the citizens. Representatives of Indonesia's Agency for Meteorology, Climatology, and Geophysics (BMKG) supported as the fact that mobility of Jakarta's citizen and commuters were reduced. With utilizing Weather Data Acquisition System managed by BMKG, this research compared fluctuations of Jakarta's air quality during two periods of time: Pre-PSBB and During-PSBB. This study proved that Jakarta's air quality has positively improved compared to the previous year, although in the lower range of unhealthy level.

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