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• Genomics and the future of conservation genetics
  openalex Fred W. Allendorf, Paul A. Hohenlohe, Gordon Luikart 2010-09-17 置信度 0.72 GenomicsBiologyConservation geneticsConservation biologyBiodiversity
• A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
  The modulation of DNA-protein interactions by methylation of protein-binding sites in DNA and the occurrence in genomic imprinting, X chromosome inactivation, and fragile X syndrome of different methylation patterns in DNA of different chromosomal origin have …
  openalex Marianne Frommer, Louise E. McDonald, David Millar, Christina M. Collis 等 1992-03-01 置信度 0.72 DNA methylation5-MethylcytosineBiologygenomic DNADNA
• A simple and rapid method for the preparation of plant genomic DNA for PCR analysis
  K. Edwards, C. Johnstone, C. Thompson; A simple and rapid method for the preparation of plant genomic DNA for PCR analysis, Nucleic Acids Research, Volume
  openalex Keith J. Edwards, CN Johnstone, C. Thompson 1991-01-01 置信度 0.72 BiologySection (typography)Library sciencePlant scienceSimple (philosophy)
• Genomic Selection for Crop Improvement
  ABSTRACT Despite important strides in marker technologies, the use of marker‐assisted selection has stagnated for the improvement of quantitative traits. Biparental mating designs for the detection of loci affecting these traits (quantitative trait loci [QTL])…
  openalex Elliot L. Heffner, Mark E. Sorrells, Jean‐Luc Jannink 2009-01-01 置信度 0.72 BiologyQuantitative trait locusGenomic selectionSelection (genetic algorithm)Heritability
• Universal and rapid salt-extraction of high quality genomic DNA for PCR- based techniques
  A very simple, fast, universally applicable and reproducible method to extract high quality megabase genomic DNA from different organisms is described. We applied the same method to extract high quality complex genomic DNA from different tissues (wheat, barley…
  openalex S. Aljanabi 1997-11-15 置信度 0.72 Biologygenomic DNADNA extractionDNACloning (programming)
• Systematic identification of genomic markers of drug sensitivity in cancer cells
  openalex Mathew J. Garnett, Elena J. Edelman, Sonja J. Heidorn, Chris Greenman 等 2012-03-01 置信度 0.72 CancerPharmacogenomicsBiologyCancer cellBiomarker
• GMAP: a genomic mapping and alignment program for mRNA and EST sequences
  MOTIVATION: We introduce GMAP, a standalone program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets.…
  openalex Ting‐Di Wu, C.K. Watanabe 2005-02-22 置信度 0.72 Computer scienceComputational biologyProbabilistic logicSequence (biology)Genetics
• The re-emergence of natural products for drug discovery in the genomics era
  openalex Alan L. Harvey, RuAngelie Edrada‐Ebel, Ronald J. Quinn 2015-01-23 置信度 0.72 Drug discoveryNatural productComputational biologyNatural (archaeology)Natural Product Research
• Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma
  Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC cases by DNA methylati…
  openalex Adrian Ally, Miruna Balasundaram, Rebecca Carlsen, Eric Chuah 等 2017-06-01 置信度 0.72 BiologyHepatocellular carcinomaCancer researchExome sequencingDNA methylation
• Integrated genomic characterization of oesophageal carcinoma
  Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern…
  openalex 2017-01-01 置信度 0.72 AdenocarcinomaCancer researchEsophagusPathologyCancer
• Big Data: Astronomical or Genomical?
  Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: as…
  openalex Zachary Stephens, Skylar Y. Lee, Faraz Faghri, Roy H. Campbell 等 2015-07-07 置信度 0.72 Big dataGenomicsData scienceBiologyComputational genomics
• Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma
  We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with characteristic low neoplastic cellularity. Deep whole-exome sequencing revealed recurrent somatic mutation…
  openalex Benjamin J. Raphael, Ralph H. Hruban, Andrew J. Aguirre, Richard A. Moffitt 等 2017-08-01 置信度 0.72 GNAS complex locusKRASCDKN2ACancer researchBiology
• Toward a Shared Vision for Cancer Genomic Data
  This FAIRsharing record describes: The National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is a data sharing The National Cancer Institute's Genomic Data Commons (GDC) was created to promote precision medicine in oncology. It supports the import and…
  openalex Robert L. Grossman, Allison P. Heath, Vincent Ferretti, Harold Varmus 等 2016-09-21 置信度 0.72 MedicineCancerMEDLINEInternal medicineBiology
• Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations.
  We developed bulked segregant analysis as a method for rapidly identifying markers linked to any specific gene or genomic region. Two bulked DNA samples are generated from a segregating population from a single cross. Each pool, or bulk, contains individuals t…
  openalex Richard W. Michelmore, Ilan Paran, Rick Kesseli 1991-11-01 置信度 0.72 Bulked segregant analysisGeneticsBiologyLocus (genetics)Population
• The genomic basis of adaptive evolution in threespine sticklebacks
  Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a h…
  openalex Felicity C. Jones, Manfred Grabherr, Yingguang Frank Chan, Pamela Russell 等 2012-04-01 置信度 0.72 BiologyEvolutionary biologyAdaptive evolutionBasis (linear algebra)Gene duplication
• When repeats drive the vocabulary: a Byte-Pair Encoding analysis of T2T primate genomes
  The emergence of telomere-to-telomere (T2T) genome assemblies has opened new avenues for comparative genomics, yet effective tokenization strategies for genomic sequences remain underexplored. In this pilot study, we apply Byte Pair Encoding (BPE) to nine T2T …
  arxiv Marina Popova, Iaroslav Chelombitko, Aleksey Komissarov 2025-05-13T19:27:58Z 置信度 0.78 q-bio.GNcs.AI
• On pairwise distances and median score of three genomes under DCJ
  In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness. Generalization of this measur…
  arxiv Sergey Aganezov,, Max A. Alekseyev 2012-08-01T08:20:16Z 置信度 0.78 q-bio.GNcs.DMq-bio.PE
• Leveraging State Space Models in Long Range Genomics
  Long-range dependencies are critical for understanding genomic structure and function, yet most conventional methods struggle with them. Widely adopted transformer-based models, while excelling at short-context tasks, are limited by the attention module's quad…
  arxiv Matvei Popov, Aymen Kallala, Anirudha Ramesh, Narimane Hennouni 等 2025-04-07T18:34:06Z 置信度 0.78 q-bio.GNcs.CVcs.LG
• Evidence for abundant transcription of non-coding regions in the Saccharomyces cerevisiae genome
  Background: Recent studies in a growing number of organisms have yielded accumulating evidence that a significant portion of the non-coding region in the genome is transcribed. We address this issue in the yeast Saccharomyces cerevisiae. Results: Taking into a…
  arxiv Moshe Havilio, Erez Y. Levanon, Galia Lerman, Martin Kupiec 等 2005-06-16T13:28:40Z 置信度 0.78 q-bio.GN
• GREGoR: Accelerating Genomics for Rare Diseases
  Rare diseases are collectively common, affecting approximately one in twenty individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in DNA sequencing, development of new computational and experimental a…
  arxiv Moez Dawood, Ben Heavner, Marsha M. Wheeler, Rachel A. Ungar 等 2024-12-18T21:11:13Z 置信度 0.78 q-bio.OT
• Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties
  Predicting the response of a specific cancer to a therapy is a major goal in modern oncology that should ultimately lead to a personalised treatment. High-throughput screenings of potentially active compounds against a panel of genomically heterogeneous cancer…
  arxiv Michael P. Menden, Francesco Iorio, Mathew Garnett, Ultan McDermott 等 2012-12-03T19:38:09Z 置信度 0.78 q-bio.GNcs.CEcs.LGq-bio.CB
• bioETH-Beacon: A Confidential On-Chain Genomic Beacon with Encrypted Counts, Filters, and Bounded Noise over a Fully Homomorphic EVM
  The Global Alliance for Genomics and Health (GA4GH) Beacon protocol lets researchers ask whether a genomic variant has been observed in a participating cohort and receive aggregate variant-level counts. As Beacon networks grow, two privacy risks remain: host i…
  arxiv Christos Galanopoulos, Kimon Antonios Provatas, Ilias Georgakopoulos-Soares 2026-06-18T14:49:13Z 置信度 0.78 q-bio.GNcs.CR
• A framework for cost-constrained genome rearrangement under Double Cut and Join
  The study of genome rearrangement has many flavours, but they all are somehow tied to edit distances on variations of a multi-graph called the breakpoint graph. We study a weighted 2-break distance on Eulerian 2-edge-colored multi-graphs, which generalizes wei…
  arxiv Pijus Simonaitis, Annie Chateau, Krister M. Swenson 2018-02-21T11:12:45Z 置信度 0.78 cs.DScs.DMmath.COq-bio.GN
• Detection of selective sweeps in cattle using genome-wide SNP data
  The domestication and subsequent selection by humans to create breeds of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability, breed characteristics …
  arxiv Holly R. Ramey, Jared E. Decker, Stephanie D. McKay, Megan M. Rolf 等 2012-12-11T04:50:02Z 置信度 0.78 q-bio.GNq-bio.PE
• AABAC -- Automated Attribute Based Access Control for Genomics Data
  The COVID-19 crisis has demonstrated the potential of cutting-edge genomics research. However, privacy of these sensitive pieces of information is an area of significant concern for genomics researchers. The current security models makes it difficult to create…
  arxiv David Reddick, Justin Presley, F. Alex Feltus, Susmit Shannigrahi 2022-04-10T03:42:06Z 置信度 0.78 cs.CRcs.NI
• Blockchain for Genomics: A Systematic Literature Review
  Human genomic data carry unique information about an individual and offer unprecedented opportunities for healthcare. The clinical interpretations derived from large genomic datasets can greatly improve healthcare and pave the way for personalized medicine. Sh…
  arxiv Mohammed Alghazwi, Fatih Turkmen, Joeri van der Velde, Dimka Karastoyanova 2021-11-19T10:59:32Z 置信度 0.78 cs.CR
• Relationship between metabolic and genomic diversity in sesame (Sesamum indicum L.)
  Background: Diversity estimates in cultivated plants provide a rationale for conservation strategies and support the selection of starting material for breeding programs. Diversity measures applied to crops usually have been limited to the assessment of genome…
  arxiv H. Laurentin, A. Ratzinger, P. Karlovsky 2014-11-01T11:06:36Z 置信度 0.78 q-bio.PEq-bio.GN
• Genomic regulatory architecture of human embryo retroviral LTR elements affecting evolution, development, and pathophysiology of Modern Humans
  Two distinct families of pan-primate endogenous retroviruses, namely HERVL and HERVH, infected primates germline, colonized host genomes, and evolved into the global retroviral genomic regulatory dominion (GRD) operating during human embryogenesis (HE). HE ret…
  arxiv Gennadi Glinsky 2023-10-25T08:04:58Z 置信度 0.78 q-bio.GNq-bio.MNq-bio.NCq-bio.PEq-bio.TO
• Evolutionary genomics of transposable elements in Saccharomyces cerevisiae
  Saccharomyces cerevisiae is one of the premier model systems for studying the genomics and evolution of transposable elements. The availability of the S. cerevisiae genome led to many insights into its five known transposable element families (Ty1-Ty5) in the …
  arxiv Martin Carr, Douda Bensasson, Casey M. Bergman 2012-09-01T19:56:01Z 置信度 0.78 q-bio.PEq-bio.GN
• The Mechanistic Invariance Test: Genomic Language Models Fail to Learn Positional Regulatory Logic
  Genomic language models (gLMs) have transformed computational biology, achieving state-of-the-art performance across genomic tasks. Yet a fundamental question threatens the foundation of this success: do these models learn the mechanistic principles governing …
  arxiv Bryan Cheng, Jasper Zhang 2026-04-08T00:56:26Z 置信度 0.78 q-bio.GN
• Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster
  Wolbachia are maternally-inherited symbiotic bacteria commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. Here we use whole genome resequencing data from 290 lines of Drosophila mel…
  arxiv Mark F. Richardson, Lucy A. Weinert, John J. Welch, Raquel S. Linheiro 等 2012-05-25T21:29:14Z 置信度 0.78 q-bio.PEq-bio.GN
• Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species
  Background: In the marine environment, where there are few absolute physical barriers, contemporary contact between previously isolated species can occur across great distances, and in some cases, may be inter-oceanic. [..] in the minke whale species complex […
  arxiv Ketil Malde, Bjørghild B. Seliussen, María Quintela, Geir Dahle 等 2018-09-06T13:49:32Z 置信度 0.78 q-bio.GN
• Can artificial neural networks supplant the polygene risk score for risk prediction of complex disorders given very large sample sizes?
  Genome-wide association studies (GWAS) provide a means of examining the common genetic variation underlying a range of traits and disorders. In addition, it is hoped that GWAS may provide a means of differentiating affected from unaffected individuals. This ha…
  arxiv Carlos Pinto, Michael Gill, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Elizabeth A. Heron 2019-11-20T16:08:27Z 置信度 0.78 q-bio.GN
• Predicting drug response of tumors from integrated genomic profiles by deep neural networks
  The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of anti-cancer drugs illumi…
  arxiv Yu-Chiao Chiu, Hung-I Harry Chen, Tinghe Zhang, Songyao Zhang 等 2018-05-20T04:27:09Z 置信度 0.78 stat.MLcs.LGq-bio.GN
• Distilling Genomic Models for Efficient mRNA Representation Learning via Embedding Matching
  Large Genomic Foundation Models have recently achieved remarkable results and in-vivo translation capabilities. However these models quickly grow to over a few Billion of parameters and are expensive to run when compute is limited. To overcome this challenge, …
  arxiv Rasched Haidari, Sam Martin, Maxime Allard 2026-03-27T14:07:13Z 置信度 0.78 cs.LGcs.AI
• Identifying cancer subtypes in glioblastoma by combining genomic, transcriptomic and epigenomic data
  We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering struct…
  arxiv Richard S. Savage, Zoubin Ghahramani, Jim E. Griffin, Paul Kirk 等 2013-04-12T09:06:45Z 置信度 0.78 q-bio.GNstat.ML
• BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis
  Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for finding exact-matchi…
  arxiv Can Firtina, Jisung Park, Mohammed Alser, Jeremie S. Kim 等 2021-12-16T08:18:00Z 置信度 0.78 q-bio.GN
• GenomeFingerprinter and universal genome fingerprint analysis for systematic comparative genomics
  How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing genetic category (chromo…
  arxiv Yuncan Ai, Hannan Ai, Fanmei Meng, Lei Zhao 2013-03-10T02:47:09Z 置信度 0.78 q-bio.GNcs.CEmath.NA
• Genome-on-Diet: Taming Large-Scale Genomic Analyses via Sparsified Genomics
  Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the exponential growth of…
  arxiv Mohammed Alser, Julien Eudine, Onur Mutlu 2022-11-15T14:09:39Z 置信度 0.78 cs.DSq-bio.GNq-bio.QM
• The Genomic HyperBrowser: inferential genomics at the sequence level
  The immense increase in the generation of genomic scale data poses an unmet analytical challenge, due to a lack of established methodology with the required flexibility and power. We propose a first principled approach to statistical analysis of sequence-level…
  arxiv Geir K. Sandve, Sveinung Gundersen, Halfdan Rydbeck, Ingrid K. Glad 等 2011-01-25T18:57:24Z 置信度 0.78 q-bio.GN
• Genomic reproducibility in the bioinformatics era
  In biomedical research, validation of a new scientific discovery is tied to the reproducibility of its experimental results. However, in genomics, the definition and implementation of reproducibility still remain imprecise. Here, we argue that genomic reproduc…
  arxiv Pelin Icer Baykal, Paweł P. Łabaj, Florian Markowetz, Lynn M. Schriml 等 2023-08-18T13:43:36Z 置信度 0.78 q-bio.GN
• Cancer-inspired Genomics Mapper Model for the Generation of Synthetic DNA Sequences with Desired Genomics Signatures
  Genome data are crucial in modern medicine, offering significant potential for diagnosis and treatment. Thanks to technological advancements, many millions of healthy and diseased genomes have already been sequenced; however, obtaining the most suitable data f…
  arxiv Teddy Lazebnik, Liron Simon-Keren 2023-05-01T07:16:40Z 置信度 0.78 q-bio.GNcs.LGcs.NE
• Deep Learning for Genomics: A Concise Overview
  Advancements in genomic research such as high-throughput sequencing techniques have driven modern genomic studies into "big data" disciplines. This data explosion is constantly challenging conventional methods used in genomics. In parallel with the urgent dema…
  arxiv Tianwei Yue, Yuanxin Wang, Longxiang Zhang, Chunming Gu 等 2018-02-02T12:50:25Z 置信度 0.78 q-bio.GNcs.LG
• Revolutionizing Genomics with Reinforcement Learning Techniques
  In recent years, Reinforcement Learning (RL) has emerged as a powerful tool for solving a wide range of problems, including decision-making and genomics. The exponential growth of raw genomic data over the past two decades has exceeded the capacity of manual a…
  arxiv Mohsen Karami, Khadijeh, Jahanian, Roohallah Alizadehsani 等 2023-02-26T08:43:08Z 置信度 0.78 q-bio.GNcs.AIcs.LGq-bio.QM
• Mapping to a Reference Genome Structure
  To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to a position in that reference genome. We refer to a collection of one or more ref…
  arxiv Benedict Paten, Adam Novak, David Haussler 2014-04-20T04:48:24Z 置信度 0.78 q-bio.GN
• Applied Category Theory for Genomics -- An Initiative
  The ultimate secret of all lives on earth is hidden in their genomes -- a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Ap…
  arxiv Yanying Wu 2020-09-06T21:36:58Z 置信度 0.78 q-bio.GNmath.CT
• The big challenge for livestock genomics is to make sequence data pay
  This paper will argue that one of the biggest challenges for livestock genomics is to make whole-genome sequencing and functional genomics applicable to breeding practice. It discusses potential explanations for why it is so difficult to consistently improve t…
  arxiv M. Johnsson 2023-02-02T14:55:51Z 置信度 0.78 q-bio.GN
• An introduction to reconstructing ancestral genomes
  Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also being compared and cont…
  arxiv Lior Pachter 2006-12-25T21:20:34Z 置信度 0.78 q-bio.GNq-bio.QM
• To Transformers and Beyond: Large Language Models for the Genome
  In the rapidly evolving landscape of genomics, deep learning has emerged as a useful tool for tackling complex computational challenges. This review focuses on the transformative role of Large Language Models (LLMs), which are mostly based on the transformer a…
  arxiv Micaela E. Consens, Cameron Dufault, Michael Wainberg, Duncan Forster 等 2023-11-13T02:13:58Z 置信度 0.78 q-bio.GNcs.LG
• Processing-in-memory for genomics workloads
  Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data are currently process…
  arxiv William Andrew Simon, Leonid Yavits, Konstantina Koliogeorgi, Yann Falevoz 等 2025-05-31T15:13:06Z 置信度 0.78 q-bio.GNcs.AR
• Scalable Genomics with R and Bioconductor
  This paper reviews strategies for solving problems encountered when analyzing large genomic data sets and describes the implementation of those strategies in R by packages from the Bioconductor project. We treat the scalable processing, summarization and visua…
  arxiv Michael Lawrence, Martin Morgan 2014-09-09T10:47:37Z 置信度 0.78 q-bio.GNcs.DC
• Genome Compression Against a Reference
  Being able to store and transmit human genome sequences is an important part in genomic research and industrial applications. The complete human genome has 3.1 billion base pairs (haploid), and storing the entire genome naively takes about 3 GB, which is infea…
  arxiv Anirduddha Laud, Gaurav Menghani, Madhava Keralapura 2020-10-05T19:00:23Z 置信度 0.78 q-bio.GN
• Unambiguosly expressing expectations about the content of prokaryotic genomes
  In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy and cheap. Thus it becomes increasingly feasible and interesting to perform comparative genomics analyses of new genomes to those of related organism…
  arxiv Giorgio Gonnella 2023-02-06T16:47:50Z 置信度 0.78 q-bio.GN
• genomepy: genes and genomes at your fingertips
  Analyzing a functional genomics experiment, such as ATAC-, ChIP- or RNA-sequencing, requires reference data including a genome assembly and gene annotation. These resources can generally be retrieved from different organizations and in different versions. Most…
  arxiv Siebren Frölich, Maarten van der Sande, Tilman Schäfers, Simon J. van Heeringen 2022-09-02T07:00:49Z 置信度 0.78 q-bio.GN
• Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models
  We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify the workflow for genomic model development: data collection, model tuning, infere…
  arxiv Weimin Wu, Xuefeng Song, Yibo Wen, Qinjie Lin 等 2025-09-13T03:31:55Z 置信度 0.78 q-bio.GNcs.LG
• Of Protein Size and Genomes
  An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized. Genome figures are presen…
  arxiv N. S. Santos-Magalhaes, H. M. de Oliveira 2015-02-12T17:03:36Z 置信度 0.78 q-bio.GNstat.AP
• gggenomes: effective and versatile visualizations for comparative genomics
  The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools often fail to efficien…
  arxiv Thomas Hackl, Markus Ankenbrand, Bart van Adrichem, David Wilkins 等 2024-11-05T11:39:53Z 置信度 0.78 q-bio.GN
• Zimin patterns in genomes
  Zimin words are words that have the same prefix and suffix. They are unavoidable patterns, with all sufficiently large strings encompassing them. Here, we examine for the first time the presence of k-mers not containing any Zimin patterns, defined hereafter as…
  arxiv Nikol Chantzi, Ioannis Mouratidis, Ilias Georgakopoulos-Soares 2024-10-16T20:00:33Z 置信度 0.78 q-bio.GN
• GQVis: A Dataset of Genomics Data Questions and Visualizations for Generative AI
  Data visualization is a fundamental tool in genomics research, enabling the exploration, interpretation, and communication of complex genomic features. While machine learning models show promise for transforming data into insightful visualizations, current mod…
  arxiv Skylar Sargent Walters, Arthea Valderrama, Thomas C. Smits, David Kouřil 等 2025-09-19T21:29:13Z 置信度 0.78 q-bio.GNcs.AIcs.HCcs.LG
• Understanding genomic alterations in cancer genomes using an integrative network approach
  In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, Novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and kataegis (mutation storm…
  arxiv Edwin Wang 2014-09-10T21:45:52Z 置信度 0.78 q-bio.GNq-bio.MN
• Divergence and Shannon information in genomes
  Shannon information (SI) and its special case, divergence, are defined for a DNA sequence in terms of probabilities of chemical words in the sequence and are computed for a set of complete genomes highly diverse in length and composition. We find the following…
  arxiv Hong-Da Chen, Chang-Heng Chang, Li-Ching Hsieh, Hoong-Chien Lee 2004-12-18T03:15:03Z 置信度 0.78 q-bio.GN
• EGC: a format for expressing prokaryotic genomes content expectations
  The number of available genomes of prokaryotic organisms is rapidly growing enabling comparative genomics studies. The comparison of genomes of organisms with a common phenotype, habitat or phylogeny often shows that these genomes share some common contents. C…
  arxiv Giorgio Gonnella 2023-03-15T16:55:03Z 置信度 0.78 q-bio.GN
• Are there laws of genome evolution?
  Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of ort…
  arxiv Eugene V. Koonin 2011-08-17T22:19:54Z 置信度 0.78 q-bio.PEq-bio.GNq-bio.MN
• Minimum-Cost Synthetic Genome Planning: An Algorithmic Framework
  As synthetic genomics scales toward the construction of increasingly larger genomes, computational strategies are needed to address technical feasibility. We introduce an algorithmic framework for the Minimum-Cost Synthetic Genome Planning problem, aiming to i…
  arxiv Michail Patsakis, Ioannis Mouratidis, Ilias Georgakopoulos-Soares 2025-09-07T22:46:57Z 置信度 0.78 q-bio.GN
• Information Theory of Genomes
  Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory considerations we d…
  arxiv Dmitri V. Parkhomchuk 2006-12-19T14:31:13Z 置信度 0.78 q-bio.GNq-bio.PE
• Towards a core genome: pairwise similarity searches on interspecific genomic data
  The phenomenon of gene conservation is an interesting evolutionary problem related to speciation and adaptation. Conserved genes are acted upon in evolution in a way that preserves their function despite other structural and functional changes going on around …
  arxiv Bradly J. Alicea, Marcela A. Carvallo-Pinto, Jorge L. M. Rodrigues 2008-07-21T20:38:48Z 置信度 0.78 q-bio.GNq-bio.PE
• Data Management for High-Throughput Genomics
  Today's sequencing technology allows sequencing an individual genome within a few weeks for a fraction of the costs of the original Human Genome project. Genomics labs are faced with dozens of TB of data per week that have to be automatically processed and mad…
  arxiv Uwe Roehm, Jose Blakeley 2009-09-09T18:09:17Z 置信度 0.78 cs.DBq-bio.GN
• Multimodal 3D Genome Pre-training
  Deep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored. Here, we propose MIX-HIC, the first multimodal …
  arxiv Minghao Yang, Pengteng Li, Yan Liang, Qianyi Cai 等 2025-04-12T03:31:03Z 置信度 0.78 cs.LGcs.AIq-bio.GN
• Tasks, Techniques, and Tools for Genomic Data Visualization
  Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of investigators. Addressing this n…
  arxiv Sabrina Nusrat, Theresa Harbig, Nils Gehlenborg 2019-05-08T00:53:22Z 置信度 0.78 q-bio.GNcs.HCq-bio.QM
• Nucleotide Distribution Patterns in Insect Genomes
  This work analyzed genome-wide nucleotide distribution patterns in ten insect genomes. Two internal measures were applied: (i) GC variation and (ii) third codon nucleotide preference. Although the genome size and overall GC level did not show any correlation w…
  arxiv Manoj Pratim Samanta 2007-02-18T08:17:22Z 置信度 0.78 q-bio.GN
• Genomic Interpreter: A Hierarchical Genomic Deep Neural Network with 1D Shifted Window Transformer
  Given the increasing volume and quality of genomics data, extracting new insights requires interpretable machine-learning models. This work presents Genomic Interpreter: a novel architecture for genomic assay prediction. This model outperforms the state-of-the…
  arxiv Zehui Li, Akashaditya Das, William A V Beardall, Yiren Zhao 等 2023-06-08T12:10:13Z 置信度 0.78 cs.LGq-bio.GN
• Hidden breakpoints in genome alignments
  During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain and loss occurs in a…
  arxiv Birte Kehr, Knut Reinert, Aaron E. Darling 2012-07-30T15:24:49Z 置信度 0.78 q-bio.GN
• Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis
  We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently exist major computa…
  arxiv Mohammed Alser, Joel Lindegger, Can Firtina, Nour Almadhoun 等 2022-05-16T19:43:13Z 置信度 0.78 q-bio.GNcs.ARq-bio.QM
• On the Law of Directionality of Genome Evolution
  The problem of the directionality of genome evolution is studied from the information-theoretic view. We propose that the function-coding information quantity of a genome always grows in the course of evolution through sequence duplication, expansion of code, …
  arxiv Liaofu Luo 2008-05-08T01:13:20Z 置信度 0.78 q-bio.GNq-bio.CB
• Multiclass Disease Predictions Based on Integrated Clinical and Genomics Datasets
  Clinical predictions using clinical data by computational methods are common in bioinformatics. However, clinical predictions using information from genomics datasets as well is not a frequently observed phenomenon in research. Precision medicine research requ…
  arxiv Moeez M. Subhani, Ashiq Anjum 2020-06-14T12:23:49Z 置信度 0.78 q-bio.GNcs.AIcs.LGstat.ML
• Rubbish DNA: The functionless fraction of the human genome
  Because genomes are products of natural processes rather than intelligent design, all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called rubbish DNA. Rubbish DNA consists of junk DNA, i.e., …
  arxiv Dan Graur 2016-01-22T15:41:37Z 置信度 0.78 q-bio.GN
• Segmentation and genome annotation algorithms
  Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These algorithms take as input epigenomic datasets, such as chromatin immunoprecipitation-sequencing (ChIP-seq) measurements of histone modi…
  arxiv Maxwell W Libbrecht, Rachel CW Chan, Michael M Hoffman 2021-01-03T19:08:36Z 置信度 0.78 q-bio.GNcs.LG
• Pan-genome Analysis of the Genus Serratia
  Pan-genome analysis is a standard procedure to decipher genome heterogeneity and diversification of bacterial species. Specie evolution is traced by defining and comparing the core (conserved), accessory (dispensable) and unique (strain-specific) gene pool wit…
  arxiv Zarrin Basharat, Azra Yasmin 2016-10-13T16:32:47Z 置信度 0.78 q-bio.GN
• Reconsidering the significance of genomic word frequency
  We propose that the distribution of DNA words in genomic sequences can be primarily characterized by a double Pareto-lognormal distribution, which explains lognormal and power-law features found across all known genomes. Such a distribution may be the result o…
  arxiv Miklós Csűrös, Laurent Noé, Gregory Kucherov 2006-09-14T17:18:30Z 置信度 0.78 q-bio.GN
• Guide to k-mer approaches for genomics across the tree of life
  The wide array of currently available genomes display a wonderful diversity in size, composition and structure with many more to come thanks to several global biodiversity genomics initiatives starting in recent years. However, sequencing of genomes, even with…
  arxiv Katharine M. Jenike, Lucía Campos-Domínguez, Marilou Boddé, José Cerca 等 2024-04-01T22:58:30Z 置信度 0.78 q-bio.GN
• OmniGenBench: Automating Large-scale in-silico Benchmarking for Genomic Foundation Models
  The advancements in artificial intelligence in recent years, such as Large Language Models (LLMs), have fueled expectations for breakthroughs in genomic foundation models (GFMs). The code of nature, hidden in diverse genomes since the very beginning of life's …
  arxiv Heng Yang, Jack Cole, Ke Li 2024-10-02T17:40:44Z 置信度 0.78 q-bio.GNcs.CL
• Gosling Designer: a Platform to Democratize Construction and Sharing of Genomics Data Visualization Tools
  Analysis of genomics data is central to nearly all areas of modern biology. Despite significant progress in artificial intelligence (AI) and computational methods, these technologies require significant human oversight to generate novel and reliable biological…
  arxiv Sehi L'Yi, John Conroy, Priya Misner, David Kouřil 等 2025-10-28T18:48:02Z 置信度 0.78 q-bio.GN
• Evaluation of the Number of Different Genomes on Medium and Identification of Known Genomes Using Composition Spectra Approach
  The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study and of two algorithms for determining the presence of a particular (known) genome in this medium. The approach is based …
  arxiv Valery Kirzhner, Zeev Volkovich 2015-06-19T21:12:34Z 置信度 0.78 q-bio.GNq-bio.QM
• On Programs and Genomes
  We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from control genes or cenes. …
  arxiv Eric Werner 2011-10-24T15:49:30Z 置信度 0.78 q-bio.OTcs.CEq-bio.GN
• A Comparison of Microbial Genome Web Portals
  Microbial genome web portals have a broad range of capabilities that address a number of information-finding and analysis needs for scientists. This article compares the capabilities of the major microbial genome web portals to aid researchers in determining w…
  arxiv Peter D. Karp, Natalia Ivanova, Markus Krummenacker, Nikos Kyrpides 等 2018-10-30T17:01:34Z 置信度 0.78 q-bio.GN
• Functional and evolutionary genomics of the Streptomyces metabolism
  This thesis is focused in the study of the evolution of the metabolic repertoire of Streptomyces, which are renowned as proficient producers of bioactive Natural Products (NPs). The main goal of my work was to contribute into the understanding of the evolution…
  arxiv Pablo Cruz-Morales 2022-05-30T09:25:35Z 置信度 0.78 q-bio.GN
• wgatools: an ultrafast toolkit for manipulating whole genome alignments
  Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment (WGA) formats, offe…
  arxiv Wenjie Wei, Songtao Gui, Jian Yang, Erik Garrison 等 2024-09-13T06:39:17Z 置信度 0.78 q-bio.GN
• Biological Database of Images and Genomes: tools for community annotations linking image and genomic information
  Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable the manipulation and…
  arxiv Andrew T. Oberlin, Dominika A. Jurkovic, Mitchell F. Balish, Iddo Friedberg 2012-12-03T16:52:41Z 置信度 0.78 q-bio.GN
• Joint analysis of functional genomic data and genome-wide association studies of 18 human traits
  Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a statistical model tha…
  arxiv Joseph K. Pickrell 2013-11-19T19:12:08Z 置信度 0.78 q-bio.GN
• Protein-to-genome alignment with miniprot
  Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in alignment algorithms. The…
  arxiv Heng Li 2022-10-14T18:43:47Z 置信度 0.78 q-bio.GN
• Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects
  Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often difficult to know the a…
  arxiv Binghang Liu, Yujian Shi, Jianying Yuan, Xuesong Hu 等 2013-08-09T01:51:19Z 置信度 0.78 q-bio.GN
• Machine Learning Applications for Therapeutic Tasks with Genomics Data
  Thanks to the increasing availability of genomics and other biomedical data, many machine learning approaches have been proposed for a wide range of therapeutic discovery and development tasks. In this survey, we review the literature on machine learning appli…
  arxiv Kexin Huang, Cao Xiao, Lucas M. Glass, Cathy W. Critchlow 等 2021-05-03T21:20:20Z 置信度 0.78 cs.LGq-bio.GNq-bio.QM
• OmniGenBench: A Modular Platform for Reproducible Genomic Foundation Models Benchmarking
  The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach to decoding the genom…
  arxiv Heng Yang, Jack Cole, Yuan Li, Renzhi Chen 等 2025-05-20T14:16:25Z 置信度 0.78 q-bio.GNcs.CL
• Efficient and Scalable Fine-Tune of Language Models for Genome Understanding
  Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language foundation models, whic…
  arxiv Huixin Zhan, Ying Nian Wu, Zijun Zhang 2024-02-12T21:40:45Z 置信度 0.78 q-bio.GNcs.AIcs.LG
• Whole-Genome Phenotype Prediction with Machine Learning: Open Problems in Bacterial Genomics
  How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accuracy scores. However, attempts to extract any meaning from t…
  arxiv Tamsin James, Ben Williamson, Peter Tino, Nicole Wheeler 2025-02-11T18:25:14Z 置信度 0.78 q-bio.GNcs.LG
• Parametric Alignment of Drosophila Genomes
  The classic algorithms of Needleman--Wunsch and Smith--Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). In order to process large genomes that have undergone complex genome rearrangements, almost all existing wh…
  arxiv Colin Dewey, Peter Huggins, Kevin Woods, Bernd Sturmfels 等 2005-12-02T21:24:37Z 置信度 0.78 q-bio.GNmath.COq-bio.QM
• The Mitochondrial Genome of Cathaya argyrophylla Reaches 18.99 Mb: Analysis of Super-Large Mitochondrial Genomes in Pinaceae
  Mitochondrial genomes in the Pinaceae family are notable for their large size and structural complexity. In this study, we sequenced and analyzed the mitochondrial genome of Cathaya argyrophylla, an endangered and endemic Pinaceae species, uncovering a genome …
  arxiv Kerui Huang, Wenbo Xu, Haoliang Hu, Xiaolong Jiang 等 2024-10-09T15:51:52Z 置信度 0.78 q-bio.GN
• An Integrated Genomics Workflow Tool: Simulating Reads, Evaluating Read Alignments, and Optimizing Variant Calling Algorithms
  Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in identifying genetic va…
  arxiv Fathima Nuzla Ismail, Shanika Amarasoma 2025-04-24T18:05:08Z 置信度 0.78 q-bio.GN
• A mechanistically interpretable neural network for regulatory genomics
  Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scientists the underlying motifs (and their syntax) which drive genome regulation. Tra…
  arxiv Alex M. Tseng, Gokcen Eraslan, Tommaso Biancalani, Gabriele Scalia 2024-10-08T17:15:26Z 置信度 0.78 q-bio.GNcs.LG
• A mathematical framework for centromere-aware evaluation of human genome assemblies
  Accurate evaluation of genome assemblies within highly repetitive regions, such as centromeres, remains a major open challenge in genomics. Conventional benchmarking relies on sequence alignment, which becomes problematic in regions of high homogeneity and div…
  arxiv Luca Franco, Matteo Migliarini, Matteo Tommaso Ungaro, Egnald Çela 等 2026-06-09T10:42:49Z 置信度 0.78 q-bio.GN