A generic, cost-effective, and scalable cell lineage analysis platform.

abstract：:Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to strong selective constraint. While some studies show that highly constrained noncoding regions act to enhance transcription...

journal_title：Genome research

authors： Cheng Y,King DC,Dore LC,Zhang X,Zhou Y,Zhang Y,Dorman C,Abebe D,Kumar SA,Chiaromonte F,Miller W,Green RD,Weiss MJ,Hardison RC

更新日期：2008-12-01 00:00:00

abstract：:The repressive capacity of cytosine DNA methylation is mediated by recruitment of silencing complexes by methyl-CpG binding domain (MBD) proteins. Despite MBD proteins being associated with silencing, we discovered that a family of arthropod Copia retrotransposons have incorporated a host-derived MBD. We functionally ...

journal_title：Genome research

authors： de Mendoza A,Pflueger J,Lister R

更新日期：2019-08-01 00:00:00

abstract：:We have developed the CADLIVE (Computer-Aided Design of LIVing systEms) Simulator that provided a rule-based automatic way to convert biochemical network maps into dynamic models, which enables simulating their dynamics without going through all of the reactions down to the details of exact kinetic parameters. The sim...

journal_title：Genome research

authors： Kurata H,Masaki K,Sumida Y,Iwasaki R

更新日期：2005-04-01 00:00:00

abstract：:RNA-seq by poly(A) selection is currently the most common protocol for whole transcriptome sequencing as it provides a broad, detailed, and accurate view of the RNA landscape. Unfortunately, the utility of poly(A) libraries is greatly limited when the input RNA is degraded, which is the norm for research tissues and c...

journal_title：Genome research

authors： Cieslik M,Chugh R,Wu YM,Wu M,Brennan C,Lonigro R,Su F,Wang R,Siddiqui J,Mehra R,Cao X,Lucas D,Chinnaiyan AM,Robinson D

更新日期：2015-09-01 00:00:00

abstract：:The vomeronasal system of mice is thought to be specialized in the detection of pheromones. Two multigene families have been identified that encode proteins with seven putative transmembrane domains and that are expressed selectively in subsets of neurons of the vomeronasal organ. The products of these vomeronasal rec...

journal_title：Genome research

authors： Del Punta K,Rothman A,Rodriguez I,Mombaerts P

更新日期：2000-12-01 00:00:00

abstract：:DNA transposons, or class 2 transposable elements, have successfully propagated in a wide variety of genomes. However, it is widely believed that DNA transposon activity has ceased in mammalian genomes for at least the last 40 million years. We recently reported evidence for the relatively recent activity of hAT and H...

journal_title：Genome research

authors： Ray DA,Feschotte C,Pagan HJ,Smith JD,Pritham EJ,Arensburger P,Atkinson PW,Craig NL

更新日期：2008-05-01 00:00:00

abstract：:Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes cont...

journal_title：Genome research

authors： Fuhrmann DR,Krzywinski MI,Chiu R,Saeedi P,Schein JE,Bosdet IE,Chinwalla A,Hillier LW,Waterston RH,McPherson JD,Jones SJ,Marra MA

更新日期：2003-05-01 00:00:00

abstract：:Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced th...

journal_title：Genome research

authors： Heidel AJ,Lawal HM,Felder M,Schilde C,Helps NR,Tunggal B,Rivero F,John U,Schleicher M,Eichinger L,Platzer M,Noegel AA,Schaap P,Glöckner G

更新日期：2011-11-01 00:00:00

abstract：:Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized th...

journal_title：Genome research

authors： Nolte V,Pandey RV,Kofler R,Schlötterer C

更新日期：2013-01-01 00:00:00

abstract：:Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA se...

journal_title：Genome research

authors： van Dijk D,Sharon E,Lotan-Pompan M,Weinberger A,Segal E,Carey LB

更新日期：2017-01-01 00:00:00

abstract：:Sex chromosomes differentiated from different ancestral autosomes in various vertebrate lineages. Here, we trace the functional evolution of the XY Chromosomes of the green anole lizard (Anolis carolinensis), on the basis of extensive high-throughput genome, transcriptome and histone modification sequencing data and r...

journal_title：Genome research

authors： Marin R,Cortez D,Lamanna F,Pradeepa MM,Leushkin E,Julien P,Liechti A,Halbert J,Brüning T,Mössinger K,Trefzer T,Conrad C,Kerver HN,Wade J,Tschopp P,Kaessmann H

更新日期：2017-12-01 00:00:00

abstract：:To accelerate the molecular analysis of behavior in the honey bee (Apis mellifera), we created expressed sequence tag (EST) and cDNA microarray resources for the bee brain. Over 20,000 cDNA clones were partially sequenced from a normalized (and subsequently subtracted) library generated from adult A. mellifera brains....

journal_title：Genome research

authors： Whitfield CW,Band MR,Bonaldo MF,Kumar CG,Liu L,Pardinas JR,Robertson HM,Soares MB,Robinson GE

更新日期：2002-04-01 00:00:00

abstract：:Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from...

journal_title：Genome research

authors： West PT,Probst AJ,Grigoriev IV,Thomas BC,Banfield JF

更新日期：2018-04-01 00:00:00

abstract：:Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized...

journal_title：Genome research

authors： Shao W,Wang T

更新日期：2021-01-01 00:00:00

abstract：:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether ...

journal_title：Genome research

authors： Schmitges FW,Radovani E,Najafabadi HS,Barazandeh M,Campitelli LF,Yin Y,Jolma A,Zhong G,Guo H,Kanagalingam T,Dai WF,Taipale J,Emili A,Greenblatt JF,Hughes TR

更新日期：2016-12-01 00:00:00

abstract：:Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NF...

journal_title：Genome research

authors： Copley RR,Totrov M,Linnell J,Field S,Ragoussis J,Udalova IA

更新日期：2007-09-01 00:00:00

abstract：:The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-seq) to determine the...

journal_title：Genome research

authors： Bryan DS,Ransom M,Adane B,York K,Hesselberth JR

更新日期：2014-09-01 00:00:00

abstract：:The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to...

journal_title：Genome research

authors： Lazar J,Moreno C,Jacob HJ,Kwitek AE

更新日期：2005-12-01 00:00:00

abstract：:Forty-three yeast artificial chromosomes (YACs) from the X chromosome have been overlapped across the 4-Mb Xq21.3 region, which is homologous to a segment in Yp11.1. The region is formatted to 60-kb resolution with 57 STSs and is merged at its edges with contigs specific for X. This allows a direct comparison of marke...

journal_title：Genome research

authors： Mumm S,Molini B,Terrell J,Srivastava A,Schlessinger D

更新日期：1997-04-01 00:00:00

abstract：:A rigorous analysis of the Merck-sponsored EST data with respect to known gene sequences increases the utility of the data set and helps refine methods for building a gene index. A highly curated human transcript data base was used as a reference data set of known genes. A detailed analysis of EST sequences derived fr...

journal_title：Genome research

authors： Aaronson JS,Eckman B,Blevins RA,Borkowski JA,Myerson J,Imran S,Elliston KO

更新日期：1996-09-01 00:00:00

abstract：:Dystroglycan is a laminin binding protein, which provides a structural link between the subsarcolemmal cytoskeleton and the extracellular matrix. It is also involved in the organization of basement membranes. So far the genomic organization of the dystroglycan gene DAG1 has not been completely investigated. Here we re...

journal_title：Genome research

authors： Leeb T,Neumann S,Deppe A,Breen M,Brenig B

更新日期：2000-03-01 00:00:00

abstract：:Many missense substitutions are identified in single nucleotide polymorphism (SNP) data and large-scale random mutagenesis projects. Each amino acid substitution potentially affects protein function. We have constructed a tool that uses sequence homology to predict whether a substitution affects protein function. SIFT...

journal_title：Genome research

authors： Ng PC,Henikoff S

更新日期：2001-05-01 00:00:00

abstract：:The study of genetic variability within natural populations of pathogens may provide insight into their evolution and pathogenesis. We used a Mycobacterium tuberculosis high-density oligonucleotide microarray to detect small-scale genomic deletions among 19 clinically and epidemiologically well-characterized isolates ...

journal_title：Genome research

authors： Kato-Maeda M,Rhee JT,Gingeras TR,Salamon H,Drenkow J,Smittipat N,Small PM

更新日期：2001-04-01 00:00:00

abstract：:Human genomic data of many types are readily available, but the complexity and scale of human molecular biology make it difficult to integrate this body of data, understand it from a systems level, and apply it to the study of specific pathways or genetic disorders. An investigator could best explore a particular prot...

journal_title：Genome research

authors： Huttenhower C,Haley EM,Hibbs MA,Dumeaux V,Barrett DR,Coller HA,Troyanskaya OG

更新日期：2009-06-01 00:00:00

abstract：:In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining nucleolus-associated domains (NADs) and lamina-associated domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (M...

journal_title：Genome research

authors： Vertii A,Ou J,Yu J,Yan A,Pagès H,Liu H,Zhu LJ,Kaufman PD

更新日期：2019-08-01 00:00:00

abstract：:RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolki...

journal_title：Genome research

authors： Derr A,Yang C,Zilionis R,Sergushichev A,Blodgett DM,Redick S,Bortell R,Luban J,Harlan DM,Kadener S,Greiner DL,Klein A,Artyomov MN,Garber M

更新日期：2016-10-01 00:00:00

abstract：:Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorithm that integrates e...

journal_title：Genome research

authors： Roy S,Wapinski I,Pfiffner J,French C,Socha A,Konieczka J,Habib N,Kellis M,Thompson D,Regev A

更新日期：2013-06-01 00:00:00

abstract：:The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrat...

journal_title：Genome research

authors： Baldarelli RM,Hill DP,Blake JA,Adachi J,Furuno M,Bradt D,Corbani LE,Cousins S,Frazer KS,Qi D,Yang L,Ramachandran S,Reed D,Zhu Y,Kasukawa T,Ringwald M,King BL,Maltais LJ,McKenzie LM,Schriml LM,Maglott D,Church DM

更新日期：2003-06-01 00:00:00

abstract：:Yeasts and filamentous fungi do not have adenosine deaminase acting on RNA (ADAR) orthologs and are believed to lack A-to-I RNA editing, which is the most prevalent editing of mRNA in animals. However, during this study with the PUK1(FGRRES_01058) pseudokinase gene important for sexual reproduction in Fusarium gramine...

journal_title：Genome research

authors： Liu H,Wang Q,He Y,Chen L,Hao C,Jiang C,Li Y,Dai Y,Kang Z,Xu JR

更新日期：2016-04-01 00:00:00

abstract：:Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host plasma membrane and is involved in protein transport and trafficking. We have identified a novel subtelomeric gene famil...

journal_title：Genome research

authors： Sam-Yellowe TY,Florens L,Johnson JR,Wang T,Drazba JA,Le Roch KG,Zhou Y,Batalov S,Carucci DJ,Winzeler EA,Yates JR 3rd

更新日期：2004-06-01 00:00:00