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Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
- Terence Gall-Duncan,
- Nozomu Sato,
- Ryan K.C. Yuen,
- and Christopher E. Pearson
Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
...Terence Gall-Duncan1,2,3, Nozomu Sato1,3, Ryan K.C. Yuen1,2 and Christopher E. Pearson1,2 1Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; 2Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada ↵3...
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Research: The landscape of genomic imprinting across diverse adult human tissues
- Yael Baran,
- Meena Subramaniam,
- Anne Biton,
- Taru Tukiainen,
- Emily K. Tsang,
- Manuel A. Rivas,
- Matti Pirinen,
- Maria Gutierrez-Arcelus,
- Kevin S. Smith,
- Kim R. Kukurba,
- Rui Zhang,
- Celeste Eng,
- Dara G. Torgerson,
- Cydney Urbanek,
- the GTEx Consortium,
- Jin Billy Li,
- Jose R. Rodriguez-Santana,
- Esteban G. Burchard,
- Max A. Seibold,
- Daniel G. MacArthur,
- Stephen B. Montgomery,
- Noah A. Zaitlen,
- and Tuuli Lappalainen
Genome Res. July 2015 25: 927-936; Published in Advance May 7, 2015, doi:10.1101/gr.192278.115
...and their maternal/paternal expression were obtained from the Otago database (Morison et al. 2001) and other sources (Supplemental Text). Furthermore, since the human gene annotation is not perfect, for all novel imprinted genes wemanually verified that coverage and splicing in RNA-sequencing data was consistent...
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RESOURCE: Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans
- Suraj Peri,
- J. Daniel Navarro,
- Ramars Amanchy,
- Troels Z. Kristiansen,
- Chandra Kiran Jonnalagadda,
- Vineeth Surendranath,
- Vidya Niranjan,
- Babylakshmi Muthusamy,
- T.K.B. Gandhi,
- Mads Gronborg,
- Nieves Ibarrola,
- Nandan Deshpande,
- K. Shanker,
- H.N. Shivashankar,
- B.P. Rashmi,
- M.A. Ramya,
- Zhixing Zhao,
- K.N. Chandrika,
- N. Padma,
- H.C. Harsha,
- A.J. Yatish,
- M.P. Kavitha,
- Minal Menezes,
- Dipanwita Roy Choudhury,
- Shubha Suresh,
- Neelanjana Ghosh,
- R. Saravana,
- Sreenath Chandran,
- Subhalakshmi Krishna,
- Mary Joy,
- Sanjeev K. Anand,
- V. Madavan,
- Ansamma Joseph,
- Guang W. Wong,
- William P. Schiemann,
- Stefan N. Constantinescu,
- Lily Huang,
- Roya Khosravi-Far,
- Hanno Steen,
- Muneesh Tewari,
- Saghi Ghaffari,
- Gerard C. Blobe,
- Chi V. Dang,
- Joe G.N. Garcia,
- Jonathan Pevsner,
- Ole N. Jensen,
- Peter Roepstorff,
- Krishna S. Deshpande,
- Arul M. Chinnaiyan,
- Ada Hamosh,
- Aravinda Chakravarti,
- and Akhilesh Pandey
Genome Res. October 2003 13: 2363-2371; doi:10.1101/gr.1680803
...and Botstein 1999 ; Pandey and Mann 2000 ; Hood and Galas 2003 ). With the sequence of the human sequence already available, a large majority of protein-coding genes has been identified that pave the way for additional -wide functional studies ( Lander et al. 2001 ; Venter et al. 2001 ). Newer technologies...
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GENOME METHODS: Overlapping Genomic Sequences: A Treasure Trove of Single-Nucleotide Polymorphisms
- Patricia Taillon-Miller,
- Zhijie Gu,
- Qun Li,
- LaDeana Hillier,
- and Pui-Yan Kwok
Genome Res. July 1, 1998 8: 748-754; doi:10.1101/gr.8.7.748
.... ( 1995 ) A new DNA sequence assembly program. Nucleic Acids Res. 23 : 4992 – 4999 . ↵ Collins F.S. , Galas D. ( 1993 ) A new five-year plan for the U.S. Human Genome Program. Science 262 : 43 – 46 . ↵ Collins F.S. , Guyer M.S. , Chakravarti A. ( 1997 ) Variations on a theme: Cataloging human DNA sequence...
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REVIEW: Perspectives: sequence data base searching in the era of large-scale genomic sequencing.
- R F Smith
Genome Res. August 1996 6: 653-660; doi:10.1101/gr.6.8.653
.... Cinkosky, M.J., , Fickett, J.W. , Keen. G.M. Cinkosky, M.J., Fickett, J.W. and Keen. G.M. 1995 . A new design for the Genome Sequence Data Base. IEEE Eng. Med. Biol. 14 : 725 – 729 . Collins, F. , Galas. D. Collins, F. and Galas. D. 1993 . A new five-year plan for the U.S. Human Genome Project. Science 262...
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Chicken Special/Resources: Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
- Ivan Ovcharenko,
- Gabriela G. Loots,
- Belinda M. Giardine,
- Minmei Hou,
- Jian Ma,
- Ross C. Hardison,
- Lisa Stubbs,
- and Webb Miller
Genome Res. January 2005 15: 184-194; Published in Advance December 8, 2004, doi:10.1101/gr.3007205
...The database of genomic DNA sequence alignments and annotations (GALA; http://globin.cse.psu.edu/gala/ ) allows users to find genomic intervals that meet defined conservation thresholds, alignment-based scores, gene annotation criteria, transcription factor bindings site patterns, expression profiles...
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RESOURCE: The ENCODEdb portal: Simplified access to ENCODE Consortium data
- Laura L. Elnitski,
- Prachi Shah,
- R. Travis Moreland,
- Lowell Umayam,
- Tyra G. Wolfsberg,
- and Andreas D. Baxevanis
Genome Res. June 2007 17: 954-959; doi:10.1101/gr.5582207
..., and the Genome Alignment and Annotation Databases (GALA), which merge annotations with multi-species alignment data ( Giardine et al. 2003 ). Once a -wide data set has been generated, high-throughput analysis can be performed using tools such as Galaxy, a simple Web portal that enables users to combine data from...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
...to recognize and bind a target DNA sequence. DNaseI protection (also known as DNaseI footprinting) ( Galas and Schmitz 1978 ) is another technique for the precise localization of protein binding sites that does not require knowledge of protein identity. The technique combines the binding reaction of an EMSA...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...S3 shows how each gap was filled, and Supplemental Figure S4 details the read coverage distribution of each gap by Nanopore and HiFi reads.View this table: In this window In a new window Table 2. Error correction by using the Nanopore and PacBio consensusesComparison of CGC1 to automated GALA...
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Research: Plasma cell-free RNA characteristics in COVID-19 patients
- Yanqun Wang,
- Jie Li,
- Lu Zhang,
- Hai-Xi Sun,
- Zhaoyong Zhang,
- Jinjin Xu,
- Yonghao Xu,
- Yu Lin,
- Airu Zhu,
- Yuxue Luo,
- Haibo Zhou,
- Yan Wu,
- Shanwen Lin,
- Yuzhe Sun,
- Fei Xiao,
- Ruiying Chen,
- Liyan Wen,
- Wei Chen,
- Fang Li,
- Rijing Ou,
- Yanjun Zhang,
- Tingyou Kuo,
- Yuming Li,
- Lingguo Li,
- Jing Sun,
- Kun Sun,
- Zhen Zhuang,
- Haorong Lu,
- Zhao Chen,
- Guoqiang Mai,
- Jianfen Zhuo,
- Puyi Qian,
- Jiayu Chen,
- Huanming Yang,
- Jian Wang,
- Xun Xu,
- Nanshan Zhong,
- Jingxian Zhao,
- Junhua Li,
- Jincun Zhao,
- and Xin Jin
Genome Res. February 2022 32: 228-241; Published in Advance January 21, 2022, doi:10.1101/gr.276175.121
...-sen University, Zhuhai, Guangdong Province 519000, China; 9College of Informatics, Huazhong Agricultural University, Wuhan 430070, China; 10Shenzhen Bay Laboratory, Shenzhen 518132, China; 11Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China; 12China National...
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