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Journal Article
Farek J, Hughes D, Salerno W, Zhu Y, Pisupati A, Mansfield A, Krasheninina O, English AC, Metcalf GA, Boerwinkle E, Muzny DM, Gibbs RA, Khan Z, Sedlazeck FJ. xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments. Gigascience. 2022 ;12.
Gibbs RA, Cockerill M. Working on the assembly line. Trends Biochem Sci. 1995 ;20(4):162-3.
Liu X, White S, Peng B, Johnson AD, Brody JA, Li AH, Huang Z, Carroll A, Wei P, Gibbs RA, Klein RJ, Boerwinkle E. WGSA: an annotation pipeline for human genome sequencing studies. J Med Genet. 2016 ;53(2):111-2.
Fu Y, Mahmoud M, Muraliraman VVaibhav, Sedlazeck FJ, Treangen TJ. Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment. Gigascience. 2021 ;10(9).
James RA, Campbell IM, Chen ES, Boone PM, Rao MA, Bainbridge MN, Lupski JR, Yang Y, Eng CM, Posey JE, Shaw CA. A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics. Genome Med. 2016 ;8(1):13.
Leung YYee, Valladares O, Chou Y-F, Lin H-J, Kuzma AB, Cantwell L, Qu L, Gangadharan P, Salerno WJ, Schellenberg GD, San Wang L-. VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project. Bioinformatics. 2019 ;35(10):1768-1770.
Amendola LM, Muenzen K, Biesecker LG, Bowling KM, Cooper GM, Dorschner MO, Driscoll C, Foreman AKatherine, Golden-Grant K, Greally JM, Hindorff L, Kanavy D, Jobanputra V, Johnston JJ, Kenny EE, McNulty S, Murali P, Ou J, Powell BC, Rehm HL, Rolf B, Roman TS, Van Ziffle J, Guha S, Abhyankar A, Crosslin D, Venner E, Yuan B, Zouk H, Jarvik GP. Variant Classification Concordance using the ACMG-AMP Variant Interpretation Guidelines across Nine Genomic Implementation Research Studies. Am J Hum Genet. 2020 ;107(5):932-941.
Chandrashekar DS, Bashel B, Balasubramanya SAkshaya Ho, Creighton CJ, Ponce-Rodriguez I, Chakravarthi BVSK, Varambally S. UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses. Neoplasia. 2017 ;19(8):649-658.
Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AAl, Mahmoud M, Paulin LF, Raza MSohail, Pfeifer SP, Agustinho DPaiva, Aliyev E, Avdeyev P, Barrozo ER, Behera S, Billingsley K, Chong LChuin, Choubey D, De Coster W, Fu Y, Gener AR, Hefferon T, Henke DMorgan, Höps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRohit Raj, Kubica J, Lakra P, Lattimer D, Liew C-S, Lo B-W, Lo C, Lötter A, Majidian S, Mendem SKumar, Mondal R, Ohmiya H, Parvin N, Peralta C, Poon C-L, Prabhakaran R, Saitou M, Sammi A, Sanio P, Sapoval N, Syed N, Treangen T, Wang G, Xu T, Yang J, Zhang S, Zhou W, Sedlazeck FJ, Busby B. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Res. 2022 ;11:530.
Smolka M, Rescheneder P, Schatz MC, von Haeseler A, Sedlazeck FJ. Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol. 2015 ;16:235.
Paulin LF, Raveendran M, Harris RA, Rogers J, von Haeseler A, Sedlazeck FJ. SVhound: detection of regions that harbor yet undetected structural variation. BMC Bioinformatics. 2023 ;24(1):23.
Fuhrmann DR, Krzywinski MI, Chiu R, Saeedi P, Schein JE, Bosdet IE, Chinwalla A, Hillier LDW, Waterston RH, McPherson JD, Jones SJM, Marra MA. Software for automated analysis of DNA fingerprinting gels. Genome Res. 2003 ;13(5):940-53.
Zhang J, Wheeler DA, Yakub I, Wei S, Sood R, Rowe W, Liu PP, Gibbs RA, Buetow KH. SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol. 2005 ;1(5):e53.
Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Genome Res. 2010 ;20(2):273-80.
Chen Y, Zhao L, Wang Y, Cao M, Gelowani V, Xu M, Agrawal SA, Li Y, Daiger SP, Gibbs RA, Wang F, Chen R. SeqCNV: a novel method for identification of copy number variations in targeted next-generation sequencing data. BMC Bioinformatics. 2017 ;18(1):147.
Chowdhury M, Pedersen BS, Sedlazeck FJ, Quinlan AR, Layer RM. Searching thousands of genomes to classify somatic and novel structural variants using STIX. Nat Methods. 2022 ;19(4):445-448.
Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan M, Sofia HJ, Hutter C, Getz G, Wheeler D, Ding L. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst. 2018 ;6(3):271-281.e7.
Kwong AM, Blackwell TW, LeFaive J, de Andrade M, Barnard J, Barnes KC, Blangero J, Boerwinkle E, Burchard EG, Cade BE, Chasman DI, Chen H, Conomos MP, L Cupples A, Ellinor PT, Eng C, Gao Y, Guo X, Irvin MRyan, Kelly TN, Kim W, Kooperberg C, Lubitz SA, C Y Mak A, Manichaikul AW, Mathias RA, Montasser ME, Montgomery CG, Musani S, Palmer ND, Peloso GM, Qiao D, Reiner AP, Roden DM, M Shoemaker B, Smith JA, Smith NL, Su JLasky, Tiwari HK, Weeks DE, Weiss ST, Scott LJ, Smith AV, Abecasis GR, Boehnke M, Kang HMin. Robust, flexible, and scalable tests for Hardy-Weinberg equilibrium across diverse ancestries. Genetics. 2021 ;218(1).
Liu M, Zhong Y, Liu H, Liang D, Liu E, Zhang Y, Tian F, Liang Q, Cram DS, Wang H, Wu L, Yu F. REDBot: Natural language process methods for clinical copy number variation reporting in prenatal and products of conception diagnosis. Mol Genet Genomic Med. 2020 ;8(11):e1488.
Miller CA, Hampton O, Coarfa C, Milosavljevic A. ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads. PLoS One. 2011 ;6(1):e16327.
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC. RaGOO: fast and accurate reference-guided scaffolding of draft genomes. Genome Biol. 2019 ;20(1):224.
Mahmoud M, Doddapaneni H, Timp W, Sedlazeck FJ. PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs, and methylation. Genome Biol. 2021 ;22(1):268.
Yao J, Lin H, Van Deynze A, Doddapaneni H, Francis M, Lemos EGertrudes, Civerolo EL. PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences. BMC Microbiol. 2008 ;8:185.
Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs RA, Hardison R, Miller W. PipMaker--a web server for aligning two genomic DNA sequences. Genome Res. 2000 ;10(4):577-86.
Wohler E, Martin R, Griffith S, Rodrigues Eda S, Antonescu C, Posey JE, Coban-Akdemir Z, Jhangiani SN, Doheny KF, Lupski JR, Valle D, Hamosh A, Sobreira N. PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. Orphanet J Rare Dis. 2021 ;16(1):365.