Pall Melsted, Ph.D. - Publications

Affiliations: 
2009 Carnegie Mellon University, Pittsburgh, PA 
Area:
Mathematics, Computer Science

16/42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biology. 17: 132. PMID 27323842 DOI: 10.1186/S13059-016-0997-X  1
2016 Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. PMID 27043002 DOI: 10.1038/Nbt.3519  1
2015 Kozma R, Melsted P, Magnússon KP, Höglund J. Looking into the past - the reaction of three grouse species to climate change over the last million years using whole genome sequences. Molecular Ecology. PMID 26607571 DOI: 10.1111/Mec.13496  1
2015 Óskarsdóttir A, Másson G, Melsted P. BamHash: a checksum program for verifying the integrity of sequence data. Bioinformatics (Oxford, England). PMID 26363028 DOI: 10.1093/Bioinformatics/Btv539  1
2015 Kehr B, Melsted P, Halldórsson BV. PopIns: population-scale detection of novel sequence insertions. Bioinformatics (Oxford, England). PMID 25926346 DOI: 10.1093/Bioinformatics/Btv273  1
2014 Melsted P, Halldórsson BV. KmerStream: streaming algorithms for k-mer abundance estimation. Bioinformatics (Oxford, England). 30: 3541-7. PMID 25355787 DOI: 10.1093/Bioinformatics/Btu713  1
2012 Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y. Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Research. 22: 602-10. PMID 22207615 DOI: 10.1101/Gr.130468.111  1
2012 Perry GH, Reeves D, Melsted P, Ratan A, Miller W, Michelini K, Louis EE, Pritchard JK, Mason CE, Gilad Y. A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar. Genome Biology and Evolution. 4: 126-35. PMID 22155688 DOI: 10.1093/Gbe/Evr132  1
2012 Frieze A, Melsted P. Maximum matchings in random bipartite graphs and the space utilization of Cuckoo Hash tables Random Structures and Algorithms. 41: 334-364. DOI: 10.1002/Rsa.20427  1
2011 Melsted P, Pritchard JK. Efficient counting of k-mers in DNA sequences using a bloom filter. Bmc Bioinformatics. 12: 333. PMID 21831268 DOI: 10.1186/1471-2105-12-333  1
2011 Frieze A, Melsted P. Randomly coloring simple hypergraphs Information Processing Letters. 111: 848-853. DOI: 10.1016/J.Ipl.2011.06.001  1
2010 Perry GH, Marioni JC, Melsted P, Gilad Y. Genomic-scale capture and sequencing of endogenous DNA from feces. Molecular Ecology. 19: 5332-44. PMID 21054605 DOI: 10.1111/J.1365-294X.2010.04888.X  1
2009 Frieze A, Melsted P, Mitzenmacher M. An analysis of random-walk cuckoo hashing Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5687: 490-503. DOI: 10.1007/978-3-642-03685-9_37  1
2009 Chebolu P, Frieze A, Melsted P, Sorkin GB. Average-case analyses of Vickrey costs Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5687: 434-447. DOI: 10.1007/978-3-642-03685-9_33  1
2008 Chebolu P, Frieze A, Melsted P. Finding a maximum matching in a sparse random graph in O(n) expected time Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5125: 161-172. DOI: 10.1007/978-3-540-70575-8_14  1
2008 Chebolu P, Melsted P. PageRank and the Random Surfer Model Proceedings of the Annual Acm-Siam Symposium On Discrete Algorithms. 1010-1018.  1
Low-probability matches
2020 Björnsson E, Gunnarsdóttir K, Halldórsson GH, Sigurðsson Á, Árnadóttir GA, Jónsson H, Ólafsdóttir EF, Niehus S, Kehr B, Sveinbjörnsson G, Guðmundsdóttir S, Helgadóttir A, Andersen K, Thorleifsson G, Eyjólfsson GI, ... ... Melsted P, et al. Lifelong Reduction in LDL Cholesterol Due to a Gain-of-Function Mutation in . Circulation. Genomic and Precision Medicine. PMID 33315477 DOI: 10.1161/CIRCGEN.120.003029  0.08
2017 Eggertsson HP, Jonsson H, Kristmundsdottir S, Hjartarson E, Kehr B, Masson G, Zink F, Hjorleifsson KE, Jonasdottir A, Jonasdottir A, Jonsdottir I, Gudbjartsson DF, Melsted P, Stefansson K, Halldorsson BV. Graphtyper enables population-scale genotyping using pangenome graphs. Nature Genetics. PMID 28945251 DOI: 10.1038/Ng.3964  0.08
2017 Kehr B, Helgadottir A, Melsted P, Jonsson H, Helgason H, Jonasdottir A, Jonasdottir A, Sigurdsson A, Gylfason A, Halldorsson GH, Kristmundsdottir S, Thorgeirsson G, Olafsson I, Holm H, Thorsteinsdottir U, et al. Diversity in non-repetitive human sequences not found in the reference genome. Nature Genetics. PMID 28250455 DOI: 10.1038/Ng.3801  0.08
2016 Kehr B, Melsted P. chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts. Bioinformatics (Oxford, England). PMID 27153590 DOI: 10.1093/Bioinformatics/Btw149  0.08
2021 Melsted P, Booeshaghi AS, Liu L, Gao F, Lu L, Min KHJ, da Veiga Beltrame E, Hjörleifsson KE, Gehring J, Pachter L. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nature Biotechnology. PMID 33795888 DOI: 10.1038/s41587-021-00870-2  0.01
2021 Olafsdottir T, Stacey SN, Sveinbjornsson G, Thorleifsson G, Norland K, Sigurgeirsson B, Thorisdottir K, Kristjansson AK, Tryggvadottir L, Sarin KY, Benediktsson R, Jonasson JG, Sigurdsson A, Jonasdottir A, Kristmundsdottir S, ... ... Melsted P, et al. Loss-of-Function Variants in the Tumor Suppressor Gene PTPN14 confer increased Cancer Risk. Cancer Research. PMID 33602785 DOI: 10.1158/0008-5472.CAN-20-3065  0.01
2020 Holley G, Melsted P. Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs. Genome Biology. 21: 249. PMID 32943081 DOI: 10.1186/S13059-020-02135-8  0.01
2020 Gudbjartsson DF, Norddahl GL, Melsted P, Gunnarsdottir K, Holm H, Eythorsson E, Arnthorsson AO, Helgason D, Bjarnadottir K, Ingvarsson RF, Thorsteinsdottir B, Kristjansdottir S, Birgisdottir K, Kristinsdottir AM, Sigurdsson MI, et al. Humoral Immune Response to SARS-CoV-2 in Iceland. The New England Journal of Medicine. PMID 32871063 DOI: 10.1056/Nejmoa2026116  0.01
2020 Saevarsdottir S, Olafsdottir TA, Ivarsdottir EV, Halldorsson GH, Gunnarsdottir K, Sigurdsson A, Johannesson A, Sigurdsson JK, Juliusdottir T, Lund SH, Arnthorsson AO, Styrmisdottir EL, Gudmundsson J, Grondal GM, Steinsson K, ... ... Melsted P, et al. FLT3 stop mutation increases FLT3 ligand level and risk of autoimmune thyroid disease. Nature. PMID 32581359 DOI: 10.1038/S41586-020-2436-0  0.01
2020 Gudbjartsson DF, Helgason A, Jonsson H, Magnusson OT, Melsted P, Norddahl GL, Saemundsdottir J, Sigurdsson A, Sulem P, Agustsdottir AB, Eiriksdottir B, Fridriksdottir R, Gardarsdottir EE, Georgsson G, Gretarsdottir OS, et al. Spread of SARS-CoV-2 in the Icelandic Population. The New England Journal of Medicine. PMID 32289214 DOI: 10.1056/Nejmoa2006100  0.01
2020 Olafsdottir T, Thorleifsson G, Sulem P, Stefansson OA, Medek H, Olafsson K, Ingthorsson O, Gudmundsson V, Jonsdottir I, Halldorsson GH, Kristjansson RP, Frigge ML, Stefansdottir L, Sigurdsson JK, Oddsson A, ... ... Melsted P, et al. Genome-wide association identifies seven loci for pelvic organ prolapse in Iceland and the UK Biobank. Communications Biology. 3: 129. PMID 32184442 DOI: 10.1038/s42003-020-0857-9  0.01
2020 Jonasson K, Sigurdsson S, Yngvason HF, Ragnarsson PO, Melsted P. Algorithm 1005 Acm Transactions On Mathematical Software. 46: 1-20. DOI: 10.1145/3382191  0.01
2019 Eggertsson HP, Kristmundsdottir S, Beyter D, Jonsson H, Skuladottir A, Hardarson MT, Gudbjartsson DF, Stefansson K, Halldorsson BV, Melsted P. GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs. Nature Communications. 10: 5402. PMID 31776332 DOI: 10.1038/S41467-019-13341-9  0.01
2019 Melsted P, Ntranos V, Pachter L. The Barcode, UMI, Set format and BUStools. Bioinformatics (Oxford, England). PMID 31073610 DOI: 10.1093/Bioinformatics/Btz279  0.01
2019 Bjornsdottir G, Ivarsdottir EV, Bjarnadottir K, Benonisdottir S, Gylfadottir SS, Arnadottir GA, Benediktsson R, Halldorsson GH, Helgadottir A, Jonasdottir A, Jonasdottir A, Jonsdottir I, Kristinsdottir AM, Magnusson OT, Masson G, ... Melsted P, et al. A PRPH splice-donor variant associates with reduced sural nerve amplitude and risk of peripheral neuropathy. Nature Communications. 10: 1777. PMID 30992453 DOI: 10.1038/S41467-019-09719-4  0.01
2019 Ntranos V, Yi L, Melsted P, Pachter L. A discriminative learning approach to differential expression analysis for single-cell RNA-seq. Nature Methods. PMID 30664774 DOI: 10.1038/S41592-018-0303-9  0.01
2018 Zink F, Magnusdottir DN, Magnusson OT, Walker NJ, Morris TJ, Sigurdsson A, Halldorsson GH, Gudjonsson SA, Melsted P, Ingimundardottir H, Kristmundsdottir S, Alexandersson KF, Helgadottir A, Gudmundsson J, Rafnar T, et al. Insights into imprinting from parent-of-origin phased methylomes and transcriptomes. Nature Genetics. 50: 1542-1552. PMID 30349119 DOI: 10.1038/S41588-018-0232-7  0.01
2018 Thorolfsdottir RB, Sveinbjornsson G, Sulem P, Nielsen JB, Jonsson S, Halldorsson GH, Melsted P, Ivarsdottir EV, Davidsson OB, Kristjansson RP, Thorleifsson G, Helgadottir A, Gretarsdottir S, Norddahl G, Rajamani S, et al. Coding variants in and increase risk of atrial fibrillation. Communications Biology. 1: 68. PMID 30271950 DOI: 10.1038/s42003-018-0068-9  0.01
2018 Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L. Pseudoalignment for metagenomic read assignment. Bioinformatics (Oxford, England). 33: 2082-2088. PMID 28334086 DOI: 10.1093/Bioinformatics/Btx106  0.01
2017 Pimentel H, Bray NL, Puente S, Melsted P, Pachter L. Differential analysis of RNA-seq incorporating quantification uncertainty. Nature Methods. PMID 28581496 DOI: 10.1038/Nmeth.4324  0.01
2016 Pimentel H, Sturmfels P, Bray N, Melsted P, Pachter L. The Lair: a resource for exploratory analysis of published RNA-Seq data. Bmc Bioinformatics. 17: 490. PMID 27905880 DOI: 10.1186/S12859-016-1357-2  0.01
2016 Bray NL, Pimentel H, Melsted P, Pachter L. Erratum: Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. 34: 888. PMID 27504780 DOI: 10.1038/Nbt0816-888D  0.01
2019 Melsted P, Booeshaghi AS, Liu L, Gao F, Min KH, Beltrame E, Lu L, Hjörleifsson KE, Gehring J, Pachter L. Algorithms and infrastructure for accurate pre-processing and analysis of single-cell RNA-seq F1000research. 8. DOI: 10.7490/F1000Research.1117626.1  0
2013 Frankenberger CA, Bainer RO, Menon J, Chavarria C, Michelini K, Melsted P, Gilad Y, Rosner MR. Abstract B25: Using species-specific RNAseq reveals stromal reprogramming in triple-negative breast cancer xenografts Cancer Research. 73. DOI: 10.1158/1538-7445.Tim2013-B25  0
2011 Frieze A, Melsted P, Mitzenmacher M. An Analysis of Random-Walk Cuckoo Hashing Siam Journal On Computing. 40: 291-308. DOI: 10.1137/090770928  0
2010 Chebolu P, Frieze A, Melsted P. Finding a maximum matching in a sparse random graph in O ( n ) expected time Journal of the Acm. 57: 24. DOI: 10.1145/1734213.1734218  0
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