☰

Aaron M. Wenger, Ph.D. - Publications

Affiliations: 
2012 Stanford University, Palo Alto, CA 
Area:
Computational Biology
Tree Info Grants Similar researchers PubMed Report error

30/52 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
2023 Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Cheng YH, Ranchalis J, Mao Y, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, et al. Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition. Biorxiv : the Preprint Server For Biology. PMID 37808736 DOI: 10.1101/2023.09.26.559521  0.383
2023 Cheung WA, Johnson AF, Rowell WJ, Farrow E, Hall R, Cohen ASA, Means JC, Zion TN, Portik DM, Saunders CT, Koseva B, Bi C, Truong TK, Schwendinger-Schreck C, Yoo B, ... ... Wenger AM, et al. Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort. Nature Communications. 14: 3090. PMID 37248219 DOI: 10.1038/s41467-023-38782-1  0.373
2022 Wagner J, Olson ND, Harris L, Khan Z, Farek J, Mahmoud M, Stankovic A, Kovacevic V, Yoo B, Miller N, Rosenfeld JA, Ni B, Zarate S, Kirsche M, Aganezov S, ... ... Wenger AM, et al. Benchmarking challenging small variants with linked and long reads. Cell Genomics. 2. PMID 36452119 DOI: 10.1016/j.xgen.2022.100128  0.329
2022 Mehinovic E, Gray T, Campbell M, Ekholm J, Wenger A, Rowell W, Grudo A, Grimwood J, Korlach J, Gurnett C, Constantino JN, Turner TN. Germline mosaicism of a missense variant in KCNC2 in a multiplex family with autism and epilepsy characterized by long-read sequencing. American Journal of Medical Genetics. Part A. PMID 35366058 DOI: 10.1002/ajmg.a.62743  0.317
2022 Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, Fungtammasan A, Hwang YC, Gupta R, Wenger AM, Rowell WJ, Khan ZM, Farek J, Zhu Y, Pisupati A, Mahmoud M, et al. Curated variation benchmarks for challenging medically relevant autosomal genes. Nature Biotechnology. PMID 35132260 DOI: 10.1038/s41587-021-01158-1  0.336
2021 Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, ... ... Wenger AM, et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science (New York, N.Y.). PMID 33632895 DOI: 10.1126/science.abf7117  0.302
2020 Pauper M, Kucuk E, Wenger AM, Chakraborty S, Baybayan P, Kwint M, van der Sanden B, Nelen MR, Derks R, Brunner HG, Hoischen A, Vissers LELM, Gilissen C. Long-read trio sequencing of individuals with unsolved intellectual disability. European Journal of Human Genetics : Ejhg. PMID 33257779 DOI: 10.1038/s41431-020-00770-0  0.328
2020 Birgmeier J, Haeussler M, Deisseroth CA, Steinberg EH, Jagadeesh KA, Ratner AJ, Guturu H, Wenger AM, Diekhans ME, Stenson PD, Cooper DN, Ré C, Beggs AH, Bernstein JA, Bejerano G. AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature. Science Translational Medicine. 12. PMID 32434849 DOI: 10.1126/Scitranslmed.Aau9113  0.645
2018 Berger MJ, Wenger AM, Guturu H, Bejerano G. Independent erosion of conserved transcription factor binding sites points to shared hindlimb, vision and external testes loss in different mammals. Nucleic Acids Research. PMID 30137416 DOI: 10.1093/Nar/Gky741  0.664
2018 Chen HI, Jagadeesh KA, Birgmeier J, Wenger AM, Guturu H, Schelley S, Bernstein JA, Bejerano G. An MTF1 binding site disrupted by a homozygous variant in the promoter of ATP7B likely causes Wilson Disease. European Journal of Human Genetics : Ejhg. PMID 30087448 DOI: 10.1038/S41431-018-0221-4  0.698
2018 Jagadeesh KA, Birgmeier J, Guturu H, Deisseroth CA, Wenger AM, Bernstein JA, Bejerano G. Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 29997393 DOI: 10.1038/S41436-018-0072-Y  0.658
2018 Birgmeier J, Esplin ED, Jagadeesh KA, Guturu H, Wenger AM, Chaib H, Buckingham JA, Bejerano G, Bernstein JA. Biallelic loss-of-function WNT5A mutations in an infant with severe and atypical manifestations of Robinow syndrome. American Journal of Medical Genetics. Part A. 176: 1030-1036. PMID 29575631 DOI: 10.1002/Ajmg.A.38636  0.637
2017 Alcantara D, Timms AE, Gripp K, Baker L, Park K, Collins S, Cheng C, Stewart F, Mehta SG, Saggar A, Sztriha L, Zombor M, Caluseriu O, Mesterman R, Van Allen MI, ... ... Wenger AM, et al. Mutations of AKT3 are associated with a wide spectrum of developmental disorders including extreme megalencephaly. Brain : a Journal of Neurology. 140: 2610-2622. PMID 28969385 DOI: 10.1093/Brain/Awx203  0.635
2017 Merker JD, Wenger AM, Sneddon T, Grove M, Zappala Z, Fresard L, Waggott D, Utiramerur S, Hou Y, Smith KS, Montgomery SB, Wheeler M, Buchan JG, Lambert CC, Eng KS, et al. Long-read genome sequencing identifies causal structural variation in a Mendelian disease. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 28640241 DOI: 10.1038/Gim.2017.86  0.359
2016 Jagadeesh KA, Wenger AM, Berger MJ, Guturu H, Stenson PD, Cooper DN, Bernstein JA, Bejerano G. M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity. Nature Genetics. PMID 27776117 DOI: 10.1038/Ng.3703  0.646
2016 Balasubramanian M, Lord H, Levesque S, Guturu H, Thuriot F, Sillon G, Wenger AM, Sureka DL, Lester T, Johnson DS, Bowen J, Calhoun AR, Viskochil DH, Bejerano G, et al. Chitayat syndrome: hyperphalangism, characteristic facies, hallux valgus and bronchomalacia results from a recurrent c.266A>G p.(Tyr89Cys) variant in the ERF gene. Journal of Medical Genetics. PMID 27738187 DOI: 10.1136/Jmedgenet-2016-104143  0.608
2016 Wenger AM, Guturu H, Bernstein JA, Bejerano G. Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 27441994 DOI: 10.1038/Gim.2016.88  0.618
2014 Camp JG, Frank CL, Lickwar CR, Guturu H, Rube T, Wenger AM, Chen J, Bejerano G, Crawford GE, Rawls JF. Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Research. 24: 1504-16. PMID 24963153 DOI: 10.1101/Gr.165845.113  0.659
2014 Tuteja G, Moreira KB, Chung T, Chen J, Wenger AM, Bejerano G. Automated discovery of tissue-targeting enhancers and transcription factors from binding motif and gene function data. Plos Computational Biology. 10: e1003449. PMID 24499934 DOI: 10.1371/Journal.Pcbi.1003449  0.702
2013 Guturu H, Doxey AC, Wenger AM, Bejerano G. Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20130029. PMID 24218641 DOI: 10.1098/Rstb.2013.0029  0.642
2013 Wenger AM, Clarke SL, Notwell JH, Chung T, Tuteja G, Guturu H, Schaar BT, Bejerano G. The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. Plos Genetics. 9: e1003728. PMID 24009522 DOI: 10.1371/Journal.Pgen.1003728  0.702
2013 Hiller M, Agarwal S, Notwell JH, Parikh R, Guturu H, Wenger AM, Bejerano G. Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish. Nucleic Acids Research. 41: e151. PMID 23814184 DOI: 10.1093/Nar/Gkt557  0.663
2013 Wenger AM, Clarke SL, Guturu H, Chen J, Schaar BT, McLean CY, Bejerano G. PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome Research. 23: 889-904. PMID 23382538 DOI: 10.1101/Gr.139071.112  0.683
2013 Tuteja G, Wenger A, Moreira KB, Chung T, Bejerano G. Genomic approaches for the identification of genes and enhancers regulating placenta development Placenta. 34: A69-A70. DOI: 10.1016/J.Placenta.2013.06.210  0.675
2012 Clarke SL, VanderMeer JE, Wenger AM, Schaar BT, Ahituv N, Bejerano G. Human developmental enhancers conserved between deuterostomes and protostomes. Plos Genetics. 8: e1002852. PMID 22876195 DOI: 10.1371/Journal.Pgen.1002852  0.695
2012 Laurell T, Vandermeer JE, Wenger AM, Grigelioniene G, Nordenskjöld A, Arner M, Ekblom AG, Bejerano G, Ahituv N, Nordgren A. A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb. Human Mutation. 33: 1063-6. PMID 22495965 DOI: 10.1002/Humu.22097  0.686
2012 Birnbaum RY, Clowney EJ, Agamy O, Kim MJ, Zhao J, Yamanaka T, Pappalardo Z, Clarke SL, Wenger AM, Nguyen L, Gurrieri F, Everman DB, Schwartz CE, Birk OS, Bejerano G, et al. Coding exons function as tissue-specific enhancers of nearby genes. Genome Research. 22: 1059-68. PMID 22442009 DOI: 10.1101/Gr.133546.111  0.695
2011 Capellini TD, Handschuh K, Quintana L, Ferretti E, Di Giacomo G, Fantini S, Vaccari G, Clarke SL, Wenger AM, Bejerano G, Sharpe J, Zappavigna V, Selleri L. Control of pelvic girdle development by genes of the Pbx family and Emx2. Developmental Dynamics : An Official Publication of the American Association of Anatomists. 240: 1173-89. PMID 21455939 DOI: 10.1002/Dvdy.22617  0.662
2011 McLean CY, Reno PL, Pollen AA, Bassan AI, Capellini TD, Guenther C, Indjeian VB, Lim X, Menke DB, Schaar BT, Wenger AM, Bejerano G, Kingsley DM. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature. 471: 216-9. PMID 21390129 DOI: 10.1038/Nature09774  0.67
2010 McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnology. 28: 495-501. PMID 20436461 DOI: 10.1038/Nbt.1630  0.702
Low-probability matches (unlikely to be authored by this person)
2019 Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, ... ... Wenger AM, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10: 1784. PMID 30992455 DOI: 10.1038/S41467-018-08148-Z  0.298
2019 Corbett MA, Kroes T, Veneziano L, Bennett MF, Florian R, Schneider AL, Coppola A, Licchetta L, Franceschetti S, Suppa A, Wenger A, Mei D, Pendziwiat M, Kaya S, Delledonne M, et al. Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2. Nature Communications. 10: 4920. PMID 31664034 DOI: 10.1038/S41467-019-12671-Y  0.293
2022 Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, ... ... Wenger A, et al. The complete sequence of a human genome. Science (New York, N.Y.). 376: 44-53. PMID 35357919 DOI: 10.1126/science.abj6987  0.291
2022 Sanford Kobayashi E, Batalov S, Wenger AM, Lambert C, Dhillon H, Hall RJ, Baybayan P, Ding Y, Rego S, Wigby K, Friedman J, Hobbs C, Bainbridge MN. Approaches to long-read sequencing in a clinical setting to improve diagnostic rate. Scientific Reports. 12: 16945. PMID 36210382 DOI: 10.1038/s41598-022-20113-x  0.287
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, ... ... Wenger AM, et al. A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32541955 DOI: 10.1038/S41587-020-0538-8  0.285
2024 Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, et al. Characterization and visualization of tandem repeats at genome scale. Nature Biotechnology. PMID 38168995 DOI: 10.1038/s41587-023-02057-3  0.265
2022 Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, ... ... Wenger A, et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature. PMID 36261518 DOI: 10.1038/s41586-022-05325-5  0.261
2023 Kucuk E, van der Sanden BPGH, O'Gorman L, Kwint M, Derks R, Wenger AM, Lambert C, Chakraborty S, Baybayan P, Rowell WJ, Brunner HG, Vissers LELM, Hoischen A, Gilissen C. Comprehensive de novo mutation discovery with HiFi long-read sequencing. Genome Medicine. 15: 34. PMID 37158973 DOI: 10.1186/s13073-023-01183-6  0.261
2020 Chapman LM, Spies N, Pai P, Lim CS, Carroll A, Narzisi G, Watson CM, Proukakis C, Clarke WE, Nariai N, Dawson E, Jones G, Blankenberg D, Brueffer C, Xiao C, ... ... Wenger AM, et al. A crowdsourced set of curated structural variants for the human genome. Plos Computational Biology. 16: e1007933. PMID 32559231 DOI: 10.1371/Journal.Pcbi.1007933  0.26
2023 Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, ... ... Wenger AM, et al. The complete sequence of a human Y chromosome. Nature. PMID 37612512 DOI: 10.1038/s41586-023-06457-y  0.259
2019 Vollger MR, Logsdon GA, Audano PA, Sulovari A, Porubsky D, Peluso P, Wenger AM, Concepcion GT, Kronenberg ZN, Munson KM, Baker C, Sanders AD, Spierings DCJ, Lansdorp PM, Surti U, et al. Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads. Annals of Human Genetics. PMID 31711268 DOI: 10.1111/Ahg.12364  0.258
2022 Espejo Valle-Inclan J, Besselink NJM, de Bruijn E, Cameron DL, Ebler J, Kutzera J, van Lieshout S, Marschall T, Nelen M, Priestley P, Renkens I, Roemer MGM, van Roosmalen MJ, Wenger AM, Ylstra B, et al. A multi-platform reference for somatic structural variation detection. Cell Genomics. 2: 100139. PMID 36778136 DOI: 10.1016/j.xgen.2022.100139  0.243
2017 Robinson JT, Thorvaldsdóttir H, Wenger AM, Zehir A, Mesirov JP. Variant Review with the Integrative Genomics Viewer. Cancer Research. 77: e31-e34. PMID 29092934 DOI: 10.1158/0008-5472.Can-17-0337  0.242
2019 Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nature Biotechnology. PMID 31406327 DOI: 10.1038/S41587-019-0217-9  0.241
2021 Fukuda H, Yamaguchi D, Nyquist K, Yabuki Y, Miyatake S, Uchiyama Y, Hamanaka K, Saida K, Koshimizu E, Tsuchida N, Fujita A, Mitsuhashi S, Ohbo K, Satake Y, Sone J, ... ... Wenger AM, et al. Father-to-offspring transmission of extremely long NOTCH2NLC repeat expansions with contractions: genetic and epigenetic profiling with long-read sequencing. Clinical Epigenetics. 13: 204. PMID 34774111 DOI: 10.1186/s13148-021-01192-5  0.23
2022 Baid G, Cook DE, Shafin K, Yun T, Llinares-López F, Berthet Q, Belyaeva A, Töpfer A, Wenger AM, Rowell WJ, Yang H, Kolesnikov A, Ammar W, Vert JP, Vaswani A, et al. DeepConsensus improves the accuracy of sequences with a gap-aware sequence transformer. Nature Biotechnology. PMID 36050551 DOI: 10.1038/s41587-022-01435-7  0.219
2019 Wang YC, Olson ND, Deikus G, Shah H, Wenger AM, Trow J, Xiao C, Sherry S, Salit ML, Zook JM, Smith M, Sebra R. High-coverage, long-read sequencing of Han Chinese trio reference samples. Scientific Data. 6: 91. PMID 31201313 DOI: 10.1038/S41597-019-0098-2  0.202
2022 Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, Baybayan P, Belden B, Berrios CD, Biswell RL, Buczkowicz P, Buske O, Chakraborty S, ... ... Wenger AM, et al. Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 35305867 DOI: 10.1016/j.gim.2022.02.007  0.199
2024 Holt JM, Saunders CT, Rowell WJ, Kronenberg Z, Wenger AM, Eberle M. HiPhase: Jointly phasing small, structural, and tandem repeat variants from HiFi sequencing. Bioinformatics (Oxford, England). PMID 38269623 DOI: 10.1093/bioinformatics/btae042  0.157
2021 Pauper M, Kucuk E, Wenger AM, Chakraborty S, Baybayan P, Kwint M, van der Sanden B, Nelen MR, Derks R, Brunner HG, Hoischen A, Vissers LELM, Gilissen C. Correction: Long-read trio sequencing of individuals with unsolved intellectual disability. European Journal of Human Genetics : Ejhg. PMID 33772160 DOI: 10.1038/s41431-021-00868-z  0.129
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, ... ... Wenger AM, et al. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32699374 DOI: 10.1038/S41587-020-0640-Y  0.105
2006 Hampton SS, Brenner P, Wenger A, Chatterjee S, Izaguirre JA. Biomolecular Sampling: Algorithms, Test Molecules, and Metrics Lecture Notes in Computational Science and Engineering. 49: 103-123.  0.053
Hide low-probability matches.