Publications: Yufeng Wu

• 2024

• The Role of Exercise in Statin-Associated Muscle Symptoms Outcomes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.
  Mangone LA, Kwon OS, Johnson BT, Wu Y, Pescatello LS
  Mayo Clinic proceedings. Innovations, quality & outcomes (2024) 8(2):131-142 PMC6465106 10.1093/eurjpc/zwad229
• Computing the Bounds of the Number of Reticulations in a Tree-Child Network That Displays a Set of Trees.
  Wu Y, Zhang L
  Journal of computational biology : a journal of computational molecular cell biology (2024) 31(4):345-359 10.1089/cmb.2023.0309
• SAND: Automated Time-Domain Modeling of NMR Spectra Applied to Metabolite Quantification.
  Wu Y, Sanati O, Uchimiya M, Krishnamurthy K, Wedell J, Hoch JC, Edison AS, Delaglio F
  Analytical chemistry (2024) 96(5):1843-1851 PMC3163565 10.1186/1471-2105-12-323
• A general approach for inferring the ancestry of recent ancestors of an admixed individual.
  Zhang Y, Zhang H, Wu Y
  Proceedings of the National Academy of Sciences of the United States of America (2024) 121(2):e2316242120 PMC8551421 10.1073/pnas.2316242120

• 2023

• Evaluation of Exercise Mobile Applications for Adults with Cardiovascular Disease Risk Factors.
  Chen S, Wu Y, Bushey EL, Pescatello LS
  Journal of cardiovascular development and disease (2023) 10(12): PMC7930885 10.1016/j.mayocpiqo.2020.08.005
• Enhanced circularly polarized luminescence dissymmetry of [Ru(bpy)] complexes in a 3D chiral framework: a study of transparent thin films.
  Zhang S, Schnable D, Elgin J, Ung G, Wu Y
  Chemical communications (Cambridge, England) (2023) 59(86):12867-12870 10.1039/d3cc04083f
• 3D-printed epidermal sweat microfluidic systems with integrated microcuvettes for precise spectroscopic and fluorometric biochemical assays.
  Yang DS, Wu Y, Kanatzidis EE, Avila R, Zhou M, Bai Y, Chen S, Sekine Y, Kim J, Deng Y, Guo H, Zhang Y, Ghaffari R, Huang Y, Rogers JA
  Materials horizons (2023) 10(11):4992-5003 10.1039/d3mh00876b
• Thermomechanical Properties of Neutron Irradiated AlHf-Al Thermal Neutron Absorber Materials.
  Guillen DP, Toloczko MB, Prabhakaran R, Zhu Y, Lu Y, Wu Y
  Materials (Basel, Switzerland) (2023) 16(16): PMC10456384 10.1016/0022-3115(93)90129-M
• A fast and scalable method for inferring phylogenetic networks from trees by aligning lineage taxon strings.
  Zhang L, Abhari N, Colijn C, Wu Y
  Genome research (2023) 33(7):1053-1060 PMC6915859 10.1186/s12859-019-3209-3
• Detecting genomic deletions from high-throughput sequence data with unsupervised learning.
  Li X, Wu Y
  BMC bioinformatics (2023) 23(Suppl 8):568 PMC3106182 10.1093/bioinformatics/btr174
• Exercise for counteracting weight recurrence after bariatric surgery: a systematic review and meta-analysis of randomized controlled trials.
  Bond DS, Manuel KM, Wu Y, Livingston J, Papasavas PK, Baillot A, Pescatello LS
  Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery (2023) 19(6):641-650 PMC8725202 10.1016/j.soard.2022.12.029

• 2022

• Sample size re-estimation in Phase 2 dose-finding: Conditional power versus Bayesian predictive power.
  Liu Q, Hu G, Ye B, Wang S, Wu Y
  Pharmaceutical statistics (2022) 22(2):349-364 10.1002/pst.2275
• Cardiometabolic Biomarkers and Habitual Caffeine Consumption Associate with the Adverse Ambulatory Blood Pressure Response to Strenuous Physical Exertion among Firefighters.
  Berkowsky RS, Zaleski AL, Taylor BA, Chen MH, Gans KM, Wu Y, Parducci PM, Zhang Y, Fernandez AB, Pescatello LS
  Nutrients (2022) 14(19): PMC4656907 10.3945/jn.115.219634
• Wireless multi-lateral optofluidic microsystems for real-time programmable optogenetics and photopharmacology.
  Wu Y, Wu M, Vázquez-Guardado A, Kim J, Zhang X, Avila R, Kim JT, Deng Y, Yu Y, Melzer S, Bai Y, Yoon H, Meng L, Zhang Y, Guo H, Hong L, Kanatzidis EE, Haney CR, Waters EA, Banks AR, Hu Z, Lie F, Chamorro LP, Sabatini BL, Huang Y, Kozorovitskiy Y, Rogers JA
  Nature communications (2022) 13(1):5571 PMC8211450 10.7554/eLife.64041
• virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.
  Zaman S, Sledzieski S, Berger B, Wu YC, Bansal MS
  Journal of computational biology : a journal of computational molecular cell biology (2022) 30(1):3-20 PMC7095418 10.1089/cmb.2021.0507
• Exercise to Treat Hypertension: Late Breaking News on Exercise Prescriptions That FITT.
  Alves AJ, Wu Y, Lopes S, Ribeiro F, Pescatello LS
  Current sports medicine reports (2022) 21(8):280-288 10.1249/JSR.0000000000000983
• Joint inference of ancestry and genotypes of parents from children.
  Zhang Y, Wu Y
  iScience (2022) 25(8):104768 PMC4750478 10.1016/j.isci.2022.104768
• Implantable Aptamer-Graphene Microtransistors for Real-Time Monitoring of Neurochemical Release in Vivo.
  Wu G, Zhang N, Matarasso A, Heck I, Li H, Lu W, Phaup JG, Schneider MJ, Wu Y, Weng Z, Sun H, Gao Z, Zhang X, Sandberg SG, Parvin D, Seaholm E, Islam SK, Wang X, Phillips PEM, Castro DC, Ding S, Li DP, Bruchas MR, Zhang Y
  Nano letters (2022) 22(9):3668-3677 PMC5262197 10.1101/2020.05.25.115675
• Evaluating the Methodological Quality of Postexercise Hypotension Aerobic Exercise Interventions.
  Day C, Wu Y, Pescatello LS
  Frontiers in physiology (2022) 13:851950 PMC5064144 10.1097/HJH.0000000000002115
• Wireless, battery-free push-pull microsystem for membrane-free neurochemical sampling in freely moving animals.
  Wu G, Heck I, Zhang N, Phaup G, Zhang X, Wu Y, Stalla DE, Weng Z, Sun H, Li H, Zhang Z, Ding S, Li DP, Zhang Y
  Science advances (2022) 8(8):eabn2277 PMC4354627 10.1126/sciadv.abn2277
• Alterations of host-gut microbiome interactions in multiple sclerosis.
  Cantoni C, Lin Q, Dorsett Y, Ghezzi L, Liu Z, Pan Y, Chen K, Han Y, Li Z, Xiao H, Gormley M, Liu Y, Bokoliya S, Panier H, Suther C, Evans E, Deng L, Locca A, Mikesell R, Obert K, Newland P, Wu Y, Salter A, Cross AH, Tarr PI, Lovett-Racke A, Piccio L, Zhou Y
  EBioMedicine (2022) 76:103798 PMC6342642 10.1016/j.ebiom.2021.103798

• 2021

• Chronic cannabis smoking-enriched oral pathobiont drives behavioral changes, macrophage infiltration, and increases β-amyloid protein production in the brain.
  Luo Z, Fitting S, Robinson C, Benitez A, Li M, Wu Y, Fu X, Amato D, Ning W, Funderburg N, Wang X, Zhou Z, Yu X, Wagner A, Cong X, Xu W, Maas K, Wolf BJ, Huang L, Yu J, Scott A, Mcrae-Clark A, Hamlett ED, Jiang W
  EBioMedicine (2021) 74:103701 PMC5791180 10.2174/1570162X16666180703151208
• Differential adhesion regulates neurite placement via a retrograde zippering mechanism.
  Sengupta T, Koonce NL, Vázquez-Martínez N, Moyle MW, Duncan LH, Emerson SE, Han X, Shao L, Wu Y, Santella A, Fan L, Bao Z, Mohler WA, Shroff H, Colón-Ramos DA
  eLife (2021) 10: PMC8843091 10.7554/eLife.71171
• The Association of Socioeconomic Factors With Outcomes for Coronary Artery Bypass Surgery.
  Hannan EL, Wu Y, Cozzens K, Friedrich M, Chikwe J, Adams DH, Sundt TM, Girardi L, Smith CR, Lahey SJ, Gold JP, Wechsler A
  The Annals of thoracic surgery (2021) 114(4):1318-1325 10.1016/j.athoracsur.2021.10.006
• Do the combined blood pressure effects of exercise and antihypertensive medications add up to the sum of their parts? A systematic meta-review.
  Pescatello LS, Wu Y, Gao S, Livingston J, Sheppard BB, Chen MH
  BMJ open sport & exercise medicine (2021) 7(1):e000895 PMC7818845 10.1136/bmjsem-2020-000895
• The impact of body fat on thermoregulation during exercise in the heat: A systematic review and meta-analysis.
  Morrissey MC, Wu Y, Zuk EF, Livingston J, Casa DJ, Pescatello LS
  Journal of science and medicine in sport (2021) 24(8):843-850 10.1016/j.jsams.2021.06.004
• A comparison of two Tai Chi interventions tailored for different health outcomes.
  Wu Y, Senk C, Coll P, Glenney S, Zaborowski K, Fortinsky R, Taylor B, Park C, Benson K, McGowan M, DiBiasi S, Chen MH, Pescatello L
  Complementary therapies in medicine (2021) 59:102731 10.1016/j.ctim.2021.102731
• Development of a Novel Clinical Decision Support System for Exercise Prescription Among Patients With Multiple Cardiovascular Disease Risk Factors.
  Pescatello LS, Wu Y, Panza GA, Zaleski A, Guidry M
  Mayo Clinic proceedings. Innovations, quality & outcomes (2021) 5(1):193-203 PMC7930885 10.1016/j.mayocpiqo.2020.08.005
• Structural and developmental principles of neuropil assembly in C. elegans.
  Moyle MW, Barnes KM, Kuchroo M, Gonopolskiy A, Duncan LH, Sengupta T, Shao L, Guo M, Santella A, Christensen R, Kumar A, Wu Y, Moon KR, Wolf G, Krishnaswamy S, Bao Z, Shroff H, Mohler WA, Colón-Ramos DA
  Nature (2021) 591(7848):99-104 PMC8385650 10.1038/s41586-020-03169-5
• Bidirectional relationships between weight stigma and pediatric obesity: A systematic review and meta-analysis.
  Ma L, Chu M, Li Y, Wu Y, Yan AF, Johnson B, Wang Y
  Obesity reviews : an official journal of the International Association for the Study of Obesity (2021) 22(6):e13178 10.1111/obr.13178

• 2020

• Biomimetic Boroxine-Based Multifunctional Thermosets via One-Pot Synthesis.
  Yang X, Guo M, Wu Y, Xue S, Li Z, Zhou H, Smith AT, Sun L
  ACS applied materials & interfaces (2020) 12(50):56445-56453 10.1021/acsami.0c16736
• Depression prevalence based on the Edinburgh Postnatal Depression Scale compared to Structured Clinical Interview for DSM DIsorders classification: Systematic review and individual participant data meta-analysis.
  Lyubenova A, Neupane D, Levis B, Wu Y, Sun Y, He C, Krishnan A, Bhandari PM, Negeri Z, Imran M, Rice DB, Azar M, Chiovitti MJ, Saadat N, Riehm KE, Boruff JT, Ioannidis JPA, Cuijpers P, Gilbody S, Kloda LA, Patten SB, Shrier I, Ziegelstein RC, Comeau L, Mitchell ND, Tonelli M, Vigod SN, Aceti F, Barnes J, Bavle AD, Beck CT, Bindt C, Boyce PM, Bunevicius A, Chaudron LH, Favez N, Figueiredo B, Garcia-Esteve L, Giardinelli L, Helle N, Howard LM, Kohlhoff J, Kusminskas L, Kozinszky Z, Lelli L, Leonardou AA, Meuti V, Radoš SN, García PN, Pawlby SJ, Quispel C, Robertson-Blackmore E, Rochat TJ, Sharp DJ, Siu BWM, Stein A, Stewart RC, Tadinac M, Tandon SD, Tendais I, Töreki A, Torres-Giménez A, Tran TD, Trevillion K, Turner K, Vega-Dienstmaier JM, Benedetti A, Thombs BD
  International journal of methods in psychiatric research (2020) 30(1):e1860 PMC7992289 10.1002/mpr.1860
• Hybrid Coronary Revascularization Versus Conventional Coronary Artery Bypass Surgery: Utilization and Comparative Outcomes.
  Hannan EL, Wu Y, Cozzens K, Sundt TM, Girardi L, Chikwe J, Wechsler A, Smith CR, Gold JP, Lahey SJ, Jordan D
  Circulation. Cardiovascular interventions (2020) 13(10):e009386 10.1161/CIRCINTERVENTIONS.120.009386
• HPV-EM: an accurate HPV detection and genotyping EM algorithm.
  Inkman MJ, Jayachandran K, Ellis TM, Ruiz F, McLellan MD, Miller CA, Wu Y, Ojesina AI, Schwarz JK, Zhang J
  Scientific reports (2020) 10(1):14340 PMC7459114 10.3892/ol.2017.7327
• Inferring the ancestry of parents and grandparents from genetic data.
  Pei J, Zhang Y, Nielsen R, Wu Y
  PLoS computational biology (2020) 16(8):e1008065 PMC7449501 10.1371/journal.pcbi.1008065
• Inference of population admixture network from local gene genealogies: a coalescent-based maximum likelihood approach.
  Wu Y
  Bioinformatics (Oxford, England) (2020) 36(Suppl_1):i326-i334 PMC7355278 10.1093/bioinformatics/btaa465
• Rapid image deconvolution and multiview fusion for optical microscopy.
  Guo M, Li Y, Su Y, Lambert T, Nogare DD, Moyle MW, Duncan LH, Ikegami R, Santella A, Rey-Suarez I, Green D, Beiriger A, Chen J, Vishwasrao H, Ganesan S, Prince V, Waters JC, Annunziata CM, Hafner M, Mohler WA, Chitnis AB, Upadhyaya A, Usdin TB, Bao Z, Colón-Ramos D, La Riviere P, Liu H, Wu Y, Shroff H
  Nature biotechnology (2020) 38(11):1337-1346 PMC7642198 10.1038/s41587-020-0560-x
• Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability.
  McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD,
  Cell reports. Medicine (2020) 1(1): PMC7289043 10.1016/j.xcrm.2020.100004
• Tai Ji Quan as antihypertensive lifestyle therapy: A systematic review and meta-analysis.
  Wu Y, Johnson BT, Chen S, Chen Y, Livingston J, Pescatello LS
  Journal of sport and health science (2020) 10(2):211-221 PMC7987647 10.1016/j.jshs.2020.03.007
• The Clinical Utility of Neuromotor Exercise as Antihypertensive Lifestyle Therapy.
  Wu Y, Pescatello LS
  Current sports medicine reports (2020) 19(4):133-136 10.1249/JSR.0000000000000700
• InvBFM: finding genomic inversions from high-throughput sequence data based on feature mining.
  Wu Z, Wu Y, Gao J
  BMC genomics (2020) 21(Suppl 1):173 PMC7057458 10.1186/s12864-020-6585-1
• Detecting circular RNA from high-throughput sequence data with de Bruijn graph.
  Li X, Wu Y
  BMC genomics (2020) 21(Suppl 1):749 PMC7057571 10.1186/s12864-019-6154-7
• A draft genome sequence of the elusive giant squid, Architeuthis dux.
  da Fonseca RR, Couto A, Machado AM, Brejova B, Albertin CB, Silva F, Gardner P, Baril T, Hayward A, Campos A, Ribeiro ÂM, Barrio-Hernandez I, Hoving HJ, Tafur-Jimenez R, Chu C, Frazão B, Petersen B, Peñaloza F, Musacchia F, Alexander GC, Osório H, Winkelmann I, Simakov O, Rasmussen S, Rahman MZ, Pisani D, Vinther J, Jarvis E, Zhang G, Strugnell JM, Castro LFC, Fedrigo O, Patricio M, Li Q, Rocha S, Antunes A, Wu Y, Ma B, Sanges R, Vinar T, Blagoev B, Sicheritz-Ponten T, Nielsen R, Gilbert MTP
  GigaScience (2020) 9(1): PMC6962438 10.1093/gigascience/giz152
• Disruption of CXCR6 Ameliorates Kidney Inflammation and Fibrosis in Deoxycorticosterone Acetate/Salt Hypertension.
  Wu Y, An C, Jin X, Hu Z, Wang Y
  Scientific reports (2020) 10(1):133 PMC6954216 10.1038/s41598-019-56933-7

• 2019

• DeepSV: accurate calling of genomic deletions from high-throughput sequencing data using deep convolutional neural network.
  Cai L, Wu Y, Gao J
  BMC bioinformatics (2019) 20(1):665 PMC6909530 10.1186/s12859-019-3299-y
• Comparison of major depression diagnostic classification probability using the SCID, CIDI, and MINI diagnostic interviews among women in pregnancy or postpartum: An individual participant data meta-analysis.
  Levis B, McMillan D, Sun Y, He C, Rice DB, Krishnan A, Wu Y, Azar M, Sanchez TA, Chiovitti MJ, Bhandari PM, Neupane D, Saadat N, Riehm KE, Imran M, Boruff JT, Cuijpers P, Gilbody S, Ioannidis JPA, Kloda LA, Patten SB, Shrier I, Ziegelstein RC, Comeau L, Mitchell ND, Tonelli M, Vigod SN, Aceti F, Alvarado R, Alvarado-Esquivel C, Bakare MO, Barnes J, Beck CT, Bindt C, Boyce PM, Bunevicius A, Couto TCE, Chaudron LH, Correa H, de Figueiredo FP, Eapen V, Fernandes M, Figueiredo B, Fisher JRW, Garcia-Esteve L, Giardinelli L, Helle N, Howard LM, Khalifa DS, Kohlhoff J, Kusminskas L, Kozinszky Z, Lelli L, Leonardou AA, Lewis BA, Maes M, Meuti V, Nakić Radoš S, Navarro García P, Nishi D, Okitundu Luwa E-Andjafono D, Robertson-Blackmore E, Rochat TJ, Rowe HJ, Siu BWM, Skalkidou A, Stein A, Stewart RC, Su KP, Sundström-Poromaa I, Tadinac M, Tandon SD, Tendais I, Thiagayson P, Töreki A, Torres-Giménez A, Tran TD, Trevillion K, Turner K, Vega-Dienstmaier JM, Wynter K, Yonkers KA, Benedetti A, Thombs BD
  International journal of methods in psychiatric research (2019) 28(4):e1803 PMC7027670 10.1002/mpr.1803
• Accurate and efficient cell lineage tree inference from noisy single cell data: the maximum likelihood perfect phylogeny approach.
  Wu Y
  Bioinformatics (Oxford, England) (2019) 36(3):742-750 10.1093/bioinformatics/btz676
• GAPPadder: a sensitive approach for closing gaps on draft genomes with short sequence reads.
  Chu C, Li X, Wu Y
  BMC genomics (2019) 20(Suppl 5):426 PMC6551238 10.1186/s12864-019-5703-4
• Thioredoxin-1 confines T cell alloresponse and pathogenicity in graft-versus-host disease.
  Sofi MH, Wu Y, Schutt SD, Dai M, Daenthanasanmak A, Heinrichs Voss J, Nguyen H, Bastian D, Iamsawat S, Selvam SP, Liu C, Maulik N, Ogretmen B, Jin J, Mehrotra S, Yu XZ
  The Journal of clinical investigation (2019) 129(7):2760-2774 PMC6597211 10.1172/JCI122899
• Altered Immune Landscape and Disrupted Coral- Symbiosis in the Scleractinian Coral by Challenge.
  Zhou Z, Zhao S, Tang J, Liu Z, Wu Y, Wang Y, Lin S
  Frontiers in physiology (2019) 10:366 PMC6454040 10.3389/fphys.2019.00366
• Yoga as Antihypertensive Lifestyle Therapy: A Systematic Review and Meta-analysis.
  Wu Y, Johnson BT, Acabchuk RL, Chen S, Lewis HK, Livingston J, Park CL, Pescatello LS
  Mayo Clinic proceedings (2019) 94(3):432-446 10.1016/j.mayocp.2018.09.023

• 2018

• Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.
  Rogers RL, Zhou L, Chu C, Márquez R, Corl A, Linderoth T, Freeborn L, MacManes MD, Xiong Z, Zheng J, Guo C, Xun X, Kronforst MR, Summers K, Wu Y, Yang H, Richards-Zawacki CL, Zhang G, Nielsen R
  Mol. Biol. Evol. (2018) 35(12):2913-2927 (PMC6278860) 10.1093/molbev/msy185
• CircMarker: a fast and accurate algorithm for circular RNA detection.
  Li X, Chu C, Pei J, Măndoiu I, Wu Y
  BMC Genomics (2018) 19(Suppl 6):572 (PMC6101086) 10.1186/s12864-018-4926-0
• An improved approach for reconstructing consensus repeats from short sequence reads.
  Chu C, Pei J, Wu Y
  BMC Genomics (2018) 19(Suppl 6):566 (PMC6101065) 10.1186/s12864-018-4920-6
• Role of glutamine synthetase in angiogenesis beyond glutamine synthesis.
  Eelen G, Dubois C, Cantelmo AR, Goveia J, Brüning U, DeRan M, Jarugumilli G, van Rijssel J, Saladino G, Comitani F, Zecchin A, Rocha S, Chen R, Huang H, Vandekeere S, Kalucka J, Lange C, Morales-Rodriguez F, Cruys B, Treps L, Ramer L, Vinckier S, Brepoels K, Wyns S, Souffreau J, Schoonjans L, Lamers WH, Wu Y, Haustraete J, Hofkens J, Liekens S, Cubbon R, Ghesquière B, Dewerchin M, Gervasio FL, Li X, van Buul JD, Wu X, Carmeliet P
  Nature (2018) 561(7721):63-69 10.1038/s41586-018-0466-7
• The C-terminus of the oncoprotein TGAT is necessary for plasma membrane association and efficient RhoA-mediated signaling.
  van Unen J, Botman D, Yin T, Wu YI, Hink MA, Gadella TWJ, Postma M, Goedhart J
  BMC Cell Biol. (2018) 19(1):6 (PMC5992656) 10.1186/s12860-018-0155-2
• CLADES: A classification-based machine learning method for species delimitation from population genetic data.
  Pei J, Chu C, Li X, Lu B, Wu Y
  Mol Ecol Resour (2018) : 10.1111/1755-0998.12887
• Combination of multilocus sequence typing and pulsed-field gel electrophoresis reveals an association of molecular clonality with the emergence of extensive-drug resistance (XDR) in Salmonella.
  Cao Y, Shen Y, Cheng L, Zhang X, Wang C, Wang Y, Zhou X, Chao G, Wu Y
  Microbiol. Res. (2018) 207:170-176 10.1016/j.micres.2017.12.001
• Role of membrane-tension gated Ca flux in cell mechanosensation.
  He L, Tao J, Maity D, Si F, Wu Y, Wu T, Prasath V, Wirtz D, Sun SX
  J. Cell. Sci. (2018) 131(4): (PMC5868948) 10.1242/jcs.208470

• 2017

• Psychological well-being, dental esthetics, and psychosocial impacts in adolescent orthodontic patients: A prospective longitudinal study.
  Deng X, Wang YJ, Deng F, Liu PL, Wu Y
  Am J Orthod Dentofacial Orthop (2017) 153(1):87-96.e2 10.1016/j.ajodo.2017.05.028
• Optogenetic activation of EphB2 receptor in dendrites induced actin polymerization by activating Arg kinase.
  Locke C, Machida K, Wu Y, Yu J
  Biol Open (2017) 6(12):1820-1830 (PMC5769660) 10.1242/bio.029900
• Synthesis of Mesoporous CoS and NiCoS with Superior Supercapacitive Performance Using a Facile Solid-Phase Sulfurization.
  Jin L, Liu B, Wu Y, Thanneeru S, He J
  ACS Appl Mater Interfaces (2017) 9(42):36837-36848 10.1021/acsami.7b11453
• Neurodevelopmental disease-associated de novo mutations and rare sequence variants affect TRIO GDP/GTP exchange factor activity.
  Katrancha SM, Wu Y, Zhu M, Eipper BA, Koleske AJ, Mains RE
  Hum. Mol. Genet. (2017) 26(23):4728-4740 (PMC5886096) 10.1093/hmg/ddx355
• Formation of Holmium Oxide in Pores of Mesoporous Carbon Nanoparticles as Substrates for Neutron-Activatable Radiotherapeutics.
  Kim J, Luo ZX, Wu Y, Lu X, Jay M
  Carbon N Y (2017) 117:92-99 (PMC5619678) 10.1016/j.carbon.2017.02.085
• The balance between Gα-Cdc42/Rac and Gα/-RhoA pathways determines endothelial barrier regulation by sphingosine-1-phosphate.
  Reinhard NR, Mastop M, Yin T, Wu Y, Bosma EK, Gadella TWJ, Goedhart J, Hordijk PL
  Mol. Biol. Cell (2017) 28(23):3371-3382 (PMC5687037) 10.1091/mbc.E17-03-0136
• A Type 2 Diabetes-Associated Functional Regulatory Variant in a Pancreatic Islet Enhancer at the Locus.
  Roman TS, Cannon ME, Vadlamudi S, Buchkovich ML, Wolford BN, Welch RP, Morken MA, Kwon GJ, Varshney A, Kursawe R, Wu Y, Jackson AU, Erdos MR, Kuusisto J, Laakso M, Scott LJ, Boehnke M, Collins FS, Parker SCJ, Stitzel ML, Mohlke KL
  Diabetes (2017) 66(9):2521-2530 (PMC5860374) 10.2337/db17-0464
• Optogenetic activation of Plexin-B1 reveals contact repulsion between osteoclasts and osteoblasts.
  Deb Roy A, Yin T, Choudhary S, Rodionov V, Pilbeam CC, Wu YI
  Nat Commun (2017) 8:15831 (PMC5482063) 10.1038/ncomms15831
• Phosphorylated cortactin recruits Vav2 guanine nucleotide exchange factor to activate Rac3 and promote invadopodial function in invasive breast cancer cells.
  Rosenberg BJ, Gil-Henn H, Mader CC, Halo T, Yin T, Condeelis J, Machida K, Wu YI, Koleske AJ
  Mol. Biol. Cell (2017) 28(10):1347-1360 (PMC5426849) 10.1091/mbc.E16-12-0885
• STELLS2: fast and accurate coalescent-based maximum likelihood inference of species trees from gene tree topologies.
  Pei J, Wu Y
  Bioinformatics (2017) 33(12):1789-1797 10.1093/bioinformatics/btx079
• Symbiont-induced odorant binding proteins mediate insect host hematopoiesis.
  Benoit JB, Vigneron A, Broderick NA, Wu Y, Sun JS, Carlson JR, Aksoy S, Weiss BL
  Elife (2017) 6: (PMC5231409) 10.7554/eLife.19535

• 2016

• Kinetics of recruitment and allosteric activation of ARHGEF25 isoforms by the heterotrimeric G-protein Gαq.
  van Unen J, Yin T, Wu YI, Mastop M, Gadella TW, Goedhart J
  Sci Rep (2016) 6:36825 (PMC5105084) 10.1038/srep36825
• Evaluating Exercise Prescription and Instructional Methods Used in Tai Chi Studies Aimed at Improving Balance in Older Adults: A Systematic Review.
  Wu Y, MacDonald HV, Pescatello LS
  J Am Geriatr Soc (2016) 64(10):2074-2080 10.1111/jgs.14242
• -NOD Mice Having a Lyn Tyrosine Kinase Mutation Exhibit Abnormal Neutrophil Chemotaxis.
  Wu Y, Hannigan M, Zhan L, Madri JA, Huang CK
  J. Cell. Physiol. (2016) 232(7):1689-1695 10.1002/jcp.25583
• Coming of Age: Considerations in the Prescription of Exercise for Older Adults.
  Zaleski AL, Taylor BA, Panza GA, Wu Y, Pescatello LS, Thompson PD, Fernandez AB
  Methodist Debakey Cardiovasc J (2016) 12(2):98-104 (PMC4969034) 10.14797/mdcj-12-2-98
• Alternate promoter usage generates two subpopulations of the neuronal RhoGEF Kalirin-7.
  Miller MB, Yan Y, Wu Y, Hao B, Mains RE, Eipper BA
  J. Neurochem. (2016) 140(6):889-902 (PMC5274606) 10.1111/jnc.13749
• An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree.
  Wu Y
  Bioinformatics (2016) 32(12):i225-i233 (PMC4908345) 10.1093/bioinformatics/btw261
• Spatiotemporal analysis of RhoA/B/C activation in primary human endothelial cells.
  Reinhard NR, van Helden SF, Anthony EC, Yin T, Wu YI, Goedhart J, Gadella TW, Hordijk PL
  Sci Rep (2016) 6:25502 (PMC4857094) 10.1038/srep25502
• REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads.
  Chu C, Nielsen R, Wu Y
  PLoS ONE (2016) 11(3):e0150719 (PMC4792456) 10.1371/journal.pone.0150719
• F-actin-rich contractile endothelial pores prevent vascular leakage during leukocyte diapedesis through local RhoA signalling.
  Heemskerk N, Schimmel L, Oort C, van Rijssel J, Yin T, Ma B, van Unen J, Pitter B, Huveneers S, Goedhart J, Wu Y, Montanez E, Woodfin A, van Buul JD
  Nat Commun (2016) 7:10493 (PMC4737874) 10.1038/ncomms10493
• Rapid Remodeling of Invadosomes by Gi-coupled Receptors: DISSECTING THE ROLE OF Rho GTPases.
  Kedziora KM, Leyton-Puig D, Argenzio E, Boumeester AJ, van Butselaar B, Yin T, Wu YI, van Leeuwen FN, Innocenti M, Jalink K, Moolenaar WH
  J. Biol. Chem. (2016) 291(9):4323-33 (PMC4813461) 10.1074/jbc.M115.695940

• 2015

• Untwisting the Caenorhabditis elegans embryo.
  Christensen RP, Bokinsky A, Santella A, Wu Y, Marquina-Solis J, Guo M, Kovacevic I, Kumar A, Winter PW, Tashakkori N, McCreedy E, Liu H, McAuliffe M, Mohler W, Colón-Ramos DA, Bao Z, Shroff H
  Elife (2015) 4: (PMC4764590) 10.7554/eLife.10070
• Integration of linear and dendritic actin nucleation in Nck-induced actin comets.
  Borinskaya S, Velle KB, Campellone KG, Talman A, Alvarez D, Agaisse H, Wu YI, Loew LM, Mayer BJ
  Mol. Biol. Cell (2015) 27(2):247-59 (PMC4713129) 10.1091/mbc.E14-11-1555
• Plasma membrane restricted RhoGEF activity is sufficient for RhoA-mediated actin polymerization.
  van Unen J, Reinhard NR, Yin T, Wu YI, Postma M, Gadella TW, Goedhart J
  Sci Rep (2015) 5:14693 (PMC4592971) 10.1038/srep14693
• Labelling and optical erasure of synaptic memory traces in the motor cortex.
  Hayashi-Takagi A, Yagishita S, Nakamura M, Shirai F, Wu YI, Loshbaugh AL, Kuhlman B, Hahn KM, Kasai H
  Nature (2015) 525(7569):333-8 (PMC4634641) 10.1038/nature15257
• A local VE-cadherin and Trio-based signaling complex stabilizes endothelial junctions through Rac1.
  Timmerman I, Heemskerk N, Kroon J, Schaefer A, van Rijssel J, Hoogenboezem M, van Unen J, Goedhart J, Gadella TW, Yin T, Wu Y, Huveneers S, van Buul JD
  J. Cell. Sci. (2015) 128(16):3041-54 10.1242/jcs.168674
• WormGUIDES: an interactive single cell developmental atlas and tool for collaborative multidimensional data exploration.
  Santella A, Catena R, Kovacevic I, Shah P, Yu Z, Marquina-Solis J, Kumar A, Wu Y, Schaff J, Colón-Ramos D, Shroff H, Mohler WA, Bao Z
  BMC Bioinformatics (2015) 16:189 (PMC4459063) 10.1186/s12859-015-0627-8
• Self-sustained reduction of multiple metals in a microbial fuel cell-microbial electrolysis cell hybrid system.
  Li Y, Wu Y, Liu B, Luan H, Vadas T, Guo W, Ding J, Li B
  Bioresour. Technol. (2015) 192:238-46 10.1016/j.biortech.2015.05.030
• Interplay between chemotaxis and contact inhibition of locomotion determines exploratory cell migration.
  Lin B, Yin T, Wu YI, Inoue T, Levchenko A
  Nat Commun (2015) 6:6619 (PMC4391292) 10.1038/ncomms7619
• Integrative analysis of 111 reference human epigenomes.
  Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning A, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Abdennur N, Adli M, Akerman M, Barrera L, Antosiewicz-Bourget J, Ballinger T, Barnes MJ, Bates D, Bell RJ, Bennett DA, Bianco K, Bock C, Boyle P, Brinchmann J, Caballero-Campo P, Camahort R, Carrasco-Alfonso MJ, Charnecki T, Chen H, Chen Z, Cheng JB, Cho S, Chu A, Chung WY, Cowan C, Athena Deng Q, Deshpande V, Diegel M, Ding B, Durham T, Echipare L, Edsall L, Flowers D, Genbacev-Krtolica O, Gifford C, Gillespie S, Giste E, Glass IA, Gnirke A, Gormley M, Gu H, Gu J, Hafler DA, Hangauer MJ, Hariharan M, Hatan M, Haugen E, He Y, Heimfeld S, Herlofsen S, Hou Z, Humbert R, Issner R, Jackson AR, Jia H, Jiang P, Johnson AK, Kadlecek T, Kamoh B, Kapidzic M, Kent J, Kim A, Kleinewietfeld M, Klugman S, Krishnan J, Kuan S, Kutyavin T, Lee AY, Lee K, Li J, Li N, Li Y, Ligon KL, Lin S, Lin Y, Liu J, Liu Y, Luckey CJ, Ma YP, Maire C, Marson A, Mattick JS, Mayo M, McMaster M, Metsky H, Mikkelsen T, Miller D, Miri M, Mukamel E, Nagarajan RP, Neri F, Nery J, Nguyen T, O'Geen H, Paithankar S, Papayannopoulou T, Pelizzola M, Plettner P, Propson NE, Raghuraman S, Raney BJ, Raubitschek A, Reynolds AP, Richards H, Riehle K, Rinaudo P, Robinson JF, Rockweiler NB, Rosen E, Rynes E, Schein J, Sears R, Sejnowski T, Shafer A, Shen L, Shoemaker R, Sigaroudinia M, Slukvin I, Stehling-Sun S, Stewart R, Subramanian SL, Suknuntha K, Swanson S, Tian S, Tilden H, Tsai L, Urich M, Vaughn I, Vierstra J, Vong S, Wagner U, Wang H, Wang T, Wang Y, Weiss A, Whitton H, Wildberg A, Witt H, Won KJ, Xie M, Xing X, Xu I, Xuan Z, Ye Z, Yen CA, Yu P, Zhang X, Zhang X, Zhao J, Zhou Y, Zhu J, Zhu Y, Ziegler S, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M
  Nature (2015) 518(7539):317-30 (PMC4530010) 10.1038/nature14248
• Single-molecule tracking of small GTPase Rac1 uncovers spatial regulation of membrane translocation and mechanism for polarized signaling.
  Das S, Yin T, Yang Q, Zhang J, Wu YI, Yu J
  Proc. Natl. Acad. Sci. U.S.A. (2015) 112(3):E267-76 (PMC4311845) 10.1073/pnas.1409667112

• 2014

• Improved gene tree error correction in the presence of horizontal gene transfer.
  Bansal MS, Wu YC, Alm EJ, Kellis M
  Bioinformatics (2014) 31(8):1211-8 (PMC4393519) 10.1093/bioinformatics/btu806
• GINDEL: accurate genotype calling of insertions and deletions from low coverage population sequence reads.
  Chu C, Zhang J, Wu Y
  PLoS ONE (2014) 9(11):e113324 (PMC4244156) 10.1371/journal.pone.0113324
• Optogenetics: optical control of a photoactivatable Rac in living cells.
  Yin T, Wu YI
  Methods Mol. Biol. (2014) 1251:277-89 10.1007/978-1-4939-2080-8_15
• A coalescent-based method for population tree inference with haplotypes.
  Wu Y
  Bioinformatics (2014) 31(5):691-8 (PMC4341064) 10.1093/bioinformatics/btu710
• Phosphorylation of Dok1 by Abl family kinases inhibits CrkI transforming activity.
  Ng KY, Yin T, Machida K, Wu YI, Mayer BJ
  Oncogene (2014) 34(20):2650-9 (PMC4302068) 10.1038/onc.2014.210
• Comparative validation of the D. melanogaster modENCODE transcriptome annotation.
  Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S
  Genome Res. (2014) 24(7):1209-23 (PMC4079975) 10.1101/gr.159384.113
• Pareto-optimal phylogenetic tree reconciliation.
  Libeskind-Hadas R, Wu YC, Bansal MS, Kellis M
  Bioinformatics (2014) 30(12):i87-95 (PMC4058917) 10.1093/bioinformatics/btu289

• 2013

• An algorithm for constructing parsimonious hybridization networks with multiple phylogenetic trees.
  Wu Y
  J. Comput. Biol. (2013) 20(10):792-804 (PMC3791036) 10.1089/cmb.2013.0072
• Unambiguous identification of the second 2+ state in 12C and the structure of the Hoyle state.
  Zimmerman WR, Ahmed MW, Bromberger B, Stave SC, Breskin A, Dangendorf V, Delbar T, Gai M, Henshaw SS, Mueller JM, Sun C, Tittelmeier K, Weller HR, Wu YK
  Phys. Rev. Lett. (2013) 110(15):152502 10.1103/PhysRevLett.110.152502
• Guiding lights: recent developments in optogenetic control of biochemical signals.
  Yin T, Wu YI
  Pflugers Arch. (2013) 465(3):397-408 10.1007/s00424-013-1244-x

• 2012

• An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.
  Zhang J, Wang J, Wu Y
  BMC Bioinformatics (2012) 13 Suppl 6:S6 (PMC3358659) 10.1186/1471-2105-13-S6-S6
• Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.
  Wu Y
  Evolution (2012) 66(3):763-775 10.1111/j.1558-5646.2011.01476.x

• 2011

• SVseq: an approach for detecting exact breakpoints of deletions with low-coverage sequence data.
  Zhang J, Wu Y
  Bioinformatics (2011) 27(23):3228-34 10.1093/bioinformatics/btr563
• Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads.
  Duitama J, Kennedy J, Dinakar S, Hernández Y, Wu Y, Măndoiu II
  BMC Bioinformatics (2011) 12 Suppl 1:S53 (PMC3044311) 10.1186/1471-2105-12-S1-S53

• 2010

• Haplotype inference from short sequence reads using a population genealogical history model.
  Zhang J, Wu Y
  Pac Symp Biocomput (2010) :288-99
• New methods for inference of local tree topologies with recombinant SNP sequences in populations.
  Wu Y
  IEEE/ACM Trans Comput Biol Bioinform (2010) 8(1):182-93 10.1109/TCBB.2009.27
• Exact computation of coalescent likelihood for panmictic and subdivided populations under the infinite sites model.
  Wu Y
  IEEE/ACM Trans Comput Biol Bioinform (2010) 7(4):611-8 10.1109/TCBB.2010.2
• Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees.
  Wu Y
  Bioinformatics (2010) 26(12):i140-8 (PMC2881383) 10.1093/bioinformatics/btq198

• 2008

• A practical method for exact computation of subtree prune and regraft distance.
  Wu Y
  Bioinformatics (2008) 25(2):190-6 10.1093/bioinformatics/btn606
• Association mapping of complex diseases with ancestral recombination graphs: models and efficient algorithms.
  Wu Y
  J. Comput. Biol. (2008) 15(7):667-84 10.1089/cmb.2007.0116

• 2007

• MAPKAPK2-mediated LSP1 phosphorylation and FMLP-induced neutrophil polarization.
  Wu Y, Zhan L, Ai Y, Hannigan M, Gaestel M, Huang CK, Madri JA
  Biochem. Biophys. Res. Commun. (2007) 358(1):170-5 10.1016/j.bbrc.2007.04.104
• 'GM-gene-deletor': fused loxP-FRT recognition sequences dramatically improve the efficiency of FLP or CRE recombinase on transgene excision from pollen and seed of tobacco plants.
  Luo K, Duan H, Zhao D, Zheng X, Deng W, Chen Y, Stewart CN, McAvoy R, Jiang X, Wu Y, He A, Pei Y, Li Y
  Plant Biotechnol. J. (2007) 5(2):263-274 10.1111/j.1467-7652.2006.00237.x

• 2005

• Expression profile of osteoblast lineage at defined stages of differentiation.
  Kalajzic I, Staal A, Yang WP, Wu Y, Johnson SE, Feyen JH, Krueger W, Maye P, Yu F, Zhao Y, Kuo L, Gupta RR, Achenie LE, Wang HW, Shin DG, Rowe DW
  J. Biol. Chem. (2005) 280(26):24618-26 10.1074/jbc.M413834200

• 2004

• A requirement of MAPKAPK2 in the uropod localization of PTEN during FMLP-induced neutrophil chemotaxis.
  Wu Y, Hannigan MO, Kotlyarov A, Gaestel M, Wu D, Huang CK
  Biochem. Biophys. Res. Commun. (2004) 316(3):666-72 10.1016/j.bbrc.2004.02.107

• 2003

• Directional sensing requires G beta gamma-mediated PAK1 and PIX alpha-dependent activation of Cdc42.
  Li Z, Hannigan M, Mo Z, Liu B, Lu W, Wu Y, Smrcka AV, Wu G, Li L, Liu M, Huang CK, Wu D
  Cell (2003) 114(2):215-27

• 2001

• Transgenics in crops.
  Li Y, Wu YH, McAvoy R, Duan H, Li Y
  Biotechnol Annu Rev (2001) 7:239-60

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