Superfund Research Program

Nature Communications (impact factor: 14.919)

2024

• Amara C, Kami Reddy K, Yuntao Y, Chan Y, Piyarathna DW, Dobrolecki L, Shih D, Shi Z, Xu J, Huang S, Ellis M, Apolo A, Ballester L, Gao J, Hansel D, Lotan Y, Hodges H, Lerner S, Creighton C, Sreekumar A, Zheng W, Msaouel P, Kavuri S, Putluri N. 2024. The IL6/JAK/STAT3 signaling axis is a therapeutic vulnerability in SMARCB1-deficient bladder cancer. Nat Commun 15(1):1373. doi:10.1038/s41467-024-45132-2 PMID:38355560 PMCID:10867091

2023

• Antal CE, Oh TG, Aigner S, Luo E, Yee BA, Campos T, Tiriac H, Rothamel KL, Cheng Z, Jiao H, Wang A, Hah N, Lenkiewicz E, Lumibao JC, Truitt ML, Estepa G, Banayo E, Bashi S, Esparza E, Munoz RM, Diedrich JK, Sodir NM, Mueller JR, Fraser CR, Borazanci E, Propper D, Von Hoff DD, Liddle C, Yu RT, Atkins AR, Han H, Lowy AM, Barrett MT, Engle DD, Evan GI, Yeo GW, Downes M, Evans RM. 2023. A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer. Nat Commun 14(1):5195. doi:10.1038/s41467-023-40798-6 PMID:37673892 PMCID:PMC10482938
• Bilbao A, Munoz N, Kim J, Orton DJ, Gao Y, Poorey K, Pomraning KR, Weitz KK, Burnet MC, Nicora CD, Wilton R, Deng S, Dai Z, Oksen E, Gee A, Fasani RA, Tsalenko A, Tanjore D, Gardner J, Smith RD, Michener JK, Gladden JM, Baker ES, Petzold CJ, Kim Y, Apffel A, Magnuson JK, Burnum-Johnson KE. 2023. PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements. Nat Commun 14(1):doi:10.1038/s41467-023-37031-9

2022

• Bilbao A, Munoz N, Kim J, Orton DJ, Gao Y, Poorey K, Pomraning KR, Weitz KK, Burnet MC, Nicora CD, Wilton R, Deng S, Dai Z, Oksen E, Gee A, Fasani RA, Tsalenko A, Tanjore D, Gardner J, Smith RD, Michener JK, Gladden JM, Baker ES, Petzold CJ, Kim Y, Apffel A, Magnuson JK, Burnum-Johnson KE. 2022. PeakDecoder: A machine learning-based identification algorithm for multidimensional mass spectrometry measurements and its application for synthetic biology. Nat Commun
• King E, Maxel S, Zhang Y, Kenney KC, Cui Y, Luu E, Siegel JB, Weiss GA, Luo R, Li H. 2022. Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. Nat Commun 13(1):7282. doi:10.1038/s41467-022-35021-x PMID:36435948 PMCID:PMC9701214
• Li J, Li X, Da Y, Yu J, Long B, Zhang P, Bakker C, McCarl BA, Yuan JS, Dai S. 2022. Sustainable environmental remediation via biomimetic multifunctional lignocellulosic nano-framework. Nat Commun 13(1):4368. doi:10.1038/s41467-022-31881-5 PMID:35902555 PMCID:PMC9334262
• Maglioni S, Schiavi A, Melcher M, Brinkmann V, Luo Z, Laromaine A, Raimundo N, Meyer JN, Distelmaier F, Ventura N. 2022. Neuroligin-mediated neurodevelopmental defects are induced by mitochondrial dysfunction and prevented by lutein in C. elegans. Nat Commun doi:10.1038/s41467-022-29972-4 PMID:35551180 PMCID:PMC9098500
• Martinez-Morata I, Bostick BC, Conroy-Ben O, Duncan DT, Jones MR, Spaur M, Patterson KP, Prins SJ, Navas-Acien A, Nigra AE. 2022. Nationwide geospatial analysis of county racial and ethnic composition and public drinking water arsenic and uranium. Nat Commun 13(1):7461. doi:10.1038/s41467-022-35185-6 PMID:36460659 PMCID:PMC9718774
• Napoli M, Wu SJ, Gore BL, Abbas H, Lee K, Checker R, Dhar S, Rajapakshe K, Tan AC, Lee MG, Coarfa C, Flores ER. 2022. Np63 regulates a common landscape of enhancer associated genes in non-small cell lung cancer. Nat Commun 13:doi:10.1038/s41467-022-28202-1 PMID:35105868 PMCID:PMC8807845
• Weber AA, Yang X, Mennillo E, Ding J, Watrous JD, Jain M, Chen S, Karin M, Tukey RH. 2022. Lactational delivery of Triclosan promotes non-alcoholic fatty liver disease in newborn mice. Nat Commun 13(1):4346. doi:10.1038/s41467-022-31947-4 PMID:35896521 PMCID:PMC9329322
• Youn J, Rai N, Tagkopoulos I. 2022. Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. Nat Commun doi:10.1038/s41467-022-29993-z PMID:35487919 PMCID:PMC9055065
• Zhang L, King E, Black WB, Heckmann CM, Wolder A, Cui Y, Nicklen F, Siegel JB, Luo R, Paul CE, Li H. 2022. Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. Nat Commun 13(1):5021. doi:10.1038/s41467-022-32727-w PMID:36028482 PMCID:PMC9418148

2021

• Lai Y, Liu C, Yang Y, Hsiao Y, Ru H, Lu K. 2021. High-coverage metabolomics uncovers microbiota-driven biochemical landscape of interorgan transport and gut-brain communication in mice. Nat Commun 12(1):6000. doi:10.1038/s41467-021-26209-8 PMID:34667167 PMCID:PMC8526691
• Leman JK, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow KA, Ben-Aharon Z, Farrell D, Fell JS, Hansen WA, Harmalkar A, Jeliazkov JR, Kuenze G, Krys JD, Ljubetic A, Loshbaugh AL, Maguire J, Moretti R, Mulligan VK, Nance ML, Nguyen PT, O'Conchuir S, Roy Burman SS, Samanta R, Smith S, Teets FD, Tiemann JK, Watkins A, Woods H, Yachnin BJ, Bahl CD, Bailey-Kellogg C, Baker D, Das R, DiMaio F, Khare SD, Kortemme T, Labonte JW, Lindorff-Larsen K, Meiler J, Schief W, Schueler-Furman O, Siegel JB, Stein A, Yarov-Yarovoy V, Kuhlman B, Leaver-Fay A, Gront D, Gray JJ, Bonneau R. 2021. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nat Commun 12:doi:10.1038/s41467-021-27222-7 PMID:34845212 PMCID:PMC8630030
• Liu M, Weston P, Hurt RH. 2021. Controlling nanochannel orientation and dimensions in graphene-based nanofluidic membranes. Nat Commun 12:507. doi:10.1038/s41467-020-20837-2 PMID:33479231 PMCID:PMC7820404
• Mao H, Li L, Fan Q, Angelini A, Saha PK, Coarfa C, Rajapakshe K, Perera D, Cheng J, Wu H, Ballantyne CM, Sun Z, Pi X, Xie L. 2021. Endothelium-specific depletion of LRP1 improves glucose homeostasis through inducing osteocalcin. Nat Commun 12:doi:10.1038/s41467-021-25673-6 PMID:34489478 PMCID:PMC8421392
• Parks RM, Anderson GB, Nethery RC, Navas-Acien A, Dominici F, Kioumourtzoglou M. 2021. Tropical cyclone exposure is associated with increased hospitalization rates in older adults. Nat Commun 12:1545. doi:10.1038/s41467-021-21777-1 PMID:33750775 PMCID:PMC7943804
• van der Lelie D, Oka A, Taghavi S, Umeno J, Fan T, Merrell KE, Watson SD, Ouellette L, Liu B, Awoniyi M, Lai Y, Chi L, Lu K, Henry CS, Sartor RB. 2021. Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis. Nat Commun 12:3105. doi:10.1038/s41467-021-23460-x PMID:34050144
• Xu L, Dong Z, Chiniquy D, Pierroz G, Deng S, Gao C, Diamond S, Simmons T, Wipf HM, Caddell DF, Varoquaux N, Madera MA, Hutmacher R, Deutschbauer A, Dahlberg JA, Guerinot ML, Purdom E, Banfield JF, Taylor JW, Lemaux PG, Coleman-Derr D. 2021. Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nat Commun 12:3209. doi:10.1038/s41467-021-23553-7 PMID:34050180

2020

• Aung MT, Song Y, Ferguson KK, Cantonwine DE, Zeng L, McElrath TF, Pennathur S, Meeker JD, Mukherjee B. 2020. Application of an analytical framework for multivariate mediation analysis of environmental data. Nat Commun 11:5624. doi:10.1038/s41467-020-19335-2 PMID:33159049 PMCID:PMC7648785
• Guo Y, Ye Q, Deng P, Cao Y, He D, Zhou Z, Wang C, Zahtseva YY, Schwartz CE, Lee EY, Evers BM, Morris AJ, Liu S, She Q. 2020. Spermine synthase and MYC cooperate to maintain colorectal cancer cell survival by repressing Bim expression. Nat Commun 11:doi:10.1038/s41467-020-17067-x PMID:32591507 PMCID:PMC7320137
• Mihajlov I, Mozumder R, Bostick BC, Stute M, Mailloux BJ, Knappett PS, Choudhury I, Ahmed KM, Schlosser P, van Geen AF. 2020. Arsenic contamination of Bangladesh aquifers exacerbated by clay layers. Nat Commun 11:2244. doi:10.1038/s41467-020-16104-z PMID:32382006
• Park S, Doherty EE, Xie Y, Padyana AK, Fang F, Zhang Y, Karki A, Lebrilla CB, Siegel JB, Beal PA. 2020. High-throughput mutagenesis reveals unique structural features of human ADAR1. Nat Commun 11:5130. doi:10.1038/s41467-020-18862-2 PMID:33046702 PMCID:PMC7550611
• Takahashi Y, Zhang J, Hsu P, Ceciliato PH, Dubeaux G, Munemasa S, Ge C, Zhao Y, Hauser F, Schroeder JI. 2020. MAP3Kinase-dependent SnRK2-kinase activation is required for abscisic acid signal transduction and rapid osmotic stress response. Nat Commun 11(1):12. doi:10.1038/s41467-019-13875-y PMID:31896774 PMCID:PMC6940395

2019

• Cai D, Wang J, Gao B, Li J, Wu F, Zou JX, Xu J, Jiang Y, Zou H, Huang Z, Borowsky AD, Bold RJ, Lara PN, Li JJ, Chen X, Lam KS, To K, Kung H, Fiehn O, Zhao R, Evans RM, Chen H. 2019. RORgamma is a targetable master regulator of cholesterol biosynthesis in a cancer subtype. Nat Commun 10(1):4621. doi:10.1038/s41467-019-12529-3 PMID:31604910 PMCID:PMC6789042
• Caussy C, Tripathi A, Humphrey G, Bassirian S, Singh S, Faulkner C, Bettencourt R, Rizo E, Richards L, Xu Z, Downes M, Evans RM, Brenner DA, Sirlin CB, Knight R, Loomba R. 2019. A gut microbiome signature for cirrhosis due to nonalcoholic fatty liver disease. Nat Commun 10:1406. doi:10.1038/s41467-019-09455-9 PMID:30926798 PMCID:PMC6440960

2018

• Myers K, Tice MM, Bostick BC. 2018. Geochemical signatures reveal that arsenic(III)-photosynthesis fueled microorganisms in 3.26-billion-year-old shallow oceans. Nat Commun (in press)
• Pierce BL, Tong L, Argos M, Demanelis K, Jasmine F, Rakibuz-Zaman M, Sarwar G, Islam M, Shahriar H, Islam T, Rahman M, Yunus M, Kibriya MG, Chen LS, Ahsan H. 2018. Co-occurring expression and methylation QTLs allow detection of common causal variants and shared biological mechanisms. Nat Commun 9:doi:10.1038/s41467-018-03209-9 PMID:29476079 PMCID:PMC5824840
• Wiemels JL, Walsh KM, de Smith AJ, Metayer C, Gonseth S, Hansen HM, Francis SS, Ojha J, Smirnov I, Barcellos L, Xiao X, Morimoto L, McKean-Cowdin R, Wang R, Yu H, Hoh J, DeWan AT, Ma X. 2018. GWAS in childhood acute lymphoblastic leukemia reveals novel genetic associations at chromosomes 17q12 and 8q24.21. Nat Commun 9:8. doi:10.1038/s41467-017-02596-9 PMID:29348612 PMCID:PMC5773513
• Zhang Y, Nasser V, Pisanty O, Omary M, Wulff N, Donato MD, Tal I, Hauser F, Hao P, Roth O, Fromm H, Schroeder JI, Geisler M, Nour-Eldin HH, Shani E. 2018. A transportome-scale amiRNA-based screen identifies redundant roles of Arabidopsis ABCB6 and ABCB20 in auxin transport. Nat Commun 9:4204. doi:10.1038/s41467-018-06410-y PMID:30310073 PMCID:PMC6182007

2017

• Ferdowsi B, Ortiz C, Houssais M, Jerolmack DJ. 2017. River-bed armouring as a granular segregation phenomenon. Nat Commun 8(1):1363. doi:10.1038/s41467-017-01681-3 PMID:29118422 PMCID:PMC5678076
• Wang J, He N, Zhang N, Quan D, Zhang S, Zhang C, Yu RT, Atkins AR, Zhu R, Yang C, Cui Y, Liddle C, Downes M, Xiao H, Zheng Y, Auwerx J, Evans RM, Leng Q. 2017. NCoR1 restrains thymic negative selection by repressing Bim expression to spare thymocytes undergoing positive selection. Nat Commun 8(1):959. doi:10.1038/s41467-017-00931-8 PMID:29038463 PMCID:PMC5643384

2016

• Keune W, Hausmann J, Bolier R, Tolenaars D, Kremer A, Heidebrecht T, Joosten RP, Sunkara M, Morris AJ, Matas-Rico E, Moolenaar WH, Oude Elferink R, Perrakis A. 2016. Steroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling. Nat Commun 7:11248. doi:10.1038/ncomms11248 PMID:27075612 PMCID:PMC4834639
• Khan MR, Knappett PS, Ahmed KM, Bostick BC, Mailloux BJ, Mozumder R, Harvey CF, van Geen AF, Michael HA. 2016. Megacity pumping and preferential flow threaten groundwater quality. Nat Commun 7:12833. doi:10.1038/ncomms12833 PMID:27673729 PMCID:PMC5052627

2015

• Vijai J, Wang Z, Berndt SI, Skibola CF, Slager SL, de Sanjose S, Melbye M, Glimelius B, Bracci PM, Birmann BM, Wang SS, Brooks-Wilson AR, Lan Q, de Bakker PI, Vermeulen R, Portlock CJ, Ansell SA, Link BK, Riby J, North KE, Gu J, Hjalgrim H, Cozen W, Becker N, Teras LR, Spinelli JJ, Turner J, Zhang Y, Purdue MP, Giles GG, Kelly RS, Zeleniuch-Jacquotte A, Ennas M, Monnereau A, Bertrand KA, Albanes D, Lightfoot TJ, Chung CC, Burdett L, Hutchinson A, Lawrence C, Montalvan R, Liang L, Huang J, Ma B, Villano DJ, Maria A, Corines M, Thomas T, Novak AJ, Dogan A, Liebow M, Thompson CA, Witzig TE, Habermann TM, Weiner GJ, Smith MT, Holly EA, Jackson RD, Tinker LF, Ye Y, Adami H, Smedby KE, De Roos AJ, Hartge P, Morton LM, Severson RK, Benavente Y, Boffetta P, Brennan P, Foretova L, Maynadie M, McKay J, Staines A, Diver WR, Vajdic CM, Armstrong BK, Kricker A, Zheng T, Holford TR, Severi G, Vineis P, Ferri GM, Ricco R, Clavel J, Giovannucci E, Kraft P, Virtamo J, Smith A, Kane E, Roman E, Chiu BC, Fraumeni JF, Wu X. 2015. A genome-wide association study of marginal zone lymphoma shows association to the HLA region. Nat Commun 6:5751. doi:10.1038/ncomms6751 PMID:25569183 PMCID:PMC4287989

2014

• Lopez-Sanchez I, Dunkel Y, Roh Y, Mittal Y, De Minicis S, Muranyi A, Singh S, Shanmugam K, Aroonsakool N, Murray F, Ho SB, Seki E, Brenner DA, Ghosh P. 2014. GIV/Girdin is a central hub for profibrogenic signalling networks during liver fibrosis. Nat Commun 5:4451. doi:10.1038/ncomms5451 PMID:25043713 PMCID:PMC4107319