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Poulsen BE, Warrier T, Barkho S, Bagnall J, Romano KP, White T, Yu X, Kawate T, Nguyen PH, Raines K, Ferrara K, Golas AL, FitzGerald M, Boeszoermenyi A, Kaushik V, Serrano-Wu M, Shoresh N, Hung DT

Discovery of a Pseudomonas aeruginosa-specific small molecule targeting outer membrane protein OprH-LPS interaction by a multiplexed screen.
Cell Chem Biol. 2024;32(2):307-324.e15 - PMID: 39732052 - PMCID: PMC12117999 - DOI: 10.1016/j.chembiol.2024.12.001

Lin Z, Guo Y, Zhang R, Li Y, Wu Y, Sheen J, Liu KH

ABA-activated low-nanomolar Ca2+-CPK signalling controls root cap cycle plasticity and stress adaptation.
Nat Plants. 2024;11(1):90-104 - PMID: 39578615 - PMCID: PMC11757075 - DOI: 10.1038/s41477-024-01865-y

Mayassi T, Li C, Segerstolpe Åsa, Brown EM, Weisberg R, Nakata T, Yano H, Herbst P, Artis D, Graham DB, Xavier RJ

Spatially restricted immune and microbiota-driven adaptation of the gut.
Nature. 2024;636(8042):447-456 - PMID: 39567686 - PMCID: PMC11816900 - DOI: 10.1038/s41586-024-08216-z

Ogasawara D, Konrad DB, Tan ZY, Carey KL, Luo J, Won SJ, Li H, Carter TR, DeMeester KE, Njomen E, Schreiber SL, Xavier RJ, Melillo B, Cravatt BF

Chemical tools to expand the ligandable proteome: Diversity-oriented synthesis-based photoreactive stereoprobes.
Cell Chem Biol. 2024;31(12):2138-2155.e32 - PMID: 39547236 - PMCID: PMC11837778 - DOI: 10.1016/j.chembiol.2024.10.005

Romano KP, Bagnall J, Warrier T, Sullivan J, Ferrara K, Orzechowski M, Nguyen PH, Raines K, Livny J, Shoresh N, Hung DT

Perturbation-specific transcriptional mapping for unbiased target elucidation of antibiotics.
Proc Natl Acad Sci U S A. 2024;121(45):e2409747121 - PMID: 39467118 - PMCID: PMC11551328 - DOI: 10.1073/pnas.2409747121

Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta DR, Hasegawa N, Ohya T, Bhattarai SK, Sasajima S, Aoto Y, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridoshi Y, Sugita K, Stražar M, Avila-Pacheco J, Pierce K, Clish CB, Skelly AN, Hattori M, Nakamoto N, Caballero S, Norman JM, Olle B, Tanoue T, Suda W, Arita M, Bucci V, Atarashi K, Xavier RJ, Honda K

Commensal consortia decolonize Enterobacteriaceae via ecological control.
Nature. 2024;633(8031):878-886 - PMID: 39294375 - PMCID: PMC11424487 - DOI: 10.1038/s41586-024-07960-6

Zhang Y, Cao Y, Jiang W, Ma Q, Shin J, Sun H, Cui J, Chen Y, Giraldo JP, Strano MS, Lowry GV, Sheen J, Marelli B

Polymeric Nanocarriers Autonomously Cross the Plant Cell Wall and Enable Protein Delivery for Stress Sensing.
Adv Mater. 2024;36(41):e2409356 - PMID: 39149770 - PMCID: PMC11466712 - DOI: 10.1002/adma.202409356

Chou WM, Lin WL, Sheen JF

Determination of chlorothalonil in vegetables/fruits using liquid chromatography-tandem mass spectrometry with a discharge adapter interface.
Rapid Commun Mass Spectrom. 2024;38(15):e9770 - PMID: 38773864 - DOI: 10.1002/rcm.9770

Deguine J, Xavier RJ

B cell tolerance and autoimmunity: Lessons from repertoires.
J Exp Med. 2024;221(9):ePub - PMID: 39093312 - PMCID: PMC11296956 - DOI: 10.1084/jem.20231314

Shehadeh F, Felix L, Kalligeros M, Shehadeh A, Fuchs BB, Ausubel FM, Sotiriadis PP, Mylonakis E

Machine learning-assisted high-throughput screening for Anti-MRSA compounds.
IEEE/ACM Trans Comput Biol Bioinform. 2024;21(6):1911-1921 - PMID: 39058605 - DOI: 10.1109/TCBB.2024.3434340

Neale I, Reddy C, Tan ZY, Li B, Nag PP, Park J, Park J, Carey KL, Graham DB, Xavier RJ

Small-molecule probe for IBD risk variant GPR65 I231L alters cytokine signaling networks through positive allosteric modulation.
Sci Adv. 2024;10(29):eadn2339 - PMID: 39028811 - PMCID: PMC11259170 - DOI: 10.1126/sciadv.adn2339

Seetharaman A, Galagali H, Linarte E, Liu MHX, Cohen JD, Chetal K, Sadreyev R, Tate AJ, Montgomery TA, Ruvkun G

Caenorhabditis elegans SynMuv B gene activity is down-regulated during a viral infection to enhance RNA interference.
bioRxiv. 2024;:ePub - PMID: 39071373 - PMCID: PMC11275910 - DOI: 10.1101/2024.07.12.603258

Yanagi KS, Jochim B, Kunjo SO, Breen P, Ruvkun G, Lehrbach N

Mutations in nucleotide metabolism genes bypass proteasome defects in png-1/NGLY1-deficient Caenorhabditis elegans.
PLoS Biol. 2024;22(7):e3002720 - PMID: 38991033 - PMCID: PMC11265709 - DOI: 10.1371/journal.pbio.3002720

Trsan T, Peng V, Krishna C, Ohara TE, Beatty WL, Sudan R, Kanai M, Krishnamoorthy P, Rodrigues PF, Fachi JL, Grajales-Reyes G, Jaeger N, Fitzpatrick JAJ, Cella M, Gilfillan S, Nakata T, Jaiswal A, Stappenbeck TS, Daly MJ, Xavier RJ, Colonna M

The centrosomal protein FGFR1OP controls myosin function in murine intestinal epithelial cells.
Dev Cell. 2024;59(18):2460-2476.e10 - PMID: 38942017 - PMCID: PMC11421975 - DOI: 10.1016/j.devcel.2024.06.001

Parada-Kusz M, Clatworthy AE, Goering ER, Blackwood SM, Shigeta JY, Mashin E, Salm EJ, Choi C, Combs S, Lee JSW, Rodriguez-Osorio C, Clish C, Tomita S, Hung DT

3-Hydroxykynurenine targets kainate receptors to promote defense against infection.
Nat Chem Biol. 2024;20(12):1586-1596 - PMID: 38898166 - PMCID: PMC12204212 - DOI: 10.1038/s41589-024-01635-z

Kumbhari A, Cheng TNH, Ananthakrishnan AN, Kochar B, Burke KE, Shannon K, Lau H, Xavier RJ, Smillie CS

Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases.
Cell Host Microbe. 2024;32(7):1147-1162.e12 - PMID: 38917808 - PMCID: PMC11239293 - DOI: 10.1016/j.chom.2024.05.022

Meisel JD, Wiesenthal PP, Mootha VK, Ruvkun G

CMTR-1 RNA methyltransferase mutations activate widespread expression of a dopaminergic neuron-specific mitochondrial complex I gene.
Curr Biol. 2024;34(12):2728-2738.e6 - PMID: 38810637 - PMCID: PMC11265314 - DOI: 10.1016/j.cub.2024.04.079

Romano KP, Bagnall J, Warrier T, Sullivan J, Ferrara K, Orzechowski M, Nguyen PH, Raines K, Livny J, Shoresh N, Hung DT

Perturbation-Specific Transcriptional Mapping facilitates unbiased target elucidation of antibiotics.
bioRxiv. 2024;:ePub - PMID: 38712067 - PMCID: PMC11071498 - DOI: 10.1101/2024.04.25.590978

Ding J, Garber JJ, Uchida A, Lefkovith A, Carter GT, Vimalathas P, Canha L, Dougan M, Staller K, Yarze J, Delorey TM, Rozenblatt-Rosen O, Ashenberg O, Graham DB, Deguine J, Regev A, Xavier RJ

An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission.
Nat Commun. 2024;15(1):3344 - PMID: 38637492 - PMCID: PMC11026436 - DOI: 10.1038/s41467-024-47647-0

Fang Z, Pazienza LT, Zhang J, Tam CP, Szostak JW

Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension.
J Am Chem Soc. 2024;146(15):10632-10639 - PMID: 38579124 - PMCID: PMC11027144 - DOI: 10.1021/jacs.4c00323

Li C, Stražar M, Mohamed AMT, Pacheco JA, Walker RL, Lebar T, Zhao S, Lockart J, Dame A, Thurimella K, Jeanfavre S, Brown EM, Ang QY, Berdy B, Sergio D, Invernizzi R, Tinoco A, Pishchany G, Vasan RS, Balskus E, Huttenhower C, Vlamakis H, Clish C, Shaw SY, Plichta DR, Xavier RJ

Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria.
Cell. 2024;187(8):1834-1852.e19 - PMID: 38569543 - PMCID: PMC11071153 - DOI: 10.1016/j.cell.2024.03.014

Poulsen BE, Warrier T, Barkho S, Bagnall J, Romano KP, White T, Yu X, Kawate T, Nguyen PH, Raines K, Ferrara K, Golas A, Fitzgerald M, Boeszoermenyi A, Kaushik V, Serrano-Wu M, Shoresh N, Hung DT

"Multiplexed screen identifies a Pseudomonas aeruginosa -specific small molecule targeting the outer membrane protein OprH and its interaction with LPS".
bioRxiv. 2024;:ePub - PMID: 38559044 - PMCID: PMC10980007 - DOI: 10.1101/2024.03.16.585348

Brandt M, Cao Z, Krishna C, Reedy JL, Gu X, Dutko RA, Oliver BA, Tusi BK, Park J, Richey L, Segerstolpe Å, Litwiler S, Creasey EA, Carey KL, Vyas JM, Graham DB, Xavier RJ

Translational genetics identifies a phosphorylation switch in CARD9 required for innate inflammatory responses.
Cell Rep. 2024;43(3):113944 - PMID: 38489265 - PMCID: PMC11008285 - DOI: 10.1016/j.celrep.2024.113944

Radakovic A, Lewicka A, Todisco M, Aitken HRM, Weiss Z, Kim S, Bannan A, Piccirilli JA, Szostak JW

Structure-guided aminoacylation and assembly of chimeric RNAs.
bioRxiv. 2024;:ePub - PMID: 38464152 - PMCID: PMC10925264 - DOI: 10.1101/2024.03.02.583109

Pust MM, Rocha Castellanos DM, Rzasa K, Dame A, Pishchany G, Assawasirisin C, Liss A, Fernandez-Del Castillo C, Xavier RJ

Absence of a pancreatic microbiome in intraductal papillary mucinous neoplasm.
Gut. 2024;73(7):1131-1141 - PMID: 38429112 - PMCID: PMC11187374 - DOI: 10.1136/gutjnl-2023-331012

Todisco M, Ding D, Szostak JW

Transient states during the annealing of mismatched and bulged oligonucleotides.
Nucleic Acids Res. 2024;52(5):2174-2187 - PMID: 38348869 - PMCID: PMC10954449 - DOI: 10.1093/nar/gkae091

Warnhoff K, Bhattacharya S, Snoozy J, Breen PC, Ruvkun G

Hypoxia-inducible factor induces cysteine dioxygenase and promotes cysteine homeostasis in Caenorhabditis elegans
Elife. 2024;12:ePub - PMID: 38349720 - PMCID: PMC10942545 - DOI: 10.7554/eLife.89173

Neo DM, Clatworthy AE, Hung DT

A dual-plasmid CRISPR/Cas9-based method for rapid and efficient genetic disruption in Mycobacterium abscessus.
J Bacteriol. 2024;206(3):e0033523 - PMID: 38319218 - PMCID: PMC10955840 - DOI: 10.1128/jb.00335-23

Freeman MW, Halvorsen YD, Bond M, Murphy B, Isaacsohn J

Results from a Phase 1 Study Assessing the Pharmacokinetics of the Aldosterone Synthase Inhibitor Baxdrostat in Participants with Varying Degrees of Renal Function.
Clin Pharmacol Drug Dev. 2024;13(4):410-418 - PMID: 38311833 - DOI: 10.1002/cpdd.1371

Ding D, Fang Z, Kim SC, O'Flaherty DK, Jia X, Stone TB, Zhou L, Szostak JW

Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying.
J Am Chem Soc. 2024;146(6):3861-3871 - PMID: 38293747 - PMCID: PMC10870715 - DOI: 10.1021/jacs.3c11158

Sturm A, Sun P, Avila-Pacheco J, Clatworthy AE, Bloom-Ackermann Z, Wuo MG, Gomez JE, Jin S, Clish CB, Kiessling LL, Hung DT

Genetic factors affecting storage and utilization of lipids during dormancy in Mycobacterium tuberculosis.
MBio. 2024;15(2):e0320823 - PMID: 38236034 - PMCID: PMC10865790 - DOI: 10.1128/mbio.03208-23

Sella Y, Broderick NA, Stouffer KM, McEwan DL, Ausubel FM, Casadevall A, Bergman A

Preliminary evidence for chaotic signatures in host-microbe interactions.
mSystems. 2024;9(2):e0111023 - PMID: 38197647 - PMCID: PMC10878097 - DOI: 10.1128/msystems.01110-23

Meisel JD, Miranda M, Skinner OS, Wiesenthal PP, Wellner SM, Jourdain AA, Ruvkun G, Mootha VK

Hypoxia and intra-complex genetic suppressors rescue complex I mutants by a shared mechanism.
Cell. 2024;187(3):659-675.e18 - PMID: 38215760 - PMCID: PMC10919891 - DOI: 10.1016/j.cell.2023.12.010

Sheen J

The new horizon of plant auxin signaling via cell-surface co-receptors.
Cell Res. 2024;34(5):343-344 - PMID: 38182889 - PMCID: PMC11061107 - DOI: 10.1038/s41422-023-00921-0

Schirmer M, Stražar M, Avila-Pacheco J, Rojas-Tapias DF, Brown EM, Temple E, Deik A, Bullock K, Jeanfavre S, Pierce K, Jin S, Invernizzi R, Pust MM, Costliow Z, Mack DR, Griffiths AM, Walters T, Boyle BM, Kugathasan S, Vlamakis H, Hyams J, Denson L, Clish CB, Xavier RJ

Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course.
Cell Host Microbe. 2024;32(2):209-226.e7 - PMID: 38215740 - PMCID: PMC10923022 - DOI: 10.1016/j.chom.2023.12.013

Zhernakova DV, Wang D, Liu L, Andreu-Sánchez S, Zhang Y, Ruiz-Moreno AJ, Peng H, Plomp N, Del Castillo-Izquierdo Á, Gacesa R, Lopera-Maya EA, Temba GS, Kullaya VI, van Leeuwen SS, Lifelines Cohort Study, Xavier RJ, de Mast Q, Joosten LAB, Riksen NP, Rutten JHW, Netea MG, Sanna S, Wijmenga C, Weersma RK, Zhernakova A, Harmsen HJM, Fu J

Host genetic regulation of human gut microbial structural variation.
Nature. 2024;625(7996):813-821 - PMID: 38172637 - PMCID: PMC10808065 - DOI: 10.1038/s41586-023-06893-w

Tellier J, Tarasova I, Nie J, Smillie CS, Fedele PL, Cao WHJ, Groom JR, Belz GT, Bhattacharya D, Smyth GK, Nutt SL

Unraveling the diversity and functions of tissue-resident plasma cells.
Nat Immunol. 2024;25(2):330-342 - PMID: 38172260 - DOI: 10.1038/s41590-023-01712-w
Total: 37