Genomics, Genetics, & Epigenetics Recent Publications

• Expanding the spectrum of novel candidate genes using trio exome sequencing and identification of monogenic cause in 27.5% of 320 families with steroid-resistant nephrotic syndrome.Schneider R, Shril S, Buerger F, Deutsch K, Yousef K, Frank CN, Onuchic-Whitford AC, Kitzler TM, Mao Y, Klämbt V, Zahoor MY, Lemberg K, Majmundar AJ, Mansour B, Saida K, Seltzsam S, Kolvenbach CM, Merz LM, Mertens ND, Hermle T, Mann N, Pantel D, Halawi AA, Bao A, Schierbaum L, Schneider S, Salmanullah D, Ben-Dov IZ, Sagiv I, Eid LA, Awad HSH, Al Saffar M, Soliman NA, Nabhan MM, Kari JA, El Desoky S, Shalaby MA, Ooda S, Fathy HM, Mane S, Lifton RP, Somers MJG, Hildebrandt F. Genes Dis. 2025 Mar; 2024 Mar 28. PMID: 39584075.
• Identification of coilin interactors reveals coordinated control of Cajal body number and structure.Arias Escayola D, Zhang C, Nischwitz E, Schärfen L, Dörner K, Straube K, Kutay U, Butter F, Neugebauer KM. J Cell Biol. 2025 Feb 3; 2024 Nov 27. PMID: 39602297.
• Noise-aware dynamic image denoising and positron range correction for Rubidium-82 cardiac PET imaging via self-supervision.Xie H, Guo L, Velo A, Liu Z, Liu Q, Guo X, Zhou B, Chen X, Tsai YJ, Miao T, Xia M, Liu YH, Armstrong IS, Wang G, Carson RE, Sinusas AJ, Liu C. Med Image Anal. 2025 Feb; 2024 Nov 20. PMID: 39579623.
• Mechanisms of thiazide-induced hypertension treatment: insights from gene expression and histological analysis in malignant stroke-prone spontaneously hypertensive rats.Khan S, Ahmad B, Khan MWZ, Fatima SM, Nawaz MU. J Hypertens. 2025 Jan 1; 2024 Nov 28. PMID: 39625002.
• GPR68 supports AML cells through the calcium/calcineurin pro-survival pathway and confers chemoresistance by mediating glucose metabolic symbiosis.He X, Hawkins C, Lawley L, Phan TM, Park I, Joven N, Zhang J, Wunderlich M, Mizukawa B, Pei S, Patel A, VanOudenhove J, Halene S, Fang J. Biochim Biophys Acta Mol Basis Dis. 2025 Jan; 2024 Nov 8. PMID: 39522891.
• Meta-analysis: The utility of the anterior quadratus lumborum block in abdominal surgery.Evans BGA, Ihnat JMH, Zhao KL, Kim L, Pierson D, Yu CT, Lin HM, Li J, Golshan M, Ayyala HS. Am J Surg. 2025 Jan; 2024 Oct 18. PMID: 39454308.
• Retrospective analysis of nail findings in the National Registry for Ichthyosis and Related Disorders database.Curtis KL, Echeandia-Francis C, Falotico JM, Luo A, Qiu Y, Grover C, Piraccini BM, Choate KA, Lipner SR. J Am Acad Dermatol. 2025 Jan; 2024 Sep 14. PMID: 39278313.
• Varying the intensity of cystoscopic surveillance for high-risk non-muscle-invasive bladder cancer.Su ZT, Florissi IS, Mahon KM, Li T, Rezaee ME, Singla N, Patel SH, Townsend JP, Kates MR. BJU Int. 2025 Jan; 2024 Aug 29. PMID: 39210627.
• Asparagine synthetase and G-protein coupled estrogen receptor are critical responders to nutrient supply in KRAS mutant colorectal cancer.Lu L, Zhang Q, Aladelokun O, Berardi D, Shen X, Marin A, Garcia-Milian R, Roper J, Khan SA, Johnson CH. Int J Cancer. 2025 Jan 1; 2024 Jul 22. PMID: 39039782.
• DNA methylation profiles of cancer-related fatigue associated with markers of inflammation and immunometabolism.Xiao C, Peng G, Conneely KN, Zhao H, Felger JC, Wommack EC, Higgins KA, Shin DM, Saba NF, Bruner DW, Miller AH. Mol Psychiatry. 2025 Jan; 2024 Jul 9. PMID: 38977918.
• Enhancing patient representation learning with inferred family pedigrees improves disease risk prediction.Huang X, Arora J, Erzurumluoglu AM, Stanhope SA, Lam D, Zhao H, Ding Z, Wang Z, de Jong J. J Am Med Inform Assoc. 2024 Dec 26; 2024 Dec 26. PMID: 39723811.
• Author Correction: π-HuB: the proteomic navigator of the human body.He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X, Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, Faridi P, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y, Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, Kelleher NL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, Mann M, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y, Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P, Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R, Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, Winkler R, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, Yates J, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, Zheng YZ, Zhong Q, Zhu Y. Nature. 2024 Dec 23; 2024 Dec 23. PMID: 39715925.
• An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.Li C, Bonder MJ, Syed S, Jensen M, Gerstein MB, Zody MC, Chaisson MJP, Talkowski ME, Marschall T, Korbel JO, Eichler EE, Lee C, Shi X. Genome Res. 2024 Dec 23; 2024 Dec 23. PMID: 39638559.
• Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships.Kudron M, Gevirtzman L, Victorsen A, Lear BC, Gao J, Xu J, Samanta S, Frink E, Tran-Pearson A, Huynh C, Vafeados D, Hammonds A, Fisher W, Wall M, Wesseling G, Hernandez V, Lin Z, Kasparian M, White K, Allada R, Gerstein M, Hillier L, Celniker SE, Reinke V, Waterston RH. Genome Res. 2024 Dec 23; 2024 Dec 23. PMID: 39438113.
• Divergent brain solute clearance in rat models of cerebral amyloid angiopathy and Alzheimer's disease.Koundal S, Chen X, Gursky Z, Lee H, Xu K, Liang F, Xie Z, Xu F, Lin HM, Van Nostrand WE, Gu X, Elkin R, Tannenbaum A, Benveniste H. iScience. 2024 Dec 20; 2024 Nov 23. PMID: 39720539.
• A New Perspective on Drugs for Duchenne Muscular Dystrophy: Proposals for Better Respiratory Outcomes and Improved Regulatory Pathways.Birnkrant DJ, Black JB, Sheehan DW, Baker HM, DiBartolo ML, Katz SL. Paediatr Drugs. 2024 Dec 20; 2024 Dec 20. PMID: 39707120.
• A role for the kinetochore protein, NUF2, in ribosome biogenesis.Brown TJ, Pichurin J, Parrado CR, Kabeche L, Baserga SJ. Mol Biol Cell. 2024 Dec 20; 2024 Dec 20. PMID: 39705402.
• Protocol for detecting glycoRNAs using metabolic labeling and northwestern blot.Li L, Zhang N, Pantoja C, Wang Y, Lu J. STAR Protoc. 2024 Dec 20; 2024 Sep 19. PMID: 39298321.
• Genetic Analysis of Epidermal Inclusion Cysts Reveals NEK9 as a Common Driver of Comedogenesis and Cyst Formation.Ellis KT, Myung P, Cohen J, Choate KA. J Invest Dermatol. 2024 Dec 18; 2024 Dec 18. PMID: 39706256.
• Digital phenotyping from wearables using AI characterizes psychiatric disorders and identifies genetic associations.Liu JJ, Borsari B, Li Y, Liu SX, Gao Y, Xin X, Lou S, Jensen M, Garrido-Martín D, Verplaetse TL, Ash G, Zhang J, Girgenti MJ, Roberts W, Gerstein M. Cell. 2024 Dec 18; 2024 Dec 18. PMID: 39706190.
• Seven years of Non-invasive Follicular Thyroid Neoplasm with Papillary-like Nuclear Features (NIFTP): Rate of Acceptance and Variation of Diagnostic Approaches Across Different Continents.Williams MD, Liu Z, Rossi ED, Agarwal S, Ryška A, Ghuzlan AA, Bychkov A, Baloch Z, Chernock R, Chiosea SL, Cipriani NA, Erkilic S, Fridman M, Hang JF, Harahap AS, Jung CK, Kakudo K, Khalil M, Khanafshar E, Kumarasinghe P, Lloyd R, Nguyen TP, Ocal IT, Prasad ML, Pusztaszeri M, Rana C, Sadow P, Sajed DP, Seethala R, Tallini G, Vuong HG, Yegen G, LiVolsi VA, Nikiforov YE. J Clin Endocrinol Metab. 2024 Dec 18. PMID: 38874075.
• The New Sydenham Society's Atlas of Portraits of Diseases of the Skin - an Educational Tool.Bolognia JL, Braverman IM. Clin Dermatol. 2024 Dec 17; 2024 Dec 17. PMID: 39701437.
• Commentary.Bolognia JL. Clin Dermatol. 2024 Dec 17; 2024 Dec 17. PMID: 39701435.
• De novo variants disrupt an LDB1-regulated transcriptional network in congenital ventriculomegaly.Allington G, Mehta NH, Dennis E, Mekbib KY, Reeves B, Kiziltug E, Chen S, Zhao S, Duy PQ, Saleh M, Ang LC, Fan B, Nelson-Williams C, Moreno-de-Luca A, Haider S, Lifton RP, Alper SL, McGee S, Jin SC, Kahle KT. Brain. 2024 Dec 16; 2024 Dec 16. PMID: 39680505.
• A Genome-wide Association Study of Susceptibility to Upper Urinary Tract Infections.Flatby HM, Ravi A, Liyanarachi KV, Afset JE, Rasheed H, Brumpton BM, Hveem K, Åsvold BO, DeWan AT, Solligård E, Damås JK, Rogne T. J Infect Dis. 2024 Dec 16. PMID: 38713594.
• Clinical outcomes among patients with mitral valve regurgitation undergoing Impella-supported high-risk PCI.Abu-Much A, Grines CL, Chen S, Batchelor WB, Zhao D, Falah B, Maini AS, Redfors B, Bellumkonda L, Bharadwaj AS, Moses JW, Truesdell AG, Zhang Y, Zhou Z, Baron SJ, Lansky AJ, Basir MB, O'Neill WW, Cohen DJ. Int J Cardiol. 2024 Dec 15; 2024 Sep 11. PMID: 39270940.
• Vascular Endothelial Cells Derived from Transgene-Free Pig Induced Pluripotent Stem Cells for Vascular Tissue Engineering.Batty L, Park J, Qin L, Riaz M, Lin Y, Xu Z, Gao X, Li X, Lopez C, Zhang W, Hoareau M, Fallon ME, Huang Y, Luo H, Luo J, Ménoret S, Li P, Jiang Z, Smith P, Sachs DH, Tellides G, Ignacio Anegon, Pober JS, Liu P, Qyang Y. Acta Biomater. 2024 Dec 14; 2024 Dec 14. PMID: 39681154.
• Validation of the NCCN/Yale criteria for the identification of CDH1 pathogenic variant carriers.Lerner BA, Giner-Calabuig M, Carraway C, Richardson M, Krahn K, Susswein L, Nielsen SM, Karam R, Xicola RM, Llor X. J Med Genet. 2024 Dec 14; 2024 Dec 14. PMID: 39674581.
• Endometrial stromal cell signaling and microRNA exosome content in women with adenomyosis.Zipponi M, Cacciottola L, Camboni A, Stratopoulou CA, Taylor HS, Dolmans MM. Mol Hum Reprod. 2024 Dec 14; 2024 Dec 14. PMID: 39673794.
• Genetic variants in folate metabolism-related genes, serum folate and hepatocellular carcinoma survival: the Guangdong Liver Cancer Cohort study.Li Y, Shu J, Tan P, Dong X, Zhang M, He T, Yang Z, Zhang X, Giovannucci EL, Liu Z, Zhou Z, Li Q, Xu Y, Xu X, Peng T, Lu J, Zhang Y, Zhu H, Fang A. Br J Nutr. 2024 Dec 14; 2024 Nov 7. PMID: 39506332.
• Effect of Single vs. Double Blind Peer Review: A Difference-in-Difference Analysis.Atwani R, Barake C, Lee M, Saade G, Taylor H, Huang JC, Kawakita T. Am J Obstet Gynecol MFM. 2024 Dec 12; 2024 Dec 12. PMID: 39674506.
• Mood lability and depression limit oral contraceptive therapy in endometriosis.Cevik EC, Taylor HS. Fertil Steril. 2024 Dec 11; 2024 Dec 11. PMID: 39672361.
• Financial Toxicity Among Patients With Advanced Solid Tumors Participating in Early-Phase Clinical Trials.Blanter J, Van Hyfte G, Ahmad M, Xu S, Hapanowicz O, Fazilov G, Lu A, Lucas N, Wu K, Shelton G, DeMerchant M, Lachowicz M, Kier M, Werner M, Eder JP, Galsky MD, Marron TU, Smith CB, LoRusso PM, Hofstatter E, Doroshow DB. JCO Oncol Pract. 2024 Dec 11; 2024 Dec 11. PMID: 39661920.
• DNA nanodevice for analysis of force-activated protein extension and interactions.Zhou K, Chung M, Cheng J, Powell JT, Yan Q, Liu J, Xiong Y, Schwartz MA, Lin C. bioRxiv. 2024 Dec 11; 2024 Dec 11. PMID: 39554144.
• A Retrospective Study to Investigate the Relationship Between Body Mass Index and Hemodynamic Characteristics in Hypertensive Patients.Xiao W, Han P, Song L, Yang J, Zhou L, Deng X, Ma ZJ, Lang Y, Zhao H, Zhao Y, Chen H, Zhang W, Huang H, Sun N. J Clin Hypertens (Greenwich). 2024 Dec 10; 2024 Dec 10. PMID: 39654491.
• Climate Effects on Belowground Tea Litter Decomposition Depend on Ecosystem and Organic Matter Types in Global Wetlands.Trevathan-Tackett SM, Kepfer-Rojas S, Malerba M, Macreadie PI, Djukic I, Zhao J, Young EB, York PH, Yeh SC, Xiong Y, Winters G, Whitlock D, Weaver CA, Watson A, Visby I, Tylkowski J, Trethowan A, Tiegs S, Taylor B, Szpikowski J, Szpikowska G, Strickland VL, Stivrins N, Sousa AI, Sinutok S, Scheffel WA, Santos R, Sanderman J, Sánchez-Carrillo S, Sanchez-Cabeza JA, Rymer KG, Ruiz-Fernandez AC, Robroek BJM, Roberts T, Ricart AM, Reynolds LK, Rachlewicz G, Prathep A, Pinsonneault AJ, Pendall E, Payne R, Ozola I, Onufrock C, Ola A, Oberbauer SF, Numbere AO, Novak AB, Norkko J, Norkko A, Mozdzer TJ, Morgan P, Montemayor DI, Martin CW, Malone SL, Major M, Majewski M, Lundquist CJ, Lovelock CE, Liu S, Lin HJ, Lillebo A, Li J, Kominoski JS, Khuroo AA, Kelleway JJ, Jinks KI, Jerónimo D, Janousek C, Jackson EL, Iribarne O, Hanley T, Hamid M, Gupta A, Guariento RD, Grudzinska I, da Rocha Gripp A, González Sagrario MA, Garrison LM, Gagnon K, Gacia E, Fusi M, Farrington L, Farmer J, de Assis Esteves F, Escapa M, Domańska M, Dias ATC, de Los Santos CB, Daffonchio D, Czyryca PM, Connolly RM, Cobb A, Chudzińska M, Christiaen B, Chifflard P, Castelar S, Carneiro LS, Cardoso-Mohedano JG, Camden M, Caliman A, Bulmer RH, Bowen J, Boström C, Bernal S, Berges JA, Benavides JC, Barry SC, Alatalo JM, Al-Haj AN, Adame MF. Environ Sci Technol. 2024 Dec 10; 2024 Nov 25. PMID: 39587399.
• Monitoring sewage and effluent water is an effective approach for the detection of the mobile colistin resistance genes (mcr) and associated bacterial hosts in the human population and environment in the USA.Hassan J, Osman M, Xu T, Naas T, Schiff SJ, Mann D, Esseili MA, Deng X, Kassem II. Environ Pollut. 2024 Dec 9; 2024 Dec 9. PMID: 39662581.
• Piwi regulates the usage of alternative transcription start sites in the Drosophila ovary.Chen J, Liu N, Qi H, Neuenkirchen N, Huang Y, Lin H. Nucleic Acids Res. 2024 Dec 9; 2024 Dec 9. PMID: 39657757.
• Improved Prediction of Ligand-Protein Binding Affinities by Meta-modeling.Lee HJ, Emani PS, Gerstein MB. J Chem Inf Model. 2024 Dec 9; 2024 Nov 22. PMID: 39576762.
• Modeling and predicting single-cell multi-gene perturbation responses with scLAMBDA.Wang G, Liu T, Zhao J, Cheng Y, Zhao H. bioRxiv. 2024 Dec 8; 2024 Dec 8. PMID: 39677694.
• High-Throughput Quantification of miRNA-3'-Untranslated-Region Regulatory Effects.Mastriano S, Kanoria S, Rennie W, Liu C, Li D, Cheng J, Ding Y, Lu J. bioRxiv. 2024 Dec 6; 2024 Dec 6. PMID: 39677669.
• Molecular characteristics of advanced colorectal cancer and multi-hit PIK3CA mutations.Yasin F, Sokol E, Vasan N, Pavlick DC, Huang RSP, Pelletier M, Levy MA, Pusztai L, Lacy J, Zhang JY, Ross JS, Cecchini M. Oncologist. 2024 Dec 6. PMID: 39401325.
• E-box independent chromatin recruitment turns MYOD into a transcriptional repressor.Nicoletti C, Massenet J, Pintado-Urbanc AP, Connor LJ, Nicolau M, Sundar S, Xu M, Schmitt A, Zhang W, Fang Z, Chan TCI, Tapscott SJ, Cheung TH, Simon MD, Caputo L, Puri PL. bioRxiv. 2024 Dec 5; 2024 Dec 5. PMID: 39677796.
• Race and Clinical Outcomes in Hormone Receptor-Positive, HER2-Negative, Node-Positive Breast Cancer in the Randomized RxPONDER Trial.Abdou Y, Barlow WE, Gralow JR, Meric-Bernstam F, Albain KS, Hayes DF, Lin NU, Perez EA, Goldstein LJ, Chia SKL, Dhesy-Thind S, Rastogi P, Alba E, Delaloge S, Schott AF, Shak S, Sharma P, Lew DL, Miao J, Unger JM, Tripathy D, Hortobagyi GN, Pusztai L, Kalinsky K. J Natl Cancer Inst. 2024 Dec 5; 2024 Dec 5. PMID: 39656951.
• Bayesian subtyping for multi-state brain functional connectome with application on preadolescent brain cognition.Chen T, Zhao H, Tan C, Constable T, Yip S, Zhao Y. Biostatistics. 2024 Dec 4; 2024 Dec 4. PMID: 39656842.
• Elevated IL-22 as a result of stress-induced gut leakage suppresses septal neuron activation to ameliorate anxiety-like behavior.Xia M, Lu J, Lan J, Teng T, Shiao R, Sun H, Jin Z, Liu X, Wang J, Wu H, Wang C, Yi H, Qi Q, Li J, Schneeberger M, Shen W, Lu B, Chen L, Ilanges A, Zhou X, Yu X. Immunity. 2024 Dec 4; 2024 Dec 4. PMID: 39644894.
• Deep learning analysis of fMRI data for predicting Alzheimer's Disease: A focus on convolutional neural networks and model interpretability.Zhou X, Kedia S, Meng R, Gerstein M. PLoS One. 2024; 2024 Dec 4. PMID: 39630834.
• Dysregulation in keratinocytes drives systemic lupus erythematosus onset.Tian J, Shi L, Zhang D, Yao X, Zhao M, Kumari S, Lu J, Yu D, Lu Q. Cell Mol Immunol. 2024 Dec 3; 2024 Dec 3. PMID: 39627610.
• Development and Validation of the RSClinN+ Tool to Predict Prognosis and Chemotherapy Benefit for Hormone Receptor-Positive, Node-Positive Breast Cancer.Pusztai L, Hoag JR, Albain KS, Barlow WE, Stemmer SM, Meisner A, Hortobagyi GN, Shak S, Rae JM, Baehner R, Sharma P, Kalinsky KM. J Clin Oncol. 2024 Dec 2; 2024 Dec 2. PMID: 39621968.
• A novel multidrug-resistant Enterobacter hormaechei ST2755 isolated from a wild-caught oyster in Georgia, USA.Nasser NA, Osman M, Hassan J, Xu T, Mann D, Deng X, Kassem II. New Microbes New Infect. 2024 Dec; 2024 Nov 29. PMID: 39697810.
• Genetic/Familial High-Risk Assessment: Colorectal, Endometrial, and Gastric, Version 3.2024, NCCN Clinical Practice Guidelines In Oncology.Hodan R, Gupta S, Weiss JM, Axell L, Burke CA, Chen LM, Chung DC, Clayback KM, Felder S, Foda Z, Giardiello FM, Grady W, Gustafson S, Hagemann A, Hall MJ, Hampel H, Idos G, Joseph N, Kassem N, Katona B, Kelly K, Kieber-Emmons A, Kupfer S, Lang K, Llor X, Markowitz AJ, Prats MM, Niell-Swiller M, Outlaw D, Pirzadeh-Miller S, Samadder NJ, Shibata D, Stanich PP, Swanson BJ, Szymaniak BM, Welborn J, Wiesner GL, Yurgelun MB, Dwyer M, Darlow S, Diwan Z. J Natl Compr Canc Netw. 2024 Dec. PMID: 39689429.
• π-HuB: the proteomic navigator of the human body.He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X, Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, Faridi P, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y, Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, Kelleher NL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, Mann M, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y, Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P, Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R, Vizcaíno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, Winkler R, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, Yates J, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, Zheng YZ, Zhong Q, Zhu Y. Nature. 2024 Dec; 2024 Dec 11. PMID: 39663494.
• Discovery of Gene Fusions in Driver-Negative Cancer Samples From the National Cancer Institute-Molecular Analysis for Therapy Choice Screening Cohort.Kaluziak ST, Codd EM, Purohit R, Melli B, Kalyan P, Fordham JA, Kirkpatrick G, McShane LM, Chang TC, Yang G, Wang J, Williams PM, Karlovich C, Sklar J, Iafrate AJ. JCO Precis Oncol. 2024 Dec; 2024 Dec 5. PMID: 39637335.
• Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling.Liu Z, Grigas AT, Sumner J, Knab E, Davis CM, O'Hern CS. Protein Sci. 2024 Dec. PMID: 39548730.
• 16S rRNA target sequencing of human tumors validates findings of Lachnoclostridium abundance in human melanomas that are heavily CD8+ T-cell infiltrated.Lu L, Johnson C, Khan S, Kluger H. Eur J Cancer. 2024 Dec; 2024 Oct 24. PMID: 39477777.
• Global, regional, and national burden of injuries, and burden attributable to injuries risk factors, 1990 to 2019: results from the Global Burden of Disease study 2019.Public Health. 2024 Dec; 2024 Oct 24. PMID: 39454232.
• Impacts of land-use and land-cover changes on temperature-related mortality.Orlov A, De Hertog SJ, Havermann F, Guo S, Manola I, Lejeune Q, Schleussner CF, Thiery W, Pongratz J, Humpenöder F, Popp A, Aunan K, Armstrong B, Royé D, Cvijanovic I, Lavigne E, Achilleos S, Bell M, Masselot P, Sera F, Vicedo-Cabrera AM, Gasparrini A, Mistry MN. Environ Epidemiol. 2024 Dec; 2024 Oct 21. PMID: 39439814.
• Splicing the Difference: Harnessing the Complexity of the Transcriptome in Hematopoiesis.Maul-Newby HM, Halene S. Exp Hematol. 2024 Dec; 2024 Oct 10. PMID: 39393608.
• Steering research on mRNA splicing in cancer towards clinical translation.Anczukow O, Allain FH, Angarola BL, Black DL, Brooks AN, Cheng C, Conesa A, Crosse EI, Eyras E, Guccione E, Lu SX, Neugebauer KM, Sehgal P, Song X, Tothova Z, Valcárcel J, Weeks KM, Yeo GW, Thomas-Tikhonenko A. Nat Rev Cancer. 2024 Dec; 2024 Oct 9. PMID: 39384951.
• Contemporary Approach to the Diagnosis and Classification of Myelodysplastic Neoplasms/Syndromes-Recommendations From the International Consortium for Myelodysplastic Neoplasms/Syndromes (MDS [icMDS]).Aakash F, Gisriel SD, Zeidan AM, Bennett JM, Bejar R, Bewersdorf JP, Borate UM, Boultwood J, Brunner AM, Buckstein R, Carraway HE, Churpek JE, Daver NG, DeZern AE, Efficace F, Fenaux P, Figueroa ME, Garcia-Manero G, Gore SD, Greenberg PL, Griffiths EA, Halene S, Hourigan CS, Kim TK, Kim N, Komrokji RS, Kutchroo VK, List AF, Little RF, Majeti R, Nazha A, Nimer SD, Odenike O, Padron E, Patnaik MM, Platzbecker U, Della Porta MG, Roboz GJ, Sallman DA, Santini V, Sanz G, Savona MR, Sekeres MA, Stahl M, Starczynowski DT, Steensma DP, Taylor J, Abdel-Wahab O, Wei AH, Xie Z, Xu ML, Hasserjian RP, Loghavi S. Mod Pathol. 2024 Dec; 2024 Sep 23. PMID: 39322118.
• Datopotamab-deruxtecan in early-stage breast cancer: the sequential multiple assignment randomized I-SPY2.2 phase 2 trial.Khoury K, Meisel JL, Yau C, Rugo HS, Nanda R, Davidian M, Tsiatis B, Chien AJ, Wallace AM, Arora M, Rozenblit M, Hershman DL, Zimmer A, Clark AS, Beckwith H, Elias AD, Stringer-Reasor E, Boughey JC, Nangia C, Vaklavas C, Omene C, Albain KS, Kalinsky KM, Isaacs C, Tseng J, Roussos Torres ET, Thomas B, Thomas A, Sanford A, Balassanian R, Ewing C, Yeung K, Sauder C, Sanft T, Pusztai L, Trivedi MS, Outhaythip A, Li W, Onishi N, Asare AL, Beineke P, Norwood P, Brown-Swigart L, Hirst GL, Matthews JB, Moore B, Fraser Symmans W, Price E, Beedle C, Perlmutter J, Pohlmann P, Shatsky RA, DeMichele A, Yee D, van 't Veer LJ, Hylton NM, Esserman LJ. Nat Med. 2024 Dec; 2024 Sep 14. PMID: 39277671.
• Association of Medicare eligibility with access to cardiac surgical care by patients identifying as other than non-Hispanic White: a regression discontinuity analysis.Arndt M, Lin HM, Strand ED, Fisher C, Schonberger RB. Br J Anaesth. 2024 Dec; 2024 Sep 14. PMID: 39277456.
• Reconstructing human-specific regulatory functions in model systems.Baumgartner M, Ji Y, Noonan JP. Curr Opin Genet Dev. 2024 Dec; 2024 Sep 12. PMID: 39270593.
• Aplastic anemia in association with multiple myeloma: clinical and pathophysiological insights.Muradashvili T, Liu Y, VanOudenhove J, Gu SX, Krause DS, Montanari F, Carlino MJ, Mancuso R, Stempel JM, Halene S, Zeidan AM, Podoltsev NA, Neparidze N. Leuk Lymphoma. 2024 Dec; 2024 Sep 3. PMID: 39225418.
• Phosphoenolpyruvate carboxykinase-2 (PCK2) is a therapeutic target in triple-negative breast cancer.Gunasekharan V, Lin HK, Marczyk M, Rios-Hoyo A, Campos GE, Shan NL, Ahmed M, Umlauf S, Gareiss P, Raaisa R, Williams R, Cardone R, Siebel S, Kibbey R, Surovtseva YV, Pusztai L. Breast Cancer Res Treat. 2024 Dec; 2024 Aug 23. PMID: 39177932.
• Empowering the biomedical research community: Innovative SAS deployment on the All of Us Researcher Workbench.Humes I, Shyr C, Dillon M, Liu Z, Peterson J, Jeor CS, Malkes J, Master H, Mapes B, Azuine R, Mack N, Abdelbary B, Gamble-George J, Goldmann E, Cook S, Choupani F, Baskir R, McMaster S, Lunt C, Watson K, Lee M, Schwartz S, Munshi R, Glazer D, Banks E, Philippakis A, Basford M, Roden D, Harris PA. J Am Med Inform Assoc. 2024 Dec 1. PMID: 39135439.
• The single-cell opioid responses in the context of HIV (SCORCH) consortium.Ament SA, Campbell RR, Lobo MK, Receveur JP, Agrawal K, Borjabad A, Byrareddy SN, Chang L, Clarke D, Emani P, Gabuzda D, Gaulton KJ, Giglio M, Giorgi FM, Gok B, Guda C, Hadas E, Herb BR, Hu W, Huttner A, Ishmam MR, Jacobs MM, Kelschenbach J, Kim DW, Lee C, Liu S, Liu X, Madras BK, Mahurkar AA, Mash DC, Mukamel EA, Niu M, O'Connor RM, Pagan CM, Pang APS, Pillai P, Repunte-Canonigo V, Ruzicka WB, Stanley J, Tickle T, Tsai SA, Wang A, Wills L, Wilson AM, Wright SN, Xu S, Yang J, Zand M, Zhang L, Zhang J, Akbarian S, Buch S, Cheng CS, Corley MJ, Fox HS, Gerstein M, Gummuluru S, Heiman M, Ho YC, Kellis M, Kenny PJ, Kluger Y, Milner TA, Moore DJ, Morgello S, Ndhlovu LC, Rana TM, Sanna PP, Satterlee JS, Sestan N, Spector SA, Spudich S, Tilgner HU, Volsky DJ, White OR, Williams DW, Zeng H. Mol Psychiatry. 2024 Dec; 2024 Jun 15. PMID: 38879719.
• SenNet recommendations for detecting senescent cells in different tissues.Suryadevara V, Hudgins AD, Rajesh A, Pappalardo A, Karpova A, Dey AK, Hertzel A, Agudelo A, Rocha A, Soygur B, Schilling B, Carver CM, Aguayo-Mazzucato C, Baker DJ, Bernlohr DA, Jurk D, Mangarova DB, Quardokus EM, Enninga EAL, Schmidt EL, Chen F, Duncan FE, Cambuli F, Kaur G, Kuchel GA, Lee G, Daldrup-Link HE, Martini H, Phatnani H, Al-Naggar IM, Rahman I, Nie J, Passos JF, Silverstein JC, Campisi J, Wang J, Iwasaki K, Barbosa K, Metis K, Nernekli K, Niedernhofer LJ, Ding L, Wang L, Adams LC, Ruiyang L, Doolittle ML, Teneche MG, Schafer MJ, Xu M, Hajipour M, Boroumand M, Basisty N, Sloan N, Slavov N, Kuksenko O, Robson P, Gomez PT, Vasilikos P, Adams PD, Carapeto P, Zhu Q, Ramasamy R, Perez-Lorenzo R, Fan R, Dong R, Montgomery RR, Shaikh S, Vickovic S, Yin S, Kang S, Suvakov S, Khosla S, Garovic VD, Menon V, Xu Y, Song Y, Suh Y, Dou Z, Neretti N. Nat Rev Mol Cell Biol. 2024 Dec; 2024 Jun 3. PMID: 38831121.
• Reliable detection of stochastic epigenetic mutations and associations with cardiovascular aging.Markov Y, Levine M, Higgins-Chen AT. Geroscience. 2024 Dec; 2024 May 13. PMID: 38736015.
• Impact of GLP-1 Receptor Agonist Use in Patients With Steatotic Liver Disease and Type 2 Diabetes: A Retrospective Cohort Study.Wood M, Kennedy AG, Khan S, Hitt JR, Davis K, Reddy SS, Gilbert MP. J Pharm Pract. 2024 Dec; 2024 May 8. PMID: 38720191.
• Origins of lineage-specific elements via gene duplication, relocation, and regional rearrangement in Neurospora crassa.Wang Z, Wang YW, Kasuga T, Hassler H, Lopez-Giraldez F, Dong C, Yarden O, Townsend JP. Mol Ecol. 2024 Dec; 2023 Oct 16. PMID: 37843462.
• Race and Intention to Breastfeed are the Strongest Predictors of Exclusive Breastfeeding: a Retrospective Study.Sartor L, Pyram-Vincent C, Lin HM, Ouyang Y, Wax DB, Beilin Y. J Racial Ethn Health Disparities. 2024 Dec; 2023 Oct 5. PMID: 37796430.
• An international survey on the knowledge, attitudes and clinical patterns of use of medical cannabis for cancer care: The TASMAN study.Trapani D, Nidhamalddin SJ, Gandini S, Filetti M, Altuna SC, Carnevale Schianca A, Petrillo A, Murthy SM, Girardi F, Bezuidenhout JB, El Bairi K, Lombardi P, Khan SZ, Lengyel CG, Seeber A, Hussain S, Seid FU, Elfaham E, Odhiambo AO, Coskun Y, Baker HS, Chowdhury AR, Genazzani A, Daniele G, Porzio G, Curigliano G, Giusti R. Eur J Cancer. 2024 Nov 30; 2024 Nov 30. PMID: 39647216.
• Ezrin drives adaptation of monocytes to the inflamed lung microenvironment.Gudneppanavar R, Di Pietro C, H Öz H, Zhang PX, Cheng EC, Huang PH, Tebaldi T, Biancon G, Halene S, Hoppe AD, Kim C, Gonzalez AL, Krause DS, Egan ME, Gupta N, Murray TS, Bruscia EM. Cell Death Dis. 2024 Nov 29; 2024 Nov 29. PMID: 39613751.
• Identification of HER2-positive breast cancer molecular subtypes with potential clinical implications in the ALTTO clinical trial.Rediti M, Venet D, Joaquin Garcia A, Maetens M, Vincent D, Majjaj S, El-Abed S, Di Cosimo S, Ueno T, Izquierdo M, Piccart M, Pusztai L, Loi S, Salgado R, Viale G, Rothé F, Sotiriou C. Nat Commun. 2024 Nov 29; 2024 Nov 29. PMID: 39613746.
• Congenital perineal hernia: a systematic review of case reports.Khan MWZ, Ahmad M, Iftikhar S, Mohmand AK, Esmat M, Qudrat S, Ikram J, Khan S, Tu L. Hernia. 2024 Nov 29; 2024 Nov 29. PMID: 39611977.
• GABA(A) receptor π forms channels that stimulate ERK through a G-protein-dependent pathway.Wang Y, Zhang Y, Li W, Salovska B, Zhang J, Li T, Li H, Liu Y, Kaczmarek LK, Pusztai L, Klein DE. Mol Cell. 2024 Nov 28; 2024 Nov 28. PMID: 39642883.
• Circulating tumor-reactive KIR(+)CD8(+) T cells suppress anti-tumor immunity in patients with melanoma.Lu BY, Lucca LE, Lewis W, Wang J, Nogueira CV, Heer S, Rayon-Estrada V, Axisa PP, Reeves SM, Buitrago-Pocasangre NC, Pham GH, Kojima ML, Wei W, Aizenbud L, Bacchiocchi A, Zhang L, Walewski JJ, Chiang V, Olino K, Clune J, Halaban R, Kluger Y, Coyle AJ, Kisielow J, Obermair FJ, Kluger HM, Hafler DA. Nat Immunol. 2024 Nov 28; 2024 Nov 28. PMID: 39609626.
• Overall Survival with Pembrolizumab in Early-Stage Triple-Negative Breast Cancer.Schmid P, Cortes J, Dent R, McArthur H, Pusztai L, Kümmel S, Denkert C, Park YH, Hui R, Harbeck N, Takahashi M, Im SA, Untch M, Fasching PA, Mouret-Reynier MA, Foukakis T, Ferreira M, Cardoso F, Zhou X, Karantza V, Tryfonidis K, Aktan G, O'Shaughnessy J. N Engl J Med. 2024 Nov 28; 2024 Sep 15. PMID: 39282906.
• Rare germline variants in cancer-relevant genes are associated with breast cancer risk in young women with high-risk family history.Rozenblit M, Qing T, Ye Y, Zhao H, Hofstatter E, Singh V, Reisenbichler E, Murray M, Pusztai L. Breast Cancer Res Treat. 2024 Nov 27; 2024 Nov 27. PMID: 39602012.
• Setdb1-loss induces type-I interferons and immune clearance of melanoma.McGeary MK, Damsky W, Daniels AJ, Lang SM, Xu Q, Song E, Huet-Calderwood C, Lou HJ, Paradkar S, Micevic G, Kaech SM, Calderwood DA, Turk BE, Yan Q, Iwasaki A, Bosenberg MW. Cancer Immunol Res. 2024 Nov 26; 2024 Nov 26. PMID: 39589394.
• Optimal Annual COVID-19 Vaccine Boosting Dates Following Previous Booster Vaccination or Breakthrough Infection.Townsend JP, Hassler HB, Dornburg A. Clin Infect Dis. 2024 Nov 26; 2024 Nov 26. PMID: 39589144.
• Transcription factor-dependent regulatory networks of sexual reproduction in Fusarium graminearum.Kim W, Kim D-W, Wang Z, Liu M, Townsend JP, Trail F. mBio. 2024 Nov 26; 2024 Nov 26. PMID: 39589130.
• Clonal hematopoiesis of indeterminate potential is associated with increased risk of immune checkpoint inhibitor myocarditis in a prospective study of a cardio-oncology cohort.Jaber Chehayeb R, Singh J, Matute-Martinez C, Chen NW, Guajardo AF, Lin D, Jayakrishnan R, Christofides A, Leveille E, Im Y, Biancon G, VanOudenhove J, Ibrahim E, Ardasheva A, Jha A, Hwa J, Halene S, Kwan JM. Cardiooncology. 2024 Nov 26; 2024 Nov 26. PMID: 39587635.
• The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus.Kojima ML, Hoppe C, Giraldez AJ. Nat Rev Genet. 2024 Nov 25; 2024 Nov 25. PMID: 39587307.
• CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis.Liu T, Long W, Cao Z, Wang Y, He CH, Zhang L, Strittmatter SM, Zhao H. Brief Bioinform. 2024 Nov 22. PMID: 39592241.
• A new and promising C-phycocyanin-producing cyanobacterial strain, Cyanobium sp. MMK01: practical strategy towards developing a methodology to achieve C-phycocyanin with ultra-high purity.Shafiei M, Shafiei M, Mohseni Sani N, Guo W, Guo S, Vali H, Akbari Noghabi K. Front Microbiol. 2024; 2024 Nov 21. PMID: 39640854.
• A Longitudinal Study of Loneliness Before the End of the COVID-19 Pandemic: Trajectories, Predictors, and Impact on Chinese Adolescent Mental Health.Wang J, Zhang W, Song P, Wang T, Yao Y, Chen Y, Lin H, Yang X, Chen X, Fu C. Psychol Res Behav Manag. 2024; 2024 Nov 21. PMID: 39588180.
• Solvent-mediated analgesia via the suppression of water permeation through TRPV1 ion channels.Liu Y, He Y, Tong J, Guo S, Zhang X, Luo Z, Sun L, Chang C, Zhuang B, Liu X. Nat Biomed Eng. 2024 Nov 21; 2024 Nov 21. PMID: 39572786.
• The cell-type underpinnings of the human functional cortical connectome.Zhang XH, Anderson KM, Dong HM, Chopra S, Dhamala E, Emani PS, Gerstein MB, Margulies DS, Holmes AJ. Nat Neurosci. 2024 Nov 21; 2024 Nov 21. PMID: 39572742.
• Paying to publish: A cross-sectional analysis of article processing charges and journal characteristics among 87 pathology journals.Clark LM, Wang DK, Adkins BD, Fitzhugh VA, Walker PD, Khan SS, Fadare O, Stephens LD, Coogan AC, Booth GS, Jacobs JW. Acad Pathol. 2024 Oct-Dec; 2024 Nov 20. PMID: 39640271.
• Suboptimal Titration of Heart Failure Medications in Pediatric Patients: Baseline Data from ACTION.Nandi D, Wright LK, Sublett-Smith J, Brax A, Bansal N, Almond CS, Azeka E, Butts R, Chen S, Conway J, Cunningham C, Fisher LA, Hall EK, Hunter T, Kobayashi R, Patterson D, Peng DM, Simpson KE, Ryan TD, Spinner JA, Wisotzkey B, Zangwill S, Gajarski RJ, O'Connor M. J Card Fail. 2024 Nov 20; 2024 Nov 20. PMID: 39577739.
• GENCODE 2025: reference gene annotation for human and mouse.Mudge JM, Carbonell-Sala S, Diekhans M, Martinez JG, Hunt T, Jungreis I, Loveland JE, Arnan C, Barnes I, Bennett R, Berry A, Bignell A, Cerdán-Vélez D, Cochran K, Cortés LT, Davidson C, Donaldson S, Dursun C, Fatima R, Hardy M, Hebbar P, Hollis Z, James BT, Jiang Y, Johnson R, Kaur G, Kay M, Mangan RJ, Maquedano M, Gómez LM, Mathlouthi N, Merritt R, Ni P, Palumbo E, Perteghella T, Pozo F, Raj S, Sisu C, Steed E, Sumathipala D, Suner MM, Uszczynska-Ratajczak B, Wass E, Yang YT, Zhang D, Finn RD, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress ML, Birney E, Martin FJ, Frankish A. Nucleic Acids Res. 2024 Nov 20; 2024 Nov 20. PMID: 39565199.
• Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT.Baysoy A, Tian X, Zhang F, Renauer P, Bai Z, Shi H, Li H, Tao B, Yang M, Enninful A, Gao F, Wang G, Zhang W, Tran T, Patterson NH, Bao S, Dong C, Xin S, Zhong M, Rankin S, Guy C, Wang Y, Connelly JP, Pruett-Miller SM, Chi H, Chen S, Fan R. bioRxiv. 2024 Nov 19; 2024 Nov 19. PMID: 39605490.
• Angioimmunoblastic T-cell lymphoma: Current Diagnostic Insights and Advances.Matsumoto NP, Xu ML. Hum Pathol. 2024 Nov 19; 2024 Nov 19. PMID: 39571692.
• Molecular adaptation to neoadjuvant immunotherapy in triple-negative breast cancer.Denkert C, Schneeweiss A, Rey J, Karn T, Hattesohl A, Weber KE, Rachakonda S, Braun M, Huober J, Jank P, Sinn HP, Zahm DM, Felder B, Hanusch C, Teply-Szymanski J, Marmé F, Fehm T, Thomalla J, Sinn BV, Stiewe T, Marczyk M, Blohmer JU, van Mackelenbergh M, Schem C, Staib P, Link T, Müller V, Stickeler E, Stover DG, Solbach C, Metzger-Filho O, Jackisch C, Geyer CE Jr, Fasching PA, Pusztai L, Nekljudova V, Untch M, Loibl S. Cell Rep Med. 2024 Nov 19. PMID: 39566464.
• Hormone Receptor Positive HER2-negative/MammaPrint High-2 Breast Cancers Closely Resemble Triple Negative Breast Cancers.Rios-Hoyo A, Xiong K, Dai J, Yau C, Marczyk M, Garcia-Milian R, Wolf DM, Huppert LA, Nanda R, Hirst GL, Cobain EF, van 't Veer LJ, Esserman LJ, Pusztai L. Clin Cancer Res. 2024 Nov 19; 2024 Nov 19. PMID: 39561272.
• Decoy-resistant IL-18 reshapes the tumor microenvironment and enhances rejection by anti-CTLA-4 in renal cell carcinoma.Schoenfeld DA, Djureinovic D, Su DG, Zhang L, Lu BY, Kamga L, Mann JE, Huck JD, Hurwitz M, Braun DA, Jilaveanu L, Ring AM, Kluger HM. JCI Insight. 2024 Nov 19; 2024 Nov 19. PMID: 39561007.
• Multi-platform biomarkers of response to an immune checkpoint inhibitor in the neoadjuvant I-SPY 2 trial for early-stage breast cancer.Campbell MJ, Wolf DM, Yau C, Brown-Swigart L, Wulfkuhle J, Gallagher IR, Zhu Z, Bolen J, Vandenberg S, Hoyt C, Mori H, Borowsky A, Sit L, Perlmutter J, Asare SM, Nanda R, Liu MC, Yee D, DeMichele AM, Hylton NM, Pusztai L, Berry DA, Hirst GL, Petricoin EF, Veer LV, Esserman L. Cell Rep Med. 2024 Nov 19; 2024 Nov 6. PMID: 39510069.
• Individual and System Level Factors Contributing to Guideline Non-Adherent Surgical Antibiotic Prophylaxis at a Tertiary Health Care System: A Qualitative Analysis.Bardia A, Melnick ER, McCall T, Zhao X, Lin HM, Fisher C, Burg MM, Schonberger RB. Anesthesiology. 2024 Nov 18; 2024 Nov 18. PMID: 39556527.