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Original Research Papers
Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling
Ooi SK, Sato S, Tomomori-Sato C, Zhang Y, Wen Z, Banks CAS, Washburn MP, Unruh JR, Florens L, Conaway RC, Conaway JW.  Proc Natl Acad Sci U S A. 2021;118:e2107277118. doi: 2107277110.2107271073/pnas.2107277118.
Original Data
Tumor-initiating stem cell shapes its microenvironment into an immunosuppressive barrier and pro-tumorigenic niche
He X, Smith SE, Chen S, Li H, Wu D, Meneses-Giles PI, Wang Y, Hembree M, Yi K, Zhao X, Guo F, Unruh JR, Maddera LE, Yu Z, Scott A, Perera A, Wang Y, Zhao C, Bae K, Box A, Haug JS, Tao F, Hu D, Hansen DM, Qian P, Saha S, Dixon D, Anant S, Zhang D, Lin EH, Sun W, Wiedemann LM, Li L. Cell Rep. 2021;36:109674.doi: 10.1016/j.celrep.2021.109674.
Original Data
Identification of rare, transient post-mitotic cell states that are induced by injury and required for whole-body regeneration in Schmidtea mediterranea
Benham-Pyle BW, Brewster CE, Kent AM, Mann FG, Jr., Chen S, Scott AR, Box AC, Sánchez Alvarado A. Nat Cell Biol. 2021;23:939-952.
Original Data
Decellularization enables functional analysis of ECM remodeling in planarian regeneration
Sonpho E, Mann FG, Jr., Levy M, Ross EJ, Guerrero-Hernandez C, Florens L, Saraf A, Doddihal V, Ounjai P, Sánchez Alvarado A. Mol Cell Proteomics. 2021:100137.
Original Data
The embryonic trunk neural crest microenvironment regulates the plasticity and invasion of human neuroblastoma via TrkB signaling
Kasemeier-Kulesa JC, Spengler JA, Muolo CE, Morrison JA, Woolley TE, Schnell S, Kulesa PM. [published ahead of print August 21 2021]. Dev Biol. 2021.
Original Data
Proteome plasticity in response to persistent environmental change
Domnauer M, Zheng F, Li L, Zhang Y, Chang CE, Unruh JR, Conkright-Fincham J, McCroskey S, Florens L, Zhang Y, Seidel C, Fong B, Schilling B, Sharma R, Ramanathan A, Si K, Zhou C. Mol Cell. 2021;81:3294-3309 e3212.
Original Data
The Planarian Anatomy Ontology: A resource to connect data within and across experimental platforms
Nowotarski SH, Davies EL, Robb SMC, Ross EJ, Matentzoglu N, Doddihal V, Mir M, McClain M, Sánchez Alvarado A. Development. 2021;148:dev196097. doi: 196010.191242/dev.196097.
Original Data
Redistribution of centrosomal proteins by centromeres and Polo kinase controls partial nuclear envelope breakdown in fission yeast
Bestul AJ, Yu Z, Unruh JR, Jaspersen SL. Mol Biol Cell. 2021;32:1487-1500.
Original Data
Biphasic co-flow through a sudden expansion or contaction of Hele-Shaw channel
Rubinstien BY, Zusmanovich D, Li Z, Leshansky AM. Phys Rev Fluids. 2021;6:074201. doi: 10.1103/PhysRevFluids.6.074201.
Branchiomeric Muscle Development Requires Proper Retinoic Acid Signaling
Wang Q, Xu L, Miura J, Saha MK, Uemura Y, Sandell LL, Trainor PA, Yamashiro T, Kurosaka H. Front Cell Dev Biol. 2021;9:596838. doi: 596810.593389/fcell.592021.596838.
Analysis of lamprey meis genes reveals that conserved inputs from hox, Meis and Pbx proteins control their expression in the hindbrain and neural tube
Parker HJ, De Kumar B, Pushel I, Bronner ME, Krumlauf R. Dev Biol. 2021:61-76.
Original Data
Pleiotropic function of the oca2 gene underlies the evolution of sleep loss and albinism in cavefish
O'Gorman M, Thakur S, Imrie G, Moran RL, Choy S, Sifuentes-Romero I, Bilandzija H, Renner KJ, Duboue E, Rohner N, McGaugh SE, Keene AC, Kowalko JE. [published ahead of print July 23 2021]. Curr Biol. 2021.
Original Data
Image3C, a multimodal image-based and label independent integrative method for single-cell analysis
Accorsi A, Box AC, Peuss R, Wood C, Sanchez Alvarado A, Rohner N. eLife. 2021;10. doi: 10.7554/eLife.65372.
Original Data
Highly contiguous assemblies of 101 drosophilid genomes
Kim BY, Wang JR, Miller DE, Barmina O, Delaney E, Thompson A, Comeault AA, Peede D, D'Agostino ER, Pelaez J, Aguilar JM, Haji D, Matsunaga T, Armstrong EE, Zych M, Ogawa Y, Stamenkovic-Radak M, Jelic M, Veselinovic MS, Tanaskovic M, Eric P, Gao JJ, Katoh TK, Toda MJ, Watabe H, Watada M, Davis JS, Moyle LC, Manoli G, Bertolini E, Kostal V, Hawley RS, Takahashi A, Jones CD, Price DK, Whiteman N, Kopp A, Matute DR, Petrov DA. eLife. 2021;10:e66405. doi: 66410.67554/eLife.66405.
Original Data
Synergistic role of retinoic acid signaling and Gata3 during primitive choanae formation
Kurosaka H, Mushiake J, Mithun S, Wu Y, Wang Q, Kikuchi M, Nakaya A, Yamamoto S, Inubushi T, Koga S, Sandell LL, Trainor P, Yamashiro T. [published ahead of print July 18 2021]. Hum Mol Genet. 2021.
Repeated evolution of circadian clock dysregulation in cavefish populations
Mack KL, Jaggard JB, Persons JL, Roback EY, Passow CN, Stanhope BA, Ferrufino E, Tsuchiya D, Smith SE, Slaughter BD, Kowalko J, Rohner N, Keene AC, McGaugh SE. PLoS Genet. 2020;17:e1009642.
Original Data
The SESAME complex regulates cell senescence through the generation of acetyl-CoA
Chen W, Yu X, Wu Y, Tang J, Yu Q, Lv X, Zha Z, Hu B, Li X, Chen J, Ma L, Workman JL, Li S. Nat Metab. 2021;3:983-1000. doi: 10.1038/s42255-021-00412-9.
Immature Follicular Origins and Disrupted Oocyte Growth Pathways Contribute to Decreased Gamete Quality During Reproductive Juvenescence in Mice
Kusuhara A, Babayev E, Zhou LT, Singh VP, Gerton JL, Duncan FE. Frontiers. 2021;9:Article 693742. doi: 693710.693389/fcell.692021.693742.
Original Data
A physicochemical model of odor sampling
Gronowitz ME, Liu A, Qiu Q, Yu CR, Cleland TA. PLoS Comput Biol. 2021;17:e1009054. doi: 10.1371/journal.pcbi.1009054.
Original Data
DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning
Quadir F, Roy RS, Halfmann R, Cheng J. Sci Rep. 2021;11:12295. doi 10.1038/s41598-021-91827-7.
K63-linked ubiquitination of DYRK1A by TRAF2 alleviates Sprouty2 mediated degradation of EGFR
Zhang P, Zhang Z, Fu Y, Zhang Y, Washburn MP, Florens L, Wu M, Huang C, Hou Z, Mohan M. Cell Death Dis. 2021;12:608.
Original Data
A role for the Cockayne Syndrome B (CSB)-Elongin ubiquitin ligase complex in signal-dependent RNA Polymerase II transcription
Weems JC, Slaughter BD, Unruh JR, Weaver KJ, Miller BD, Delventhal KM, Conaway JW, Conaway RC. J Biol Chem. 2021;297:100862.
Original Data
Encoding innately recognized odors via a generalized population code
Qiu Q, Wu Y, Ma L, Yu CR. Curr Biol. 2021;31:1813-1825 e1814.
Original Data
Adaptive cell invasion maintains lateral line organ homeostasis in response to environmental changes.
Peloggia J, Munch D, Meneses-Giles P, Romero-Carvajal A, Lush ME, Lawson ND, McClain M, Pan YA, Piotrowski T. Dev Cell. 2021.
Original Data
Canonical and early lineage-specific stem cell types identified in planarian SirNeoblasts
Niu K, Xu H, Xiong YZ, Zhao Y, Gao C, Seidel CW, Pan X, Ying Y, Lei K. Cell Regen. 2021;10:15.
Original Data
Ocular elongation and retraction in foveated reptiles
Rasys AM, Pau SH, Irwin KE, Luo S, Kim H, Wahle MA, Trainor PA, Menke DB, Lauderdale JD. [published ahead of print April 19 2021]. Dev Dyn. 2021.
The structure, function and evolution of a complete human chromosome 8
Logsdon GA, Vollger MR, Hsieh P, Mao Y, Liskovykh MA, Koren S, Nurk S, Mercuri L, Dishuck PC, Rhie A, de Lima LG, Dvorkina T, Porubsky D, Harvey WT, Mikheenko A, Bzikadze AV, Kremitzki M, Graves-Lindsay TA, Jain C, Hoekzema K, Murali SC, Munson KM, Baker C, Sorensen M, Lewis AM, Surti U, Gerton JL, Larionov V, Ventura M, Miga KH, Phillippy AM, Eichler EE. T [published ahead of print April 9 2021]. Nature. 2021.
Original Data
Med23 Regulates Sox9 Expression during Craniofacial Development
Dash S, Bhatt S, Falcon KT, Sandell LL, Trainor PA. J Dent Res. 2021;100:406-414.
Original Data
Acquisition of innate odor preference depends on spontaneous and experiential activities during critical period
Qiu Q, Wu Y, Ma L, Xu W, Hills MJ, Ramalingam V, Yu CR. eLife. 2021;10:e60546. doi: 10.7554/eLife.60546.
Original Data
DNA replication, transcription, and H3K56 acetylation regulate copy number and stability at tandem repeats
Salim D, Bradford WD, Rubinstein B, Gerton JL. G3 (Bethesda). 2021:jkab082. doi:010.1093/g1093journal/jkab1082.
Original Data
Plasticity in parental effects confers rapid larval thermal tolerance in the estuarine anemone Nematostella vectensis
Rivera HE, Chen CY, Gibson MC, Tarrant AM. J Exp Biol. 2021;224: jeb236745. doi: 236710.231242/jeb.236745.
Original Data
Double emulsions with ultrathin shell by microfluidic step-emulsification
Ge X, Rubinstein BY, He Y, Bruce FNO, Li L, Leshansky AM, Li Z. [published ahead of print March 9 2021]. Lab Chip. 2021.
A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution
Warren WC, Boggs TE, Borowsky R, Carlson BM, Ferrufino E, Gross JB, Hillier L, Hu Z, Keene AC, Kenzior A, Kowalko JE, Tomlinson C, Kremitzki M, Lemieux ME, Graves-Lindsay T, McGaugh SE, Miller JT, Mommersteeg MTM, Moran RL, Peuss R, Rice ES, Riddle MR, Sifuentes-Romero I, Stanhope BA, Tabin CJ, Thakur S, Yamamoto Y, Rohner N. Nat Commun. 2021;12:1447.
Original Data
The methyltransferase SETD2 couples transcription and splicing by engaging mRNA processing factors through its SHI domain
Bhattacharya S, Levy MJ, Zhang N, Li H, Florens L, Washburn MP, Workman JL. Nat Commun. 2021;12:1443. doi: 1410.1038/s41467-41021-21663-w.
Original Data
Multiple Niche Compartments Orchestrate Stepwise Germline Stem Cell Progeny Differentiation
Tu R, Duan B, Song X, Chen S, Scott A, Hall K, Blanck J, DeGraffenreid D, Li H, Perera A, Haug J, Xie T. Curr Biol. 2021;31:827-839 e823.
Original Data
Base-resolution models of transcription-factor binding reveal soft motif syntax
Avsec Z, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Nat Genet. 2021;53:354-366.
Original Data
Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression
Singh NP, De Kumar B, Paulson A, Parrish ME, Scott C, Zhang Y, Florens L, Krumlauf R. [published ahead of print March 4 2021]. Dev Biol. 2021;9.
Original Data
TATA and paused promoters active in differentiated tissues have distinct expression characteristics
Ramalingam V, Natarajan M, Johnston J, Zeitlinger J. Mol Syst Biol. 2021;17:e9866.
Original Data
Mechanistic inferences from analysis of measurements of protein phase transitions in live cells
Posey AE, Ruff KM, Lalmansingh JM, Kandola TS, Lange JJ, Halfmann R, Pappu RV. [published ahead of print February 5 2021]. J Mol Biol. 2021:166848.
Original Data
Identification of Stem Cells from Large Cell Populations with Topological Scoring
Sardiu ME, Box AC, Haug JS, Washburn MP. Mol Omics. 2021;17:59-65.
Metabolic regulation of telomere silencing by SESAME complex-catalyzed H3T11 phosphorylation
Zhang S, Yu X, Zhang Y, Xue X, Yu Q, Zha Z, Gogol M, Workman JL, Li S. Nat Commun. 2021;12:594. doi: 510.1038/s41467-41020-20711-41461.
Harnessing Ionic Selectivity In Acetyltransferase Chemoproteomic Probes
Jing Y, Montano JL, Levy M, Lopez JE, Kung PP, Richardson P, Krajewski K, Florens L, Washburn MP, Meier JL. ACS Chem Biol. 2021;16:27-34.
Original Data
NOTCH Signaling Controls Ciliary Body Morphogenesis and Secretion by Directly Regulating Nectin Protein Expression
Pang J, Le L, Zhou Y, Tu R, Hou Q, Tsuchiya D, Thomas N, Wang Y, Yu Z, Alexander R, Thexton M, Lewis B, Corbin T, Durnin M, Li H, Ashery-Padan R, Yan D, Xie T. Cell Rep. 2021;34:108603. doi: 108610.101016/j.celrep.102020.108603.
Original Data
Protocol for mouse trophoblast stem cell isolation, differentiation and cytokine detection
Singh VP, Gerton JL. STAR Protoc. 2021;2:100242. doi: 10.1016/ j.xpro.2020.100242.
Original Data
Crosstalk between codon optimality and cis-regulatory elements dictates mRNA stability
Medina-Munoz SG, Kushawah G, Castellano LA, Diez M, DeVore ML, Salazar MJB, Bazzini AA. [published ahead of print January 7 2021]. Genome Biol. 2021;22:14.
Original Data
Combined inhibition of RNA polymerase I and mTORC1/2 synergize to combat oral squamous cell carcinoma
Shi S, Luo H, Wang L, Li H, Liang Y, Xia J, Wang Z, Cheng B, Huang L, Liao G, Xu B. Biomed Pharmacother. 2021;133:110906. doi: 110910.111016/j.biopha.112020.110906.
Original Data
Reviews, Commentaries, Chapters or Books
The 2021 FASEB Virtual Science Research Conference on Protein Aggregation: Function, Dysfunction, and Disease, June 23-25, 2021
Hatters DM, Halfmann R, Baum J. T. FASEB J. 2021;35:e21884.
Nucleotide Metabolism Behind Epigenetics
Suganuma T, Workman JL. Front Endocrinol (Lausanne). 2021;12:731648.
Segmentation and patterning of the vertebrate hindbrain
Krumlauf R, Wilkinson DG. Development. 2021;148,dev186460. doi:10.1242/dev.186460.
Meiosis in Quarantine discussions lead to an action plan to increase diversity and inclusion within the genetics community
Billmyre KK, Bravo Nunez MA, Bishop DK, Cole F. PLoS Genet. 2021;17:e1009648. doi: 10.1371/journal.pgen.1009648.
Husbandry Techniques for a Research Colony of Veiled Chameleons (Chamaeleo calyptratus)
Jewell D, Muensch A, Kupronis R, Baumann DP. Husbandry Techniques for a Research Colony of Veiled Chameleons (Chamaeleo calyptratus). Lab Anim Sci Prof. 2021;9:52-55.
Faulty ribosome biogenesis underlies the ANE syndrome ribosomopathy
Gerton JL. Proc Natl Acad Sci U S A. 2021;118:e2107030118.
Lipid metabolism in adaptation to extreme nutritional challenges
Olsen L, Thum E, Rohner N. Dev Cell. 2021;56:1417-1429.
Meiosis: The elusive sister chromatid repair
Billmyre KK, Hughes SE. Curr Biol. 2021;31:R454-R456.
Unceasingly searching for answers - an interview with Claudio Stern
Sánchez-Alvarado A. Int J Dev Biol. 2021;65:131-136.
Synaptonemal Complex
Lake CM, Hawley RS. Curr Biol Quick Guide. 2021;31:R225-R227.
Live Imaging of the Neural Crest Cell Epithelial-to-Mesenchymal Transition in the Chick Embryo
McKinney MC, Kulesa PM. Methods Mol Biol. 2021;2179:107-114.
Original Data
Modelling Cell Invasion: A Review of What JD Murray and the Embryo Can Teach Us
Kulesa PM, Kasemeier-Kulesa JC, Morrison JA, McLennan R, McKinney MC, Bailey C. Bull Math Biol. 2021;83:26.
Anatomy of the fungal microtubule organizing center, the spindle pole body
Jaspersen SL. Curr Opin Struct Biol. 2021;66:22-31.
In Situ Hematopoietic Stem Cell Imaging
Venkatraman A, Smith SE, Pinho S, Zhao M, Li L, Frenette P. Methods Mol Biol. 2021;2185:373-382.
Mechanics of a molecular mousetrap-- nucleation-limited innate immune signaling
Gama AR, Miller T, Halfmann R. [published ahead of print January 19 2021].  Biophys J. 2021.
Acknowledging the use of human cadaveric tissues in research papers: Recommendations from anatomical journal editors.
Iwanaga J, Singh V, Ohtsuka A, Hwang Y, Kim HJ, Morys J, Ravi KS, Ribatti D, Trainor PA, Sanudo JR, Apaydin N, Sengul G, Albertine KH, Walocha JA, Loukas M, Duparc F, Paulsen F, Del Sol M, Adds P, Hegazy A, Tubbs RS. Clin Anat. 2021;34:2-4.
© 2021 Stowers Institute for Medical Research