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Original Research Papers
An anti-inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish
Denans N, Tran NTT, Swall ME, Diaz DC, Blanck J, Piotrowski T. Nat Commun. 2022;13:5356 doi: 10.1038/s41467-022-33015-3.
Original Data
Lamb-type solution and properties of unsteady Stokes equation
Fouxon I, Leshansky A, Rubinstein B, Or Y. Phys Rev Fluids. 2022;7:094103 doi: 10.1103/PhysRevFluids.7.094103.
Protocol to detect RNAs from tissue sections in mice using Y-branched probe in-situ hybridization
Wu Y, Yu CR. STAR Protoc. 2022;3:101686 doi: 10.1016/j.xpro.2022.101686.
A freeze-substitution approach with solvent-based glyoxal fixative to prevent distortion of ocular structures
Pang J, Zhao X, Deng F, Tsuchiya D, Malloy S, Parmely T, Xie T, Wang Y.  [published ahead of print September 16 2022]. J Histotechnol. 2022:1-10.
Original Data
Elevated levels of the methyltransferase SETD2 causes transcription and alternative splicing changes resulting in oncogenic phenotypes
Bhattacharya S, Reddy D, Zhang N, Li H, Workman J.  Front Cell Dev Biol. 2022;10:945668 doi: 10.3389/fcell.2022.945668.
Original Data
An apical protein, Pcr2, is required for persistent movement by the human parasite Toxoplasma gondii
Munera Lopez J, Tengganu IF, Liu J, Murray JM, Arias Padilla LF, Zhang Y, Brown PT, Florens L, Hu K. PLoS Pathog. 2022;18:e1010776 doi: 10.1371/journal.ppat.1010776.
Original Data
Dual control of formin-nucleated actin assembly bythe chromatin and ER in mouse oocytes
Wang H, Hu J, Yi K, Ma Z, Song X, Lee Y, Kalab P, Bershadsky AD, Miao Y, Li R. [published ahead of print August 19 2022]. Curr Biol. 2022.
Dynamic regulation and requirement for ribosomal RNA transcription during mammalian development
Falcon KT, Watt KEN, Dash S, Zhao R, Sakai D, Moore EL, Fitriasari S, Childers M, Sardiu ME, Swanson S, Tsuchiya D, Unruh J, Bugarinovic G, Li L, Shiang R, Achilleos A, Dixon J, Dixon MJ, Trainor PA. Proc Natl Acad Sci U S A. 2022;119:e2116974119 doi: 10.1073/pnas.2116974119.
Original Data
iCodon customizes gene expression based on the codon composition
Diez M, Medina-Munoz SG, Castellano LA, da Silva Pescador G, Wu Q, Bazzini AA. Sci Rep. 2022;12:12126 doi: 10.1038/s41598-022-15526-7.
Original Data
Single-cell transcriptomics and gene-regulatory networks modulated by Wntless in mammalian midline facial formation and clefts
Gu R, Zhang S, Saha SK, Ji Y, Reynolds K, McMahon M, Sun B, Islam M, Trainor PA, Chen Y, Xu Y, Chai Y, Burkart-Waco D, Zhou CJ. [published ahead of print July 4 2022].  Development. 2022.
Nucleolin loss of function leads to aberrant Fibroblast Growth Factor signaling and craniofacial anomalies
Dash S, Trainor PA. [published ahead of print June 29 2022]. Development. 2022;149.
Original Data
A nucleation barrier spring-loads the CBM signalosome for binary activation
Rodriguez Gama A, Miller T, Lange JJ, Unruh JR, Halfmann R. eLife. 2022;11:e79826. doi: 10.7554/eLife.79826.
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Liver-derived cell lines from cavefish Astyanax mexicanus as an in vitro model for studying metabolic adaptation
Krishnan J, Wang Y, Kenzior O, Hassan H, Olsen L, Tsuchiya D, Kenzior A, Peuss R, Xiong S, Wang Y, Zhao C, Rohner N. Sci Rep. 2022;12:10115. doi: 10110.11038/s41598-10022-14507-10110.
Original Data
The architecture and operating mechanism of a cnidarian stinging organelle​
Karabulut A, McClain M, Rubinstein B, Sabin KZ, McKinney SA, Gibson MC. Nat Commun. 2022;13:3494. doi: 10.1038/s41467-41022-31090.
Original Data
Molecular characterization of a flatworm Girardia isolate from Guanajuato, Mexico
Duncan EM, Nowotarski SH, Guerrero-Hernandez C, Ross EJ, D'Orazio JA, Clubes de Ciencia Mexico Workshop for Developmental B. [published ahead of print June 17 2022]. Dev Biol 2022.
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The metabolome of Mexican cavefish shows a convergent signature highlighting sugar, antioxidant, and Ageing-Related metabolites
Medley JK, Persons J, Biswas T, Olsen L, Peuss R, Krishnan J, Xiong S, Rohner N. eLife. 2022;11:e74539. doi: 74510.77554/eLife.74539.
Original Data
Nature of the Poynting Vector Field Singularities in Resonant Light Scattering by Nanoparticles
Tribelsky MI, Rubinstein BY. Nanomaterials (Basel). 2022;12:1878. doi: 1810.3390/nano12111878.
Mediator recruits the cohesin loader Scc2 to RNA Pol II transcribed genes and promotes sister chromatid cohesion
Mattingly M, Seidel C, Munoz S, Hao Y, Zhang Y, Wen Z, Florens L, Uhlmann F, Gerton JL. [published ahead of print June 3 2022]. Curr Biol. 2022;32.
Original Data
Island-specific evolution of a sex-primedautosome in a sexual planarian
Guo L, Bloom JS, Dols-Serrate D, Boocock J, Ben-David E, Schubert OT, Kozuma K, Ho K, Warda E, Chui C, Wei Y, Leighton D, Lemus Vergara T, Riutort M, Sánchez Alvarado A, Kruglyak L. [published ahead of print June 1 2022]. Nature. 2022;606:329-334.
The 3′ Pol II pausing at replication-dependenthistone genes is regulated by Mediator throughCajal bodies’ association with histone locus bodies
Suzuki H, Abe R, Shimada M, Hirose T, Hirose H, Noguchi K, Ike Y, Yasui N, Furugori K, Yamaguchi Y, Toyoda A, Suzuki Y, Yamamoto T, Saitoh N, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Takahashi H. Nat Commun. 2022;13:2905. doi: 2910.1038/s41467-41022-30632-w.
Hmx gene conservation identifies the origin of vertebrate cranial ganglia
Papadogiannis V, Pennati A, Parker HJ, Rothbacher U, Patthey C, Bronner ME, Shimeld SM. [published ahead of print May 19 2022]. Nature. 2022.
Original Data
Genome-wide analysis of cis-regulatory changes in the metabolic adaptation of cavefish
Krishnan J, Seidel CW, Zhang N, Singh NP, VanCampen J, Peuss R, Xiong S, Kenzior A, Li H, Conaway JW, Rohner N. Nat Genet. 2022;54:684-693.
Original Data
UBAP2/UBAP2L regulate UV-induced ubiquitylation of RNA polymerase II and are the human orthologues of yeast Def1
Herlihy AE, Boeing S, Weems JC, Walker J, Dirac-Svejstrup AB, Lehner MH, Conaway RC, Conaway JW, Svejstrup JQ. DNA Repair (Amst). 2022;115:103343. doi: 103310.101016/j.dnarep.102022.103343.
Original Data
In-depth Satellitome Analyses of 37 Drosophila species illuminate repetitive DNA evolution in the Drosophila genus
de Lima LG, Ruiz-Ruano FJ. Genome Biol Evol. [published ahead of print May 6 2022]. 2022.
Original Data
Robust and sensitive in situ RNA detection method using Yn-situ
Wu Y, Xu W, Yu Z, Wang Y, Yu CR. Cell Rep Methods. 2022;2:100201. doi: 100210.101016/j.crmeth.102022.100201.
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Lack of VMP1 Impairs Hepatic Lipoprotein Secretion and Promotes Nonalcoholic Steatohepatitis
Jiang X, Fulte S, Deng F, Chen S, Xie Y, Chao X, He XC, Zhang Y, Li T, Li F, McCoin C, Morris EM, Thyfault J, Liu W, Li L, Davidson NO, Ding WX, Ni HM. Lack of VMP1 Impairs Hepatic Lipoprotein Secretion and Promotes Nonalcoholic Steatohepatitis. [Published ahead of print April 23 2022]. J Hepatol. 2022.
Maximal Dependence Capturing as a Principle of Sensory Processing
Raj R, Dahlen D, Duyck K, Yu CR. Front Comput Neurosci. 2022;16:857653.
Enhanced lipogenesis through Ppary helps cavefish adapt to food scarcity
Xiong S, Wang W, Kenzior A, Olsen L, Krishnan J, Persons J, Medley K, Peuss R, Wang Y, Chen S, Zhang N, Thomas N, Miles JM, Sánchez Alvarado A, Rohner N. [published ahead of print April 8 2022].Curr Biol. 2022.
Original Data
Complete genomic and epigenetic maps of human centromeres
Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. [published ahead of print April 1 2022]. Science. 2022;376:eabl4178.
Original Data
The complete sequence of a human genome
Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sovic I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. Science. 2022;376:44-53.
Original Data
From telomere to telomere: The transcriptional and epigenetic state of human repeat elements
Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, Olson D, Rosen J, Smit AFA, Straight AF, Vollger MR, Wheeler TJ, Schatz MC, Eichler EE, Phillippy AM, Timp W, Miga KH, O'Neill RJ. [published ahead of print April 1 2022]. Science. 2022;376:eabk3112.
Original Data
Quantitative analysis of nuclear pore complex organization in Schizosaccharomyces pombe
Varberg JM, Unruh JR, Bestul AJ, Khan AA, Jaspersen SL. [published ahead of print April 1 2022]. Life Sci Alliance. 2022;5:e202201423. doi: 10.26508/lsa.202201423
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H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function
Li J, Bergmann L, Rafael de Almeida A, Webb KM, Gogol MM, Voigt P, Liu Y, Liang H, Smolle MM. Nucleic Acids Res. 2022;50:2549-2565.
Original Data
Single-cell transcriptome analysis reveals three sequential phases of gene expression during zebrafish sensory hair cell regeneration
Baek S, Tran NTT, Diaz DC, Tsai YY, Acedo JN, Lush ME, Piotrowski T. [published ahead of print 3-28-2022]. Dev Cell. 2022;57:1-21. doi: 10.1016/j.devcel.2022.1003.1001.
Original Data
Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum
Hollin T, Abel S, Falla A, Pasaje CFA, Bhatia A, Hur M, Kirkwood JS, Saraf A, Prudhomme J, de Souza A, Florens L, Niles JC, Le Roch KG. Nat Commun. 2022;13:1275. doi: 1210.1038/s41467-41022-28981-41467.
Original Data
A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function in telomerase biogenesis
Paez-Moscoso DJ, Ho DV, Pan L, Hildebrand K, Jensen KL, Levy MJ, Florens L, Baumann P. Nat Commun. 2022;13:1067. doi: 1010.1038/s41467-41022-28545-41469.
Original Data
MPTAC links alkylation damage signaling to sterol biosynthesis
Suganuma T, Workman JL. Redox Biol. 2022;51:102270. doi: 102210.101016/j.redox.102022.102270.
Original Data
Cytidine acetylation yields a hypoinflammatory synthetic messenger RNA
Nance KD, Gamage ST, Alam MM, Yang A, Levy MJ, Link CN, Florens L, Washburn MP, Gu S, Oppenheim JJ, Meier JL. Cell Chem Biol. 2022;29:312-320 e317.
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Hybridization underlies localized trait evolution in cavefish
Moran RL, Jaggard JB, Roback EY, Kenzior A, Rohner N, Kowalko JE, Ornelas-Garcia CP, McGaugh SE, Keene AC. iScience. 2022;25:103778. doi: 103710.101016/j.isci.102022.103778.
Cell Sorter Cleaning Practices and Their Impact on Instrument Sterility
Box A, Holmes L, DeLay M, Adams D, Bergeron A, Clise-Dwyer K, Cochran M, del Rio Guerra R, Handley M, Meyer M, Meyer EM, Saluk A, Brundage K.  J Biomol Tech (JBT). 2022;33:e2675d2674. doi: 2610.7171/2673fc2671f2675fe.e2675d2674.
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MOCS2 links nucleotide metabolism to nucleoli function
Suganuma T, Swanson SK, Gogol M, Garrett TJ, Florens L, Workman JL. J Mol Cell Biol. 2022;13:838-840.
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Impact of cilia-related genes on mitochondrial dynamics during Drosophila spermatogenesis
Bauerly E, Akiyama T, Staber C, Yi K, Gibson MC. Dev Biol. 2022;482:17-27.
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A High-throughput Automated ELISA Assay for Detection of IgG Antibodies to the SARS-CoV-2 Spike Protein
Conkright-Fincham J, Tomomori-Sato C, McGhee R, Leslie EM, Beucher CJ, Weems LE, Sato S, Redwine WB, Weaver KJ, Miller BD, Delventhal KM, Kary JJ, Koebbe AB, Dean A, Witt JL, Remy LM, Parmely TJ, Zhao C, Wang Y, Conaway JW, Unruh JR. Bio-protocol. 2022;12:e4301. doi: 4310.21769/BioProtoc.24301.
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Single-cell reconstruction with spatial context of migrating neural crest cells and their microenvironments during vertebrate head and neck formation
Morrison JA, McLennan R, Teddy JM, Scott AR, Kasemeier-Kulesa JC, Gogol MM, Kulesa PM. Development. 2021;148:dev19468. doi: 19410.11242/dev.199468.
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Retinoic Acid Deficiency Underlies the Etiology of Midfacial Defects
Wu Y, Kurosaka H, Wang Q, Inubushi T, Nakatsugawa K, Kikuchi M, Ohara H, Tsujimoto T, Natsuyama S, Shida Y, Sandell LL, Trainor PA, Yamashiro T. J Dent Res. 2022:220345211062049.
PCR amplicons to determine human centromeric array copy number reveal wide-spread size variation and instability in cancer
de Lima LG, Howe E, Singh VP, Potapova T, Li H, Xu B, Castle J, Crozier S, Harrison CJ, Clifford SC, Miga KH, Ryan SL, Gerton JL. Cell Genom. 2022;1:100064. doi: 10.1016/j.xgen.2021.100064.
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Comprehensive Structure and Functional Adaptations of the Yeast Nuclear Pore Complex
Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP. Cell. 2022;185:361-378 e325.
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Optimized CRISPR-RfxCas13d system for RNA targeting in zebrafish embryos
Hernandez-Huertas L, Kushawah G, Diaz-Moscoso A, Tomas-Gallardo L, Moreno-Sanchez I, da Silva Prescador G, Bazzini AA, Moreno-Mateos MA. STAR-Protocol. 2022;3:101058.  doi: 10.1016/j.xpro.2021.101058..
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Reviews, Commentaries, Chapters or Books
Drug Resistance and Evolvability in an Emerging Human Fungal Pathogen
Billmyre RB. mBio. 2022:e0187622 doi: 10.1128/mbio.01876-22.
Poor eyesight reveals a new vision gene
Biswas T, Krishnan J, Rohner N. eLife. 2022;11 doi: 10.7554/eLife.81520.
p57Kip2 indirectly regulates AGM HSCs
Mao X, Li L. Blood. 2022;140:411-412.
What can we learn from selfish loci that break Mendel's law?
Zanders SE. PLoS Biol. 2022;20:e3001700. doi: 10.1371/journal.pbio.3001700.
Standardized annotation of translated open reading frames
Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Alba MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S. Nat Biotechnol. 2022;40:994-999.
Beyond Moco Biosynthesis-Moonlighting Roles of MoaE and MOCS2
Suganuma T. Molecules. 2022;27:3733. doi: 3710.3390/molecules27123733.
Diversification and Functional Evolution of HOX Proteins
Singh NP, Krumlauf R. Front Cell Dev Biol. 2022;10:798812. doi: 798810.793389/fcell.792022.798812.
Developmental biology is poised to discover altogether new principles in biology in the 21st century
Sánchez Alvarado A. Dev Biol. 2022;488:47-53.
RNA Polymerases I and III in development and disease
Watt KE, Macintosh J, Bernard G, Trainor PA. [published ahead of print April 16 2022]. Semin Cell Dev Biol. 2022.
Split-GFP Complementation to Study the Nuclear Membrane Proteome Using Microscopy
Shelton SN, Smith SE, Jaspersen SL. In: MW Goldberg, ed. Methods Mol Biol 2022/04/13 ed. New York, NY: Humana; 2022;2502 205-213.
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Heat Therapy Can Improve Hepatic Mitochondrial Function and Glucose Control
Johnson CN, Jensen RS, Von Schulze AT, Geiger PC. [published ahead of print April 9 2022]. Exerc Sport Sci Rev. 2022.
Schmidtea happens:Re-establishing the planarian as a model for studying the mechanisms of regeneration
Newmark PA, Sánchez Alvarado A. Curr Top Dev Biol. 2022;147:307-344.
Epithelial to mesenchymal transition during mammalian neural crest cell delamination
Zhao R, Trainor P. Epithelial to mesenchymal transition during mammalian neural crest cell delamination. [published ahead of print March 9 2022]. Semin Cell Dev Biol. 2022.
Cornelia de Lange syndrome and the Cohesin complex: Abstracts from the 9th Biennial Scientific and Educational Virtual Symposium 2020
Oliver C, Groves L, Hansen BD, Salehi M, Kheradmand S, Carrico CS, Caudill P, Mattingly M, Dorsett D, Chea S, Singh VP, Krantz ID, Huisman S, Deardorff MA, Kline AD. Abstracts from the 9th Biennial Scientific and Educational Virtual Symposium 2020. Am J Med Genet A. 2022;188A:1005-1014.
Standardized Statement for the Ethical Use of Human Cadaveric Tissues in Anatomy Research Papers: Recommendations from Anatomical Journal Editors-in-Chief
Iwanaga J, Singh V, Takeda S, Ogeng'o J, Kim HJ, Morys J, Ravi KS, Ribatti D, Trainor PA, Sanudo JR, Apaydin N, Sharma A, Smith HF, Walocha JA, Hegazy AMS, Duparc F, Paulsen F, Del Sol M, Adds P, Louryan S, Fazan VPS, Boddeti RK, Tubbs RS. Clin Anat. 2022;35:526-528.
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YTHDF3 as a new player in hematopoietic stem cell regulation
Mao X, Li L. [published ahead of print February 4 2022].  Haematologica. 2022.
Superresolution Microscopy for Visualization of Physical Contacts Between Chromosomes at Nanoscale Resolution
Yu Z, Potapova TA. Methods Mol Biol. 2022;2458:359-375.
Live Imaging of the Dynamics of Mammalian Neural Crest Cell Migration
Moore EL, Trainor PA. Methods Mol Biol. 2022;2403:263-276.
Time to synchronize our clocks: Connecting developmental mechanisms and evolutionary consequences of heterochrony
Dobreva MP, Camacho J, Abzhanov A. J Exp Zool Pt B, Mol Dev Evol. 2022;338:87-106.
Transcriptional regulation and implications for controlling Hox gene expression
Afzal Z, Krumlauf R. J Dev Biol. 2022;10:4. doi: 10.3390/jdb10010004.
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