Qing Liu, Qin Wang, Weixian Deng, Xu Wang, Mingxin Piao, Dawei Cai, Yaxing Li, William D. Barshop, Xiaolan Yu, Tingting Zhou, Bin Liu, Yoshito Oka, James Wohlschlegel, Zecheng Zuo and Chentao Lin.(2017) Molecular basis for blue light-dependent phosphorylation of Arabidopsis cryptochrome 2 Nature Communications doi:10.1038/ncomms15234.

Harris CJ, Husmann D, Liu W, Kasmi FE, Wang H, Papikian A, Pastor WA, Moissiard G, Vashisht AA, Dang JL, Wohlschlegel JA, Jacobsen SE. (2016) Arabidopsis AtMORC4 and AtMORC7 Form Nuclear Bodies and Repress a Large Number of Protein-Coding Genes PLOS Genetics doi:10.1371/journal.pgen.1005998.

Beck Josh R, Fung Connie, Straub Kurtis W, Coppens Isabelle, Vashisht Ajay A, Wohlschlegel James A, Bradley Peter J.(2013) A Toxoplasma Palmitoyl Acyl Transferase and the Palmitoylated Armadillo Repeat Protein TgARO Govern Apical Rhoptry Tethering and Reveal a Critical Role for the Rhoptries in Host Cell Invasion but Not Egress PLoS pathogens 9(2): e1003162.

Kim Myoung Shin, Machida Yuka, Vashisht Ajay A, Wohlschlegel James A, Pang Yuan-Ping, Machida Yuichi J.(2013) Regulation of error-prone translesion synthesis by Spartan/C1orf124 Nucleic acids research 41(3): 1661-1668.
Thivierge Caroline, Makil Neetha, Flamand Mathieu, Vasale Jessica J, Mello Craig C, Wohlschlegel James, Conte Darryl, Duchaine Thomas F .(2013) Tudor domain ERI-5 tethers an RNA-dependent RNA polymerase to DCR-1 to potentiate endo-RNAi Nature structural & molecular biology 20(2): 244.
Du Jiamu, Zhong Xuehua, Bernatavichute Yana V, Stroud Hume, Feng Suhua, Caro Elena, Vashisht Ajay A, Terragni Jolyon, Chin Hang Gyeong, Tu Andy, Hetzel Jonathan, Wohlschlegel James A, Pradhan Sriharsa, Patel Dinshaw J, Jacobsen Steven E .(2012) Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants Cell  151(1): 167-180.
Nie Minghua, Aslanian Aaron, Prudden John, Heideker Johanna, Vashisht Ajay A, Wohlschlegel James A, Yates John R, Boddy Michael N.(2012) Dual recruitment of Cdc48 (p97)-Ufd1-Npl4 ubiquitin-selective segregase by small ubiquitin-like modifier protein (SUMO) and ubiquitin in SUMO-targeted ubiquitin ligase-mediated genome stability functions The Journal of biological chemistry 287(35): 29610-29619.
Ausin Israel, Greenberg Maxim V C, Simanshu Dhirendra K, Hale Christopher J, Vashisht Ajay A, Simon Stacey A, Lee Tzuu-fen, Feng Suhua, Española Sophia D, Meyers Blake C, Wohlschlegel James A, Patel Dinshaw J, Jacobsen Steven E .(2012) INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis  Proceedings of the National Academy of Sciences of the United States of America 109(22): 8374-8381.
Stehling Oliver, Vashisht Ajay A, Mascarenhas Judita, Jonsson Zophonias O, Sharma Tanu, Netz Daili J A, Pierik Antonio J, Wohlschlegel James A, Lill Roland.(2012) MMS19 assembles iron-sulfur proteins required for DNA metabolism and genomic integrity Science 337(6091): 195-199.  
Chen Xiao-Fen, Lehmann Lynn, Lin Justin J, Vashisht Ajay, Schmidt Ryan, Ferrari Roberto, Huang Chengyang, McKee Robin, Mosley Amber, Plath Kathrin, Kurdistani Siavash K, Wohlschlegel James, Carey Michael.(2012) Mediator and SAGA have distinct roles in Pol II preinitiation complex assembly and function Cell reports 2(5): 1061-1067.
Lehmann Lynn, Ferrari Roberto, Vashisht Ajay A, Wohlschlegel James A, Kurdistani Siavash K, Carey Michael .(2012) Polycomb repressive complex 1 (PRC1) disassembles RNA polymerase II preinitiation complexes The Journal of biological chemistry 287(43): 35784-35794.
Caro Elena, Stroud Hume, Greenberg Maxim V C, Bernatavichute Yana V, Feng Suhua, Groth Martin, Vashisht Ajay A, Wohlschlegel James, Jacobsen Steve E.(2012) The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation-independent manner PLoS genetics 8(10): e1002995.
Thivierge Caroline, Makil Neetha, Flamand Mathieu, Vasale Jessica J, Mello Craig C, Wohlschlegel James, Conte Darryl, Duchaine Thomas F.(2012) Tudor domain ERI-5 tethers an RNA-dependent RNA polymerase to DCR-1 to potentiate endo-RNAi Nature structural & molecular biology 19(1): 90-97.
Sun Yu, Vashisht Ajay A, Tchieu Jason, Wohlschlegel James A, Dreier Lars.(2012) Voltage-dependent anion channels (VDACs) recruit Parkin to defective mitochondria to promote mitochondrial autophagy The Journal of biological chemistry 287(48): 40652-40660.
Oberholzer Michael, Langousis Gerasimos, Nguyen HoangKim T, Saada Edwin A, Shimogawa Michelle M, Jonsson Zophonias O, Nguyen Steven M, Wohlschlegel James A, Hill Kent L .(2011) Independent analysis of the flagellum surface and matrix proteomes provides insight into flagellum signaling in mammalian-infectious Trypanosoma brucei   Molecular & cellular proteomics : MCP 10(10): M111.010538.
Lin Justin J, Lehmann Lynn W, Bonora Giancarlo, Sridharan Rupa, Vashisht Ajay A, Tran Nancy, Plath Kathrin, Wohlschlegel James A, Carey Michael.(2011) Mediator coordinates PIC assembly with recruitment of CHD1  Genes & development 25(20): 2198-2209.
Smith Alias J, Chudnovsky Lorissa, Simoes-Barbosa Augusto, Delgadillo-Correa Maria G, Jonsson Zophonias O, Wohlschlegel James A, Johnson Patricia J.(2011) Novel core promoter elements and a cognate transcription factor in the divergent unicellular eukaryote Trichomonas vaginalis  Molecular and cellular biology 31(7): 1444-1458.
Lomenick Brett, Jung Gwanghyun, Wohlschlegel James A, Huang Jing.(2011) Target identification using drug affinity responsive target stability (DARTS)  Current protocols in chemical biology 3(4): 163-180.
Law Julie A, Ausin Israel, Johnson Lianna M, Vashisht Ajay A, Zhu Jian-Kang, Wohlschlegel James A, Jacobsen Steven E .(2010) A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in plants  Current biology 20(10): 951-956.
Spielewoy Nathalie, Guaderrama Marisela, Wohlschlegel James A, Ashe Mabelle, Yates John R, Wittenberg Curt.(2010) Npr2, yeast homolog of the human tumor suppressor NPRL2, is a target of Grr1 required for adaptation to growth on diverse nitrogen sources  Eukaryotic cell 9(4): 592-601.
de Miguel Natalia, Lustig Gil, Twu Olivia, Chattopadhyay Arnab, Wohlschlegel James A, Johnson Patricia J.(2010) Proteome analysis of the surface of Trichomonas vaginalis reveals novel proteins and strain-dependent differential expression  Molecular & cellular proteomics  9(7): 1554-1566.
Hernandez Alfredo, Madina Bhaskara Reddy, Ro Kevin, Wohlschlegel James A, Willard Belinda, Kinter Mike T, Cruz-Reyes Jorge.(2010) REH2 RNA helicase in kinetoplastid mitochondria: ribonucleoprotein complexes and essential motifs for unwinding and guide RNA (gRNA) binding  The Journal of biological chemistry 285(2): 1220-1228.
Vashisht Ajay A, Zumbrennen Kimberly B, Huang Xinhua, Powers David N, Durazo Armando, Sun Dahui, Bhaskaran Nimesh, Persson Anja, Uhlen Mathias, Sangfelt Olle, Spruck Charles, Leibold Elizabeth A, Wohlschlegel James A.(2009) Control of iron homeostasis by an iron-regulated ubiquitin ligase  Science 326(5953): 718-721.
Konopka Genevieve, Bomar Jamee M, Winden Kellen, Coppola Giovanni, Jonsson Zophonias O, Gao Fuying, Peng Sophia, Preuss Todd M, Wohlschlegel James A, Geschwind Daniel H.(2009) Human-specific transcriptional regulation of CNS development genes by FOXP2  Nature  (7270): 213-217.
Wohlschlegel James A.(2009) Identification of SUMO-conjugated proteins and their SUMO attachment sites using proteomic mass spectrometry  Methods in molecular biology  497(5): 33-49.
Chuang Li-Chiou, Teixeira Leonardo K, Wohlschlegel James A, Henze Martha, Yates John R, Méndez Juan, Reed Steven I.(2009) Phosphorylation of Mcm2 by Cdc7 promotes pre-replication complex assembly during cell-cycle re-entry  Molecular cell 35(2): 206-216.
Zhou Rui, Czech Benjamin, Brennecke Julius, Sachidanandam Ravi, Wohlschlegel James A, Perrimon Norbert, Hannon Gregory J.(2009) Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform  RNA 15(10): 1886-1895.
Lomenick Brett, Hao Rui, Jonai Nao, Chin Randall M, Aghajan Mariam, Warburton Sarah, Wang Jianing, Wu Raymond P, Gomez Fernando, Loo Joseph A, Wohlschlegel James A, Vondriska Thomas M, Pelletier Jerry, Herschman Harvey R, Clardy Jon, Clarke Catherine F, Huang Jing.(2009) Target identification using drug affinity responsive target stability (DARTS)  PNAS 106(51): 21984-21989.  
Machida Yuichi J, Machida Yuka, Vashisht Ajay A, Wohlschlegel James A, Dutta Anindya.(2009) The deubiquitinating enzyme BAP1 regulates cell growth via interaction with HCF-1 The Journal of biological chemistry 284(49): 34179-34188.
Zamudio Jesse R, Mittra Bidyottam, Chattopadhyay Arnab, Wohlschlegel James A, Sturm Nancy R, Campbell David A.(2009) Trypanosoma brucei spliced leader RNA maturation by the cap 1 2'-O-ribose methyltransferase and SLA1 H/ACA snoRNA pseudouridine synthase complex  Molecular and cellular biology 29(5): 1202-1211.
Bellare Priya, Small Eliza C, Huang Xinhua, Wohlschlegel James A, Staley Jonathan P, Sontheimer Erik J.(2008) A role for ubiquitin in the spliceosome assembly pathway  Nature structural & molecular biology 15(5): 444-451.
Czech Benjamin, Malone Colin D, Zhou Rui, Stark Alexander, Schlingeheyde Catherine, Dus Monica, Perrimon Norbert, Kellis Manolis, Wohlschlegel James A, Sachidanandam Ravi, Hannon Gregory J, Brennecke Julius.(2008) An endogenous small interfering RNA pathway in Drosophila  Nature 453(7196): 798-802.
Usaite Renata, Wohlschlegel James, Venable John D, Park Sung K, Nielsen Jens, Olsson Lisbeth, Yates Iii John R.(2008) Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods Journal of proteome research 7(1): 266-275.
Reed Darien E, Huang Xinhua M, Wohlschlegel James A, Levine Michael S, Senger Kate.(2008) DEAF-1 regulates immunity gene expression in Drosophila PNAS 105(24): 8351-8356.
Olson Brian L, Hock M Benjamin, Ekholm-Reed Susanna, Wohlschlegel James A, Dev Kumlesh K, Kralli Anastasia, Reed Steven I.(2008) SCFCdc4 acts antagonistically to the PGC-1alpha transcriptional coactivator by targeting it for ubiquitin-mediated proteolysis  Genes & development 22(2): 252-264.
Simoes-Barbosa Augusto, Meloni Dionigia, Wohlschlegel James A, Konarska Maria M, Johnson Patricia J.(2008) Spliceosomal snRNAs in the unicellular eukaryote Trichomonas vaginalis are structurally conserved but lack a 5'-cap structure  RNA 14(8): 1617-1631.
Motoyama Akira, Xu Tao, Ruse Cristian I, Wohlschlegel James A, Yates John R.(2007) Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides  Analytical chemistry 79(10): 3623-3634.
Zhu Wenge, Ukomadu Chinweike, Jha Sudhakar, Senga Takeshi, Dhar Suman K, Wohlschlegel James A, Nutt Leta K, Kornbluth Sally, Dutta Anindya.(2007) Mcm10 and And-1/CTF4 recruit DNA polymerase alpha to chromatin for initiation of DNA replication  Genes & development 21(18): 2288-2299.
Venable John D, Wohlschlegel James, McClatchy Daniel B, Park Sung Kyu, Yates John R.(2007) Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer  Analytical chemistry 79(8): 3056-3064.
Sadygov, R. Wohlschlegel, J. Park, S. K. Xu, T. Yates, J. R., 3rd.(2006) Central limit theorem as an approximation for intensity-based scoring function  Anal Chem 78(1): 89-95.
De Bruin, R. A. Kalashnikova, T. I. Chahwan, C. McDonald, W. H. Wohlschlegel, J. Yates, J., 3rd Russell, P. Wittenberg, C.(2006) Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback Mol Cell 23(4): 483-496.
Duchaine, T. F. Wohlschlegel, J. A. Kennedy, S. Bei, Y. Conte, D., Jr. Pang, K. Brownell, D. R. Harding, S. Mitani, S. Ruvkun, G. Yates, J. R., 3rd Mello, C. C.(2006) Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways  Cell 124(2): 343-354.
Wohlschlegel, J. A. Johnson, E. S. Reed, S. I. Yates, J. R., 3rd.(2006) Improved identification of SUMO attachment sites using C-terminal SUMO mutants and tailored protease digestion strategies  J Proteome Res 5(4): 761-770.
Raffa Grazia D, Wohlschlegel James, Yates John R, Boddy Michael N.(2006) SUMO-binding motifs mediate the Rad60-dependent response to replicative stress and self-association  The Journal of biological chemistry 281(38): 27973-27981.
Sedgwick, C. Rawluk, M. Decesare, J. Raithatha, S. Wohlschlegel, J. Semchuk, P. Ellison, M. Yates, J. Stuart, D.(2006) Saccharomyces cerevisiae Ime2 phosphorylates Sic1 at multiple PXS/T sites but is insufficient to trigger Sic1 degradation  Biochem J 399(1): 151-160.
Raffa, G. D. Wohlschlegel, J. Yates, J. R., 3rd Boddy, M. N.(2006) Sumo-binding motifs mediate the RAD60-dependent response to replicative stress and self association  J Biol Chem 281(38):27973-27981.
Martin, V. Chahwan, C. Gao, H. Blais, V. Wohlschlegel, J. Yates, J. R., 3rd McGowan, C. H. Russell, P.(2006) Sws1 is a conserved regulator of homologous recombination in eukaryotic cells  Embo J 25(11): 2564-2574.
Pebernard, S. Wohlschlegel, J. McDonald, W. H. Yates, J. R., 3rd Boddy, M. N.(2006) The Nse5-Nse6 dimer mediates DNA repair roles of the Smc5-Smc6 complex  Mol Cell Biol 26(5): 1617-1630.
Ernkvist, M. Aase, K. Ukomadu, C. Wohlschlegel, J. Blackman, R. Veitonmaki, N. Bratt, A. Dutta, A. Holmgren, L.(2006) p130-angiomotin associates to actin and controls endothelial cell shape  Febs J 273(9): 2000-2011.
Liu, J. Rivas, F. V. Wohlschlegel, J. Yates, J. R., 3rd Parker, R. Hannon, G. J.(2005) A role for the P-body component GW182 in microRNA function  Nat Cell Biol 7(12): 1261-1266.
Kaiser, P. Wohlschlegel, J.(2005) Identification of ubiquitination sites and determination of ubiquitin-chain architectures by mass spectrometry  Methods Enzymol 399: 266-277.
Venable, J. D. Dong, M. Q. Wohlschlegel, J. Dillin, A. Yates, J. R.(2004) Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra  Nat Methods  1(1): 39-45.
Wohlschlegel, J. A. Johnson, E. S. Reed, S. I. Yates, J. R., 3rd.(2004) Global analysis of protein sumoylation in Saccharomyces cerevisiae  J Biol Chem 279(44): 45662-45668.
Flick, K. Ouni, I. Wohlschlegel, J. A. Capati, C. McDonald, W. H. Yates, J. R. Kaiser, P.(2004) Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain  Nat Cell Biol 6(7): 634-641.
Jonsson, Z. O. Jha, S. Wohlschlegel, J. A. Dutta, A.(2004) Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex  Mol Cell 16(3): 465-477.
Wohlschlegel, J. A. Yates, J. R.(2003) Proteomics: where's Waldo in yeast?  Nature 425(6959): 671-672.
Wohlschlegel, J. A. Kutok, J. L. Weng, A. P. Dutta, A.(2002) Expression of geminin as a marker of cell proliferation in normal tissues and malignancies  Am J Pathol 161(1): 267-273.
Wohlschlegel, J. A. Dhar, S. K. Prokhorova, T. A. Dutta, A. Walter, J. C.(2002) Xenopus Mcm10 binds to origins of DNA replication after Mcm2-7 and stimulates origin binding of Cdc45  Mol Cell 9(2): 233-240.
Takeda, D. Y. Wohlschlegel, J. A. Dutta, A.(2001) A bipartite substrate recognition motif for cyclin-dependent kinases  J Biol Chem 276(3): 1993-1997.
Wohlschlegel, J. A. Dwyer, B. T. Takeda, D. Y. Dutta, A.(2001) Mutational analysis of the Cy motif from p21 reveals sequence degeneracy and specificity for different cyclin-dependent kinases  Mol Cell Biol 21(15): 4868-4874.
Dhar, S. K. Yoshida, K. Machida, Y. Khaira, P. Chaudhuri, B. Wohlschlegel, J. A. Leffak, M. Yates, J. Dutta, A.(2001) Replication from oriP of Epstein-Barr virus requires human ORC and is inhibited by geminin  Cell 106(3): 287-296.
Wohlschlegel, J. A. Dwyer, B. T. Dhar, S. K. Cvetic, C. Walter, J. C. Dutta, A.(2000) Inhibition of eukaryotic DNA replication by geminin binding to Cdt1  Science 290(5500): 2309-2312.
Pinto, S. Quintana, D. G. Smith, P. Mihalek, R. M. Hou, Z. H. Boynton, S. Jones, C. J. Hendricks, M. Velinzon, K. Wohlschlegel, J. A. Austin, R. J. Lane, W. S. Tully, T. Dutta, A.(1999) latheo encodes a subunit of the origin recognition complex and disrupts neuronal proliferation and adult olfactory memory when mutant  Neuron 23(1): 45-54.
Garza, A. G. Biran, R. Wohlschlegel, J. A. Manson, M. D.(1996) Mutations in motB suppressible by changes in stator or rotor components of the bacterial flagellar motor  J Mol Biol 258(2): 270-285.