Maurizio, P.L., Ferris, M.T., Keele, G.R., Miller, D.R., Shaw, G.D., Whitmore, A.C., West, A., Morrison, C.R., Noll, K.E., Plante, K.S., Cockrell, A.S., Threadgill, D.W., Pardo-Manuel de Villena, F., Baric, R.S., Heise, M.T. & Valdar, W. 2018. Bayesian diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice. G3 | Genes, Genomes, Genetics, 8(2): 427-445. 10.1534/g3.117.300438.  PMID:29187420.

Turner, S.D., Maurizio, P.L., Valdar, W., Yandell, B. & Simon, P. 2018. Dissecting the genetic architecture of shoot growth in carrot (Daucus carota L.) using a diallel mating design. G3 | Genes, Genomes, Genetics, 8(2): 411-426. 10.1534/g3.117.300235. PMID:29187419.
Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, Wang K, Devescovi G, Stillman K, Monteiro F, Rangel Alvarez B, Lundberg DS, Lu TY, Lebeis S, Jin Z, McDonald M, Klein AP, Feltcher ME, Rio TG, Grant SR, Doty SL, Ley RE, Zhao B, Venturi V, Pelletier DA, Vorholt JA, Tringe SG, Woyke T, Dangl JL. Genomic features of bacterial adaptation to plants. Nat Genet. 2018 Jan;50(1):138-150. doi: 10.1038/s41588-017-0012-9. Epub 2017 Dec 18. PMID: 29255260 DOI:10.1038/s41588-017-0012-9


Maurizio PL, Ferris MT, Keele GR, Miller DR, Shaw GD, Whitmore AC, West A, Morrison CR, Noll KE, Plante KS, Cockrell AS, Threadgill DW, Pardo-Manuel de Villena F, Baric RS, Heise MT and Valdar W. 2017. Diallel analysis reveals Mx1-dependent and Mx1-independent effects on response to influenza A virus in mice. G3: Genes, Genomes, Genetics. (accepted). bioRxiv preprint: https://dx.doi.org/10.1101/214205

Turner SD, Maurizio PL, Valdar W, Yandell BS and Simon PW. 2017. Dissecting the genetic architecture of shoot growth in carrot (Daucus carota L.) using a diallel mating design. G3: Genes, Genomes, Genetics. (accepted). bioRxiv preprint: https://dx.doi.org/10.1101/115519

Keele GR, Prokop JW, Hong H, Holl K, Littrell J, Deal A, Francic S, Cui L, Gatti DM, Broman KW, Tschannen M, Tsaih SW, Zagloul M, Kim Y, Baur B, Fox J, Robinson M, Levy S, Flister MJ, Mott R, Valdar W, Solberg Woods LC. Genetic fine-mapping and identification of candidate genes and variants for adiposity traits in outbred rats. Obesity. 2017 (Accepted). doi: 10.1002/oby.22075.

Kirk Grubbs, Rachel Bleich, Kevin Santa Maria, Scott Allen, Sherif Farag, AgBiome Team, Elizabeth Shank, and Albert Bowers. Large-scale bioinformatics analysis of Bacillus genomes uncovers conserved roles of natural products in bacterial physiology. Msystems, 2017

Corley M, Solem A, Phillips G, Lackey L, Ziehr B, Vincent HA, Mustoe AM, Ramos SBV, Weeks KM, Moorman NJ, Laederach A. An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression. Proc Natl Acad Sci U S A. 2017 Nov 6. pii: 201706539. doi: 10.1073/pnas.1706539114. [Epub ahead of print] PMID: 29109288 DOI: 10.1073/pnas.1706539114

Cancer Genome Atlas Research Network, Hepperla AJ. Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell. 2017 Nov 2;171(4):950-965.e28. PMID: 29100075 doi: 10.1016/j.cell.2017.10.014.

Hui Xiao Chao, Cere E. Poovey, Ashley A. Privette, Gavin D. Grant, Jean G. Cook, Hui Yan Chao, Jeremy E. Purvis. Orchestration of DNA Damage Checkpoint Dynamics across the Human Cell Cycle. (2017) Cell Systems. 2017 Oct 23. pii: S2405-4712(17)30436-2. doi: 10.1016/j.cels.2017.09.015. [Epub ahead of print]. PMID: 29102360

Donoghue LJ, Livraghi-Butrico A, McFadden KM, Thomas JM, Chen G, Grubb BR, O’Neal WK, Boucher RC, Kelada SN. Identification of trans Protein QTL for Secreted Airway Mucins in Mice and a Causal Role for Bpifb1. Genetics. 2017 Oct 1;207(2):801-12. doi: 10.1534/genetics.117.300211. PMID: 28851744 PMCID: PMC5629340 DOI: 10.1534/genetics.117.300211

Wang JR, Quach B, Furey TS. Correcting nucleotide-specific biases in high-throughput sequencing data. BMC Bioinformatics. 2017 Aug 1;18(1):357. doi: 10.1186/s12859-017-1766-x. PMID: 28764645 PMCID: PMC5540620 DOI: 10.1186/s12859-017-1766-x

McDaniel SL, Hepperla AJ, Huang J, Dronamraju R, Adams AT, Kulkarni VG, Davis IJ, Strahl BD. H3K36 Methylation Regulates Nutrient Stress Response in Saccharomyces cerevisiae by Enforcing Transcriptional Fidelity. Cell Reports. 2017 Jun 13;19(11):2371-2382. PMID: 28614721 PMCID: PMC5528882 doi: 10.1016/j.celrep.2017.05.057.

Oreper DGCai Y, Tarantino LM, Pardo-Manual de Villena F, Valdar W. Inbred Strain Variant Database (ISVdb): A repository for probabilistically informed sequence differences among the Collaborative Cross strains and their founders. G3 (Bethesda). 2017 Jun 7;7(6):1623-1630. doi: 10.1534/g3.117.041491. PMID: 28592645.

Woods, CT, Laederach, A. Classification of RNA structure change by ‘gazing’ at experimental data. Bioinformatics. 2017 Jun 1;33(11):1647-1655. doi: 10.1093/bioinformatics/btx041. PMID: 28130241 PMCID: PMC5447233

Quach B, Furey TS. DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter. Bioinformatics. 2017 Apr 1;33(7):956-963. doi: 10.1093/bioinformatics/btw740. PMID: 27993786 DOI: 10.1093/bioinformatics/btw740

Talkington A, Dantoin C, Durrett R. Ordinary Differential Equation Models for Adoptive Immunotherapy.  Bull Math Biol. 2017 Apr 5. doi: 10.1007/s11538-017-0263-8. [Epub ahead of print] PMID: 28382423 DOI: 10.1007/s11538-017-0263-8

Mosedale M, Kim Y, Brock WJ, Roth SE, Wiltshire T, Eaddy JS, Keele GR, Corty RW, Xie Y, Valdar W, Watkins P. Candidate risk factors and mechanisms for Tolvaptan-induced liver injury are indentified using a Collaborative Cross approach. Toxico Sci. 2017 Apr 1; 156(2):438-454. doi: 10.1093/toxsci/kfw269. PMID: 28115652.

Walsh DM, McCullough SD, Yourstone S, Jones SW, Cairns BA, Jones CD, Jaspers I, Diaz-Sanchez D.  Alterations in airway microbiota in patients with PaO2/FiO2 ratio ≤ 300 after burn and inhalation injury. PLoS One. 2017 Mar 30;12(3):e0173848. doi: 10.1371/journal.pone.0173848. eCollection 2017. PMID: 28358811 PMCID: PMC5373524 DOI: 10.1371/journal.pone.0173848

Turner, S., Maurizio, P. L., Valdar, W., Yandell, B., & Simon P. (2017) Dissecting the genetic architecture of shoot growth in carrot (Daucus carota L.) using a diallel mating design. G3 | Genes, Genomes, Genetics (accepted). bioRxiv preprint at: https://dx.doi.org/10.1101/115519

Maurizio, P. L. & Ferris, M.T. (2017). “The Collaborative Cross Resource for Systems Genetics Research of Infectious Diseases.” Methods in Molecular Biology: Systems Genetics – Methods and Protocols. Springer Science+Business Media, New York, NY. Klaus Schughart and Robert W. Williams (eds.) vol. 1488, pp579-596, eBook ISBN: 978-1-4939-6427-7, hardcover ISBN: 978-1-4939-6425-3. https://doi.org/10.1007/978-1-4939-6427-7_28


Gomez NC, Hepperla AJ, Dumitru R, Simon JM, Fang F, Davis IJ. Widespread Chromatin Accessibility at Repetitive Elements Links Stem Cells with Human Cancer. Cell Reports. 2016 Nov 1;17(6):1607-1620. PMID: 27806299 PMCID: PMC5267842 doi: 10.1016/j.celrep.2016.10.011.

Lackey P, Welch JD, Marzluff WM. TUT7 Catalyzes the Uridylation of the 3’ End of Histone mRNA for Rapid Degradation. RNA 2016 (in press).

Welch JD*, Williams LA*, DiSalvo M*, Brandt AT, Marayati R, Sims CE, Allbritton NL, Prins JF, Yeh JJ, Jones CD. Selective Single Cell Isolation for Genomics Using Microraft Arrays. Nucleic Acids Research 2016 (in press) *Equal contribution.

Mansouri K1, Abdelaziz A, Rybacka A, Roncaglioni A, Tropsha A, Varnek A, Zakharov A, Worth A, Richard AM, Grulke CM, Trisciuzzi D, Fourches D, Horvath D, Benfenati E, Muratov E, Wedebye EB, Grisoni F, Mangiatordi GF, Incisivo GM, Hong H, Ng HW, Tetko IV, Balabin I, Kancherla J, Shen J, Burton J, Nicklaus M, Cassotti M, Nikolov NG, Nicolotti O, Andersson PL, Zang Q, Politi R, Beger RD, Todeschini R, Huang R, Farag S, Rosenberg SA, Slavov S, Hu X, Judson RS. CERAPP: Collaborative Estrogen Receptor Activity Prediction Project. Environ Health Perspect. 2016 Jul;124(7):1023-33. doi: 10.1289/ehp.1510267. Epub 2016 Feb 23. PubMed PMID: 26908244.

Lyons SM, Cunningham CH, Welch JD, Groh B, Guo AY, Wei B, Whitfield ML, Xiong Y, Marzluff WF. A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues. Nucleic Acids Research 2016 July 8. doi: 10.1093/nar/gkw620 [PDF] PubMed PMID: 27402160.

Vinicius M. Alves, Eugene N. Muratov, Stephen J. Capuzzi,Regina Politi, Yen Low, Rodolpho C. Braga, Alexey V. Zakharov, Alexander Sedykh, Elena Mokshyna, Sherif Farag, Carolina H. Andrade, Victor E. Kuz’min, and Alexander Tropsha. Alarms about structural alerts. Green Chemistry, 2016 Aug 21;18(16):4348-4360. doi: 10.1039/C6GC01492E. Epub 2016 Jun 28.. PMID: 28503093 PMCID: PMC5423727 DOI: 10.1039/C6GC01492E

Taylor D, Shai S, Stanley N, Mucha PJ. “Enhanced detectability of community structure in multilayer networks through layer aggregation.” Physical Review Letters 2016 Jun 3; 116, no. 22 (2016): 228301. Epub 2016 Jun 2. PubMed PMID: 27314740.

Welch JD, Hartemink AJ, Prins JF. SLICER: Inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. Genome Biology 2016 May 23; 17:106 doi:10.1186/s13059-016-0975-3 [PDF] *Also accepted at RECOMB 2016 (doi: http://dx.doi.org/10.1101/047845 [PDF]) PubMed PMID: 27215581.

Welch JD, Hu Y, Prins JF. Robust Detection of Alternative Splicing in a Population of Single Cells. Nucleic Acids Research 2016 May 5; doi: 10.1093/nar/gkv1525 [PDF] Epub 2016 Jan 5. *Also accepted as a highlight at ISMB 2016. PubMed PMID: 26740580.

Lange EM, Ribado JV, Zuhlke KA, Johnson AM, Keele GR, Li J, Wang Y, Duan Q, Li G, Gao Z, Li Y, Xu J, Zheng SL, Cooney KA. Assessing the cumulative contribution of new and established common genetic risk factors to early-onset prostate cancer. Cancer Epidemiol Biomarkers Prev. 2016 May; 25(5): 766-72. doi: 10.1158/1055-9965.EPI-14-0995. PMID: 26671023. PMCID: PMC4873425

Stanley N, Shai S, Taylor D, Mucha PJ, “Clustering Network Layers with the Strata Multilayer Stochastic Block Model,” in IEEE Transactions on Network Science and Engineering, vol. 3, no. 2, pp. 95-105, April-June 1 2016. doi: 10.1109/TNSE.2016.2537545. 

Parry TL, Desai G, Schisler JC, Li L, Quintana MT, Stanley N, Lockyer P, Patterson C, Willis MS. “Fenofibrate unexpectedly induces cardiac hypertrophy in mice lacking MuRF1.” Cardiovascular Pathology 2016 Mar-Apr;25(2):127-40. doi: 10.1016/j.carpath.2015.09.008. Epub 2015 Oct 29. PubMed PMID: 26764147.

Kardos, J., Chai, S., Mose, L. E., Selitsky, S. R., Krishnan, B., Saito, R., … & Vincent, B. G. (2016). Claudin-low bladder tumors are immune infiltrated and actively immune suppressed. JCI Insight, 2016 Mar 17; 1(3): e85902. doi: 10.1172/jci.insight.85902.

Xu, Z., Zhang, G., Duan, Q., Chai, S., Zhang, B., Wu, C., … & Hu, M. (2016). HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. BMC research notes, 2016 Mar 11; 9(1), 1. PubMed PMID: 26969411.

Shobair, M., Dagliyan, O., Kota, P., Dang, Y. L., He, H., Stutts, M. J., & Dokholyan, N. V. (2016). Gain-of-function mutation W493R in the epithelial sodium channel allosterically reconfigures intersubunit couplingJournal of Biological Chemistry 2016 Feb 19; 291(8), 3682-3692. Paper of the Week. DOI: 10.1074/jbc.M115.678052 PubMed PMID: 26668308.

Capuzzi, SJ; Politi, R; Isayev, O; Farag, S; Tropsha, A , QSAR Modeling of Tox21 Challenge Stress Response and Nuclear Receptor Signaling Toxicity Assays. Frontiers in Environmental Science, 04 February 2016. PDF. https://doi.org/10.3389/fenvs.2016.00003.


Swanson CI, Meserve JH, McCarter PC, Thieme A, Mathew T, Elston TC, Duronio RJ. “Expression of an S phase-stabilized version of the CDK inhibitor Dacapo can alter endoreplication” Development: 2015 Dec 15; doi:10.1242/dev.115006. PubMed PMID 26493402.

Nagiec MJ, McCarter PC, Kelley JB, Dixit G, Elston TC, Dohlman HG.  “Signal inhibition by a dynamically-regulated pool of mono-phosphorylated MAPK” Mol. Biol. Cell 2015 Sep 15 26, 3359–3371. PubMed PMID: 26179917.

Lebeis SL, Herrera Paredes S, Lundberg DS, Breakfield N, Gehring J, McDonald M, et al. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science. 2015 Aug 21;349(6250):860–4. Available from: http://www.sciencemag.org/cgi/doi/10.1126/science.aaa8764 PubMed PMID: 26184915.

Coleman KE, Grant GD, Haggerty RA, Brantley K, Shibata E, Workman BD, Dutta A, Varma D, Purvis JE, Cook JG. Sequential replication-coupled destruction at G1/S ensures genome stability. Genes & Development 2015 Aug 15; 29(16):1734-46. doi: 10.1101/gad.263731.115 PubMed PMID: 26272819.

Herrera Paredes S, Lebeis SL. Giving back to the community: microbial mechanisms of plant-soil interactions. Bailey JK, editor. Funct Ecol. 2016 Jul;30(7):1043–52. Available from: http://doi.wiley.com/10.1111/1365-2435.12684

Morgan AP, Welsh CE. Informatics resources for the Collaborative Cross and related mouse populations. Mamm Genome. 2015 Jul 2. [Epub ahead of print] No abstract available. PubMed PMID: 26135136.

Solem AC, Halvorsen M, Ramos SB, Laederach A. The potential of the riboSNitch in personalized medicine. Wiley Interdiscip Rev RNA. 2015 Jun 26. doi: 10.1002/wrna.1291. [Epub ahead of print] PubMed PMID: 26115028.

Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y, Wang JR, Morgan AP, Calaway JD, Aylor DL, Yun Z, Bell TA, Buus RJ, Calaway ME, Didion JP, Gooch TJ, Hansen SD, Robinson NN, Shaw GD, Spence JS, Quackenbush CR, Barrick CJ, Nonneman RJ, Kim K, Xenakis J, Xie Y, Valdar W, Lenarcic AB, Wang W, Welsh CE, Fu CP, Zhang Z, Holt J, Guo Z, Threadgill DW, Tarantino LM, Miller DR, Zou F, McMillan L, Sullivan PF, de Villena FP. Corrigendum: Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nat Genet. 2015 May 27;47(6):690. doi: 10.1038/ng0615-690a. No abstract available. PubMed PMID: 26018903.

Welch JD, Slevin MK, Tatomer DC, Duronio RJ, Prins JF, Marzluff WF. EnD-Seq and AppEnD: sequencing 3′ ends to identify nontemplated tails and degradation intermediates. RNA. 2015 Jul;21(7):1375-89. doi: 10.1261/rna.048785.114. Epub 2015 May 26. PubMed PMID: 26015596.

Kutchko KM, Sanders W, Ziehr B, Phillips G, Solem A, Halvorsen M, Weeks KM, Moorman N, Laederach A. Multiple conformations are a conserved and regulatory feature of the RB1 5′ UTR. RNA. 2015 Jul;21(7):1274-85. doi: 10.1261/rna.049221.114. Epub 2015 May 21. PubMed PMID: 25999316.

Tsai YS, Dominguez D, Gomez SM, Wang Z. Transcriptome-wide identification and study of cancer-specific splicing events across multiple tumors. Oncotarget. 2015 Mar 30;6(9):6825-39. PubMed PMID: 25749525.

Xu Z, Duan Q, Yan S, Chen W, Li M, Lange E, Li Y. DISSCO: direct imputation of summary statistics allowing covariates. Bioinformatics. 2015 Mar 24. pii: btv168. [Epub ahead of print] PubMed PMID: 25810429.

Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci IK, Kim Y, Wang JR, Morgan AP, Calaway JD, Aylor DL, Yun Z, Bell TA, Buus RJ, Calaway ME, Didion JP, Gooch TJ, Hansen SD, Robinson NN, Shaw GD, Spence JS, Quackenbush CR, Barrick CJ, Nonneman RJ, Kim K, Xenakis J, Xie Y, Valdar W, Lenarcic AB, Wang W, Welsh CE, Fu CP, Zhang Z, Holt J, Guo Z, Threadgill DW, Tarantino LM, Miller DR, Zou F, McMillan L, Sullivan PF, Pardo-Manuel de Villena F. Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance. Nat Genet. 2015 Apr;47(4):353-60. doi: 10.1038/ng.3222. Epub 2015 Mar 2. PubMed PMID: 25730764.

Welch JD, Baran-Gale J, Perou CM, Sethupathy P, Prins JF. Pseudogenes transcribed in breast invasive carcinoma show subtype-specific expression and ceRNA potential. BMC Genomics. 2015 Feb 22;16:113. doi: 10.1186/s12864-015-1227-8. PubMed PMID: 25765044.

Didion JP, Morgan AP, Clayshulte AM, Mcmullan RC, Yadgary L, Petkov PM, Bell TA, Gatti DM, Crowley JJ, Hua K, Aylor DL, Bai L, Calaway M, Chesler EJ, French JE, Geiger TR, Gooch TJ, Garland T Jr, Harrill AH, Hunter K, McMillan L, Holt M, Miller DR, O’Brien DA, Paigen K, Pan W, Rowe LB, Shaw GD, Simecek P, Sullivan PF, Svenson KL, Weinstock GM, Threadgill DW, Pomp D, Churchill GA, Pardo-Manuel de Villena F. A multi-megabase copy number gain causes maternal transmission ratio distortion on mouse chromosome 2. PLoS Genet. 2015 Feb 13;11(2):e1004850. doi: 10.1371/journal.pgen.1004850. eCollection 2015 Feb. PubMed PMID: 25679959.

Proctor EA, Kota P, Aleksandrov AA, He L, Riordan JR, Dokholyan NV. Rational Coupled Dynamics Network Manipulation Rescues Disease-Relevant Mutant Cystic Fibrosis Transmembrane Conductance Regulator. Chem Sci. 2015 Feb;6(2):1237-1246. PubMed PMID: 25685315.

Corley M, Solem A, Qu K, Chang HY, Laederach A. Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. Nucleic Acids Res. 2015 Jan 23. pii: gkv010. [Epub ahead of print] PubMed PMID: 25618847.

Li J, Shi J, Huang W, Sun J, Wu Y, Duan Q, Luo J, Lange LA, Gordon-Larsen P, Zheng SL, Yuan W, Wang Y, Popkin BM, Mo Z, Xu J, Du S, Mohlke KL, Lange EM. Variant Near FGF5 Has Stronger Effects on Blood Pressure in Chinese With a Higher Body Mass Index. Am J Hypertens. 2015 Jan 23. pii: hpu263. [Epub ahead of print] PubMed PMID: 25618516.

Selitsky SR, Baran-Gale J, Honda M, Yamane D, Masaki T, Fannin EE, Guerra B, Shirasaki T, Shimakami T, Kaneko S, Lanford RE, Lemon SM, Sethupathy P. Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C. Sci Rep. 2015 Jan 8;5:7675. doi: 10.1038/srep07675. PubMed PMID: 25567797.

Kelley JB, Dixit G, Sheetz JB, Venkatapurapu SP, Elston TC, Dohlman HG. RGS proteins and septins cooperate to promote chemotropism by regulating polar cap mobility. Curr Biol. 2015 Feb 2;25(3):275-85. doi: 10.1016/j.cub.2014.11.047. Epub 2015 Jan 15. PubMed PMID: 25601550.

English JG, Shellhammer JP, Malahe M, McCarter PC, Elston TC, Dohlman HG. MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast. Sci Signal. 2015 Jan 13;8(359):ra5. doi: 10.1126/scisignal.2005774. PubMed PMID: 25587192.


Morgan AP, Crowley JJ, Nonneman RJ, Quackenbush CR, Miller CN, Ryan AK, Bogue MA, Paredes SH, Yourstone S, Carroll IM, Kawula TH, Bower MA, Sartor RB, Sullivan PF. The antipsychotic olanzapine interacts with the gut microbiome to cause weight gain in mouse. PLoS One. 2014 Dec 15;9(12):e115225. doi: 10.1371/journal.pone.0115225. eCollection 2014. PubMed PMID: 25506936.

Orvis T*, Hepperla A*, Walter V*, Song S, Simon J, Parker J, Wilkerson MD, Desai N, Major MB, Hayes DN, Davis IJ, Weissman B. BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization. Cancer Research. 2014 Nov 15;74(22):6486-6498. PMID: 25115300 PMCID: PMC4233181 doi: 10.1158/0008-5472.CAN-14-0061.

Blatt J, Farag S, Corey SJ, Sarrimanolis Z, Muratov E, Fourches D, Tropsha A, Janzen WP. Expanding the scope of drug repurposing in pediatrics: the Children’s Pharmacy Collaborative. Drug Discov Today. 2014 Nov;19(11):1696-8. doi: 10.1016/j.drudis.2014.08.003. Epub 2014 Aug 19. PubMed PMID: 25149597.

Hasan SS, Proctor EA, Yamashita E, Dokholyan NV, Cramer WA. Traffic within the cytochrome b6f lipoprotein complex: gating of the quinone portal. Biophys J. 2014 Oct 7;107(7):1620-8. doi: 10.1016/j.bpj.2014.08.003. PubMed PMID: 25296314.

Weiser M, Mukherjee S, Furey TS. Novel distal eQTL analysis demonstrates effect of population genetic architecture on detecting and interpreting associations. Genetics. 2014 Nov;198(3):879-93. doi: 10.1534/genetics.114.167791. Epub 2014 Sep 16. PubMed PMID: 25230953.

Baran-Gale J, Fannin EE, Kurtz CL, Sethupathy P. Beta cell 5′-shifted isomiRs are candidate regulatory hubs in type 2 diabetes. PLoS One. 2013 Sep 9;8(9):e73240. doi: 10.1371/journal.pone.0073240. eCollection 2013. PubMed PMID: 24039891.

Wang Y, Chen D, Qian H, Tsai YS, Shao S, Liu Q, Dominguez D, Wang Z. The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression. Cancer Cell. 2014 Sep 8;26(3):374-89. doi: 10.1016/j.ccr.2014.07.010. PubMed PMID: 25203323.

Miller LA, Santhanakrishnan A, Jones S, Hamlet C, Mertens K, Zhu L. J Exp Biol. 2012 Aug 1;215(Pt 15):2716-27. doi: 10.1242/jeb.064501. Reconfiguration and the reduction of vortex-induced vibrations in broad leaves. PubMed PMID: 22786650.

Gatza ML, Silva GO, Parker JS, Fan C, Perou CM. An integrated genomics approach identifies drivers of proliferation in luminal-subtype human breast cancer. Nat Genet. 2014 Oct;46(10):1051-9. doi: 10.1038/ng.3073. Epub 2014 Aug 24. PubMed PMID: 25151356.

Yourstone SM, Lundberg DS, Dangl JL, Jones CD. MT-Toolbox: improved amplicon sequencing using molecule tags. BMC Bioinformatics. 2014 Aug 22;15:284. doi: 10.1186/1471-2105-15-284. PubMed PMID: 25149069.

Mellnik J, Vasquez PA, McKinley SA, Witten J, Hill DB, Forest MG. Micro-heterogeneity metrics for diffusion in soft matter. Soft Matter. 2014 Oct 21;10(39):7781-96. doi: 10.1039/c4sm00676c. Epub 2014 Aug 21. PubMed PMID: 25144347.

Orvis T, Hepperla A, Walter V, Song S, Simon J, Parker J, Wilkerson MD, Desai N, Major MB, Hayes DN, Davis IJ, Weissman B. BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization. Cancer Res. 2014 Nov 15;74(22):6486-98. doi: 10.1158/0008-5472.CAN-14-0061. Epub 2014 Aug 12. PubMed PMID: 25115300.

Nedd S, Redler RL, Proctor EA, Dokholyan NV, Alexandrova AN. Cu,Zn-superoxide dismutase without Zn is folded but catalytically inactive. J Mol Biol. 2014 Dec 12;426(24):4112-24. doi: 10.1016/j.jmb.2014.07.016. Epub 2014 Jul 30. PubMed PMID: 25083917.

Zhao W, He X, Hoadley KA, Parker JS, Hayes DN, Perou CM. Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling. BMC Genomics. 2014 Jun 2;15:419. doi: 10.1186/1471-2164-15-419. PubMed PMID: 24888378.

Choudhury R, Roy SG, Tsai YS, Tripathy A, Graves LM, Wang Z. The splicing activator DAZAP1 integrates splicing control into MEK/Erk-regulated cell proliferation and migration. Nat Commun. 2014;5:3078. doi: 10.1038/ncomms4078. PubMed PMID: 24452013.

Haoqian Zhang*, Min Lin*, Handuo Shi, Longwen Huang, Xiaomeng Zhang, Shan Shen, Rencheng Gao, Shuke Wu, Chengzhe Tian, Zhenglin Yang, Guosheng Zhang, Siheng He, Hao Wang, Tiffany Saw, Yiwei Chen, Weiyue Ji, and Qi Ouyang. Programming a Pavlovian conditioning circuit in Escherichia coli. 2014;5:3102. doi: 10.1038/ncomms4102. PubMed PMID: 24434523.

Liu CT, Buchkovich ML, Winkler TW, Heid IM; African Ancestry Anthropometry Genetics Consortium; GIANT Consortium, Borecki IB, Fox CS, Mohlke KL, North KE, Adrienne Cupples L. Multi-ethnic fine-mapping of 14 central adiposity loci. Hum Mol Genet. 2014 Sep 1;23(17):4738-44. doi: 10.1093/hmg/ddu183. Epub 2014 Apr 23. PubMed PMID: 24760767.

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