Sen DR, Kaminski J, Barnitz AR, Kurachi M, Gerdemann U, Yates KB, Tsao HW, Godec J, LaFleur M, Brown FD, Tonnerre P, Chung RT, Tully DC, Allen TM, Frahm N, Lauer GM, Wherry EJ, Yosef N, Haining WN. The epigenetic landscape of T cell exhaustion. Science doi:10.1126/science.aae0491. (2016). Read it.

Sage PT, Ron-Harel N, Juneja VR, Sen DR, Maleri S, Sungnak W, Kuchroo VK, Haining WN, Chevrier N, Haigis M, Sharpe AH. Suppression by TFR cells leads to durable and selective inhibition of B cell effector function. Nat Immunol doi: 10.1038/ni.3578. (2016). Read it.

Provine NM, Larocca RA, Aid M, Penaloza-MacMaster P, Badamchi-Zadah A, Borducci EN, Yates KB, Abbink P, Kirilova M, Ng'ang'a D, Bramson J, Haining WN, Barouch DH. Immediate Dysfunction of Vaccine-Elicited CD8+ T cells Primed in the Absence of CD4+ T cells. J Immunol doi: 10.4049/jimmunol.1600591. (2016). Read it.

Reese TA, Bi K, Kambal A, Filali-Mouhim A, Beura LK, Bürger MC, Pulendran B, Sekaly RP, Jameson SC, Masopust D, Haining WN, Virgin HW. Sequential Infection with Common Pathogens Promotes Human-like Immune Gene Expression and Altered Vaccine Response. Cell Host Microbe doi: 10.1016/j.chom.2016.04.003. (2016). Read it.

Beura LK, Hamilton SE, Bi K, Schenkel JM, Odumade OA, Casey KA, Thompson EA, Fraser KA, Rosato PC, Filali-Mouhim A, Sekaly RP, Jenkins MK, Vezys V, Haining WN, Jameson SC, Masopust D. Normalizing the environment recapitulates adult human immune traits in laboratory mice. Nature doi: 10.1038/nature17655 (2016). Read it.

Godec J, Tan Y, Liberzon A, Tamayo P, Bhattacharya S, Butte AJ, Mesirov JP, Haining WN. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. Immunity doi:10.1016/j.immuni.2015.12.006 (2016). Read it.

Pesenacker AM, Wang AY, Singh A, Gillies J, Kim YW, Piccirillo CA, Nguyen D, Haining WN, Tebbutt SJ, Panagiotopoulos C, Levings MK. A Treg gene signature is a specific and sensitive biomarker to identify children with new onset type 1 diabetes. Diabetes doi:10.2337/db15-0572 (2016). Read it.

Tan Y, Wu F, Tamayo P, Haining WN, Mesirov JP. Constellation Map: Downstream visualization and interpretation of gene set enrichment results. F1000Res doi:10.12688/f1000research.6644.1 (2015). Read it.

Gupta PK, Godec J, Wolski D, Adland E, Yates K, Pauken KE, Cosgrove C, Ledderose C, Junger WG, Robson SC, Wherry EJ, Alter G, Goulder PJ, Klenerman P, Sharpe AH, Lauer GM, Haining WN. CD39 Expression Identifies Terminally Exhausted CD8+ T Cells. PLoS Pathog. doi: 10.1371/journal.ppat.1005177 (2015). Read it.

Kim HJ, Barnitz RA, Kreslavsky T, Brown FD, Moffett H, Lemieux ME, Kaygusuz Y, Meissner T, Holderried TA, Chan S, Kastner P, Haining WN, Cantor H. Stable inhibitory activity of regulatory T cells requires the transcription factor Helios. Science doi: 10.1126/science.aad0616 (2015). Read it.

Penaloza-MacMaster P, Barber DL, Wherry EJ, Provine NM, Teigler JE, Parentau L, Blackmore S, Borducchi EN, Larocca RA, Yates KB, Shen H, Haining WN, Sommerstein R, Pinschewer DD, Ahmed R, Barouch DH. Vaccine-elicited CD4 T cells induce immunopathology after chronic LCMV infection. Science doi: 10.1126/science.aaa2148 (2015). Read it.

Godec J,  Cowley GS, Barnitz RA, Root DE, Sharpe AH, Haining WN. Inducible RNAi in vivo reveals that the transcription factor BATF is required to initiate but not maintain the CD8+ T-cell effector differentiation. PNAS doi: 10.1073/pnas.1413291112 (2014). Read it.

Stelekati E, Shin H, Doering TA, Dolfi DV, Ziegler CG, Beiting DP, Dawson L, Liboon J, Wolski D, Ali MA, Katsikis PD, Shen H, Roos DS, Haining WN, Lauer GM, Wherry EJ. Bystander chronic infection negatively impacts development of CD8(+) T cell memory. Immunity doi:10.1016/j.immuni.2014.04.010 (2014). Read it.

Kurachi M, Barnitz RA, Yosef N, Odorizzi PM, DiIorio MA, Lemieux ME, Yates K, Godec J, Klatt MG, Regev A, Wherry EJ, Haining WN. The transcription factor BATF operates as an essential differentiation checkpoint in early effector CD8+ T cells. Nature Immunology doi: 10.1038/ni.2834 (2014). Read it.

Haining WN. Strength in numbers: comparing vaccine signatures the modular way. Nature Immunology doi: 10.1038/ni.2807 (2014). Read it.

Bachireddy P, Hainz U, Rooney M, Pozdnyakova O, Aldridge J, Zhang W, Liao X, Hodi FS, O'Connell K, Haining WN, Goldstein NR, Canning CM, Soiffer RJ, Ritz J, Hacohen N, Alyea EP, Kim HT, Wu CJ. Reversal of in situ T-cell exhaustion during effective human antileukemia responses to donor lymphocyte infusion. Blood doi: 10.1182/blood-2013-08-523001 (2014). Read it.

Tan Y, Tamayo P, Nakaya H, Pulendran B, Mesirov JP, Haining WN. Gene signatures related to B-cell proliferation predict influenza vaccine-induced antibody response. Eur J Immunol doi: 10.1002/eji.201343657 (2013). Read it.

Henrickson SE, Perro M, Loughhead SM, Senman B, Stutte S, Quigley M, Alexe G, Iannacone M, Flynn MP, Omid S, Jesnick JL, Imam S, Mempel TR, Mazo IB, Haining WN, von Andrian UH. Antigen availability determines CD8+ T cell-dendritic cell interaction kinetics and memory fate decisions. Immunity 39(3):496-507 (2013). Read it.

Barnitz RA, Imam S, Yates K, Haining WN. Isolation of RNA and the synthesis and amplification of cDNA from antigen-specific T cells for genome-wide expression analysis. Methods Mol Biol 979:161-73 (2013). Read it.

Huang AY, Haining WN, Barkauskas DS, Myers JT, Petrosiute A, Garrett AP, Singh K, Cooke KR, Kean LS. Viewing transplantation immunology through today's lens: new models, new imaging, and new insights. Biol Blood Marrow Transplant 19(1 Suppl): S44-51 (2013). Read it.

Haining WN. Thinking inside the box: how T cell inhibitory receptors signal. Nat Med 18(9):1338-9 (2012). Read it.

Butte MJ, Lee SJ, Jesneck J, Keir ME, Haining WN, Sharpe AH. CD28 costimulation regulates genome-wide effects on alternative splicing. PLoS One 7(6):e40032 (2012). Read it.

Haining WN, Pulendran B. Identifying gnostic predictors of vaccine response. Curr Opin Immunology 24(3):332-6 (2012). Read it.

Haining WN. Travels in time: Assessing the functional complexity of T cells. PNAS 109(5):1359-60 (2012). Read it.

Haining WN. The numerology of T cell functional diversity. Immunity 36(1):10-2 (2012). Read it.

Haining WN, Barnitz R. Deconvolving heterogeneity in the CD8+ T-cell response to HIV. Curr Opin HIV AIDS 7(1):38-43 (2012). Read it.

West EE, Youngblood B, Tan WG, Jin HT, Araki K, Alexe G, Konieczny BT, Calpe S, Freeman GJ, Terhorst C, Haining WN, Ahmed R. Tight Regulation of Memory CD8(+) T Cells Limits Their Effectiveness during Sustained High Viral Load. Immunity (2011). Read it.

Nakaya HI, Wrammert J, Lee EK, Racioppi L, Marie-Kunze S, Haining WN, Means AR, Kasturi SP, Khan N, Li GM, McCausland M, Kanchan V, Kokko KE, Li S, Elbein R, Mehta AK, Aderem A, Subbarao K, Ahmed R, Pulendran B. Systems biology of vaccination for seasonal influenza in humans. Nature Immunology 12(8):786-95 (2011). Read it.

Duraiswamy J, Ibegbu CC, Masopust D, Miller JD, Araki K, Doho GH, Tata P, Gupta S, Zilliox MJ, Nakaya HI, Pulendran B, Haining WN, Freeman GJ, Ahmed R. Phenotype, Function, and Gene Expression Profiles of Programmed Death-1hi CD8 T Cells in Healthy Human Adults. The Journal of Immunology 186 (2011). Read it.

Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN, McConkey ME, Habib N, Yosef N, Chang CY, Shay T, Frampton GM, Drake AC, Leskov I, Nilsson B, Preffer F, Dombkowski D, Evans JW, Liefeld T, Smutko JS, Chen J, Friedman N, Young RA, Golub TR, Regev A, Ebert BL. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144(2):296-309 (2011). Read it.

Quigley M, Pereyra F, Nilsson B, Porichis F, Fonseca C, Eichbaum Q, Julg B, Jesneck JL, Brosnahan K, Imam S, Russell K, Toth I, Piechocka-Troca A, Dolfi D, Angelosanto J, Crawford A, Shin H, Kwon DS, Francisco L, Freeman GJ, Wherry EJ, Kaufmann DE, Walker BD, Ebert BL, Haining WN. Integrative genomic analysis of HIV-specific CD8+ T cells reveals that PD-1 inhibits T cell function by upregulating BATF. Nature Medicine 16,1147-1151 (2010). Read it.

Haining WN, Wherry EJ. Integrating genomic signatures for immunologic discovery. Immunity 32(2), 152-61 (2010). Read it.

Kalia, V, Sarkar S, Subramaniam S, Haining WN, Smith KA, Ahmed R. Prolonged interleukin-2Ralpha Expression on virus-specific CD8+ T cells favors terminal-effector differentiation in vivo. Immunity 32(1): 91-103 (2010). Read it.

Blackburn SD, Shin H, Haining WN, Zou T, Workman CJ, Polley A, Betts MR, Freeman GJ, Vignali DA, Wherry EJ. Coregulation of CD8+ T cell exhaustion by multiple inhibitory receptors during chronic viral infection. Nature Immunology 10, 29-37 (2009). Read it.

Haining WN, Angelosanto J, Brosnahan K, Ross K, Hahn C, Russell K, Drury L, Norton S, Nadler L, Stegmaier K. High-throughput gene expression profiling of memory differentiation in primary human T cells. BMC Immunology 9, 44 (2008). Read it.

Haining WN, Ebert BL, Subramanian A, Wherry EJ, Eichbaum Q, Evans JW, Mak R, Rivoli S, Pretz J, Angelosanto J, Smutko JS, Walker BD, Kaech SM, Ahmed R, Nadler LM, Golub TR. Identification of an evolutionarily conserved transcriptional signature of CD8 memory differentiation that is shared by T and B Cells. Journal of Immunology 181, 1859-68 (2008). Read it.

Sarkar S, Kalia V, Haining WN, Konieczny BT, Subramaniam S, Ahmed R. Functional and genomic profiling of effector CD8 T cell subsets with distinct memory fates. Journal of Experimental Medicine 205, 625-40 (2008). Read it.

Haining WN, Davies J, Kanzler H, Drury L, Brenn T, Evans J, Angelosanto J, Rivoli S, Russell K, George S, Sims P, Neuberg D, Li X, Kutok J, Morgan J, Wen P, Demetri G, Coffman RL, Nadler LM. CpG oligonucleotides alter lymphocyte and dendritic cell trafficking in humans. Clinical Cancer Research 14, 5626-34 (2008). Read it.

Wherry EJ, Ha SJ, Kaech SM, Haining WN, Sarkar S, Kalia V, Subramaniam S, Blattman JN, Barber DL, Ahmed R. Molecular signature of CD8+ T cell exhaustion during chronic viral infection. Immunity 27, 670-86 (2007). Read it.

Haining WN, Neuberg DS, Keczkemethy HL, Evans JW, Rivoli S, Gelman R, Rosenblatt HM, Shearer WT, Guenaga J, Douek DC, Silverman LB, Sallan SE, Guinan EC, Nadler LM. Antigen-specific T-cell memory is preserved in children treated for acute lymphoblastic leukemia. Blood 106, 1749-54 (2005). Read it.