DrEvgenyZdobnov

Vejnar CE, Zdobnov EM, 2012, miRmap: Comprehensive prediction of microRNA target repression strength, NUCLEIC ACIDS RESEARCH, Vol: 40, Pages: 11673-11683, ISSN: 0305-1048

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• Citations: 269

Ambrosioni J, Junier T, Delhumeau C, Calmy A, Hirschel B, Zdobnov E, Kaiser L, Yerly Set al., 2012, Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections, AIDS, Vol: 26, Pages: 2079-2086, ISSN: 0269-9370

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• Citations: 40

Ambrosioni J, Junier T, Delhumeau C, Calmy A, Hirschel B, Zdobnov E, Kaiser L, Yerly S, Swiss HIV Cohort Studyet al., 2012, Impact of highly active antiretroviral therapy on the molecular epidemiology of newly diagnosed HIV infections., AIDS, Vol: 26, Pages: 2079-2086

OBJECTIVE: To evaluate HIV-1 transmission trends and the impact of highly active antiretroviral therapy (HAART) on newly diagnosed HIV infections in Geneva, Switzerland. DESIGN: Retrospective molecular epidemiology analysis of all newly HIV-diagnosed individuals between 2008 and 2010. METHODS: Phylogenetic analyses were performed using pol sequences of 780 newly HIV-1 diagnosed individuals between 2000 and 2010 (mandatory reporting) and 1058 individuals diagnosed before 2000. All clusters (bootstrap value >98%) including individuals diagnosed in 2008-2010 were analyzed. Recent HIV infections (<1 year) were determined by documented seroconversion and/or fraction of ambiguous nucleotides. Median viral load and HAART coverage during the study period were obtained from patients included in the Swiss HIV Cohort Study (SHCS). RESULTS: Among 142 newly diagnosed individuals during 2008-2010, 49% had a recent infection and 42% were included in transmission clusters. Among the latter, two-thirds were included in new clusters and one-third expanded previously known clusters. MSM carrying resistant strains were more frequently included in clusters. Only 1.8% of individuals diagnosed before 2000 and 10.8% diagnosed during 2000-2008 were included in clusters involving individuals diagnosed between 2008 and 2010. During 2008-2010, the median population viral load of SHCS-enrolled individuals was significantly lower for individuals diagnosed before 2000 than for those diagnosed during 2000-2008 and 2008-2010 and HAART coverage significantly higher. CONCLUSIONS: MSM with recent HIV infection are a significant source of onward transmission. Individuals diagnosed before 2000 were only exceptionally related to newly diagnosed infections between 2008 and 2010. Prevention campaigns need to be focused on improving diagnosis for recently infected individuals.

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Cordey S, Petty TJ, Schibler M, Martinez Y, Gerlach D, van Belle S, Turin L, Zdobnov E, Kaiser L, Tapparel Cet al., 2012, Identification of Site-Specific Adaptations Conferring Increased Neural Cell Tropism during Human Enterovirus 71 Infection, PLOS PATHOGENS, Vol: 8, ISSN: 1553-7366

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• Citations: 76

Li J, Waterhouse RM, Zdobnov EM, 2011, A remarkably stable <i>TipE</i> gene cluster: evolution of insect Para sodium channel auxiliary subunits, BMC EVOLUTIONARY BIOLOGY, Vol: 11, ISSN: 1471-2148

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• Citations: 13

Tapparel C, Cordey S, Junier T, Farinelli L, Van Belle S, Soccal PM, Aubert J-D, Zdobnov E, Kaiser Let al., 2011, Rhinovirus Genome Variation during Chronic Upper and Lower Respiratory Tract Infections, PLOS ONE, Vol: 6, ISSN: 1932-6203

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• Citations: 49

Dunand-Sauthier I, Santiago-Raber M-L, Capponi L, Vejnar CE, Schaad O, Irla M, Seguin-Estevez Q, Descombes P, Zdobnov EM, Acha-Orbea H, Reith Wet al., 2011, Silencing of c-Fos expression by microRNA-155 is critical for dendritic cell maturation and function, BLOOD, Vol: 117, Pages: 4490-4500, ISSN: 0006-4971

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• Citations: 111

Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubio JMC, Ribeiro JMC, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Kraus E, Mittapalli O, Margam VM, Li H-M, Meyer JM, Johnson RM, Romero-Severson J, VanZee JP, Alvarez-Ponce D, Vieira FG, Aguade M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BRet al., 2011, Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle (vol 107, pg 12168, 2010), PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 108, Pages: 6335-6336, ISSN: 0027-8424

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• Citations: 4

Papaioannou MD, Lagarrigue M, Vejnar CE, Rolland AD, Kuehne F, Aubry F, Schaad O, Fort A, Descombes P, Neerman-Arbez M, Guillou F, Zdobnov EM, Pineau C, Nef Set al., 2011, Loss of Dicer in Sertoli Cells Has a Major Impact on the Testicular Proteome of Mice, MOLECULAR & CELLULAR PROTEOMICS, Vol: 10, ISSN: 1535-9476

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• Citations: 85

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Caceres CE, Carmel L, Casola C, Choi J-H, Detter JC, Dong Q, Dusheyko S, Eads BD, Froehlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kueltz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JLet al., 2011, The Ecoresponsive Genome of <i>Daphnia pulex</i>, SCIENCE, Vol: 331, Pages: 555-561, ISSN: 0036-8075

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• Citations: 936

Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J, Kriventseva EVet al., 2011, OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011, NUCLEIC ACIDS RESEARCH, Vol: 39, Pages: D283-D288, ISSN: 0305-1048

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• Citations: 108

Waterhouse RM, Zdobnov EM, Kriventseva EV, 2011, Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi, GENOME BIOLOGY AND EVOLUTION, Vol: 3, Pages: 75-86, ISSN: 1759-6653

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• Citations: 54

Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao C, Mayhew G, Michel K, Mori A, Liu N, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi Y, Ranson H, Ribeiro JMC, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JMC, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MAT, Raikhel AS, Atkinson PWet al., 2010, Sequencing of <i>Culex quinquefasciatus</i> Establishes a Platform for Mosquito Comparative Genomics, SCIENCE, Vol: 330, Pages: 86-88, ISSN: 0036-8075

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• Citations: 347

Bartholomay LC, Waterhouse RM, Mayhew GF, Campbell CL, Michel K, Zou Z, Ramirez JL, Das S, Alvarez K, Arensburger P, Bryant B, Chapman SB, Dong Y, Erickson SM, Karunaratne SHPP, Kokoza V, Kodira CD, Pignatelli P, Shin SW, Vanlandingham DL, Atkinson PW, Birren B, Christophides GK, Clem RJ, Hemingway J, Higgs S, Megy K, Ranson H, Zdobnov EM, Raikhel AS, Christensen BM, Dimopoulos G, Muskavitch MATet al., 2010, Pathogenomics of <i>Culex quinquefasciatus</i> and Meta-Analysis of Infection Responses to Diverse Pathogens, SCIENCE, Vol: 330, Pages: 88-90, ISSN: 0036-8075

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• Citations: 124

Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubio JMC, Ribeiro JMC, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Krause E, Mittapalli O, Margam VM, Li H-M, Meyer JM, Johnson RM, Romero-Severson J, VanZee JP, Alvarez-Ponce D, Vieira FG, Aguade M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BRet al., 2010, Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 107, Pages: 12168-12173, ISSN: 0027-8424

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• Citations: 384

Junier T, Zdobnov EM, 2010, The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell, BIOINFORMATICS, Vol: 26, Pages: 1669-1670, ISSN: 1367-4803

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• Citations: 371

Cordey S, Junier T, Gerlach D, Gobbini F, Farinelli L, Zdobnov EM, Winther B, Tapparel C, Kaiser Let al., 2010, Rhinovirus Genome Evolution during Experimental Human Infection, PLOS ONE, Vol: 5, ISSN: 1932-6203

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• Citations: 41

Hovatta O, Jaconi M, Tohonen V, Bena F, Gimelli S, Bosman A, Holm F, Wyder S, Zdobnov EM, Irion O, Andrews PW, Antonarakis SE, Zucchelli M, Kere J, Feki Aet al., 2010, A Teratocarcinoma-Like Human Embryonic Stem Cell (hESC) Line and Four hESC Lines Reveal Potentially Oncogenic Genomic Changes, PLOS ONE, Vol: 5, ISSN: 1932-6203

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• Citations: 38

Hunt BG, Wyder S, Elango N, Werren JH, Zdobnov EM, Yi SV, Goodisman MADet al., 2010, Sociality Is Linked to Rates of Protein Evolution in a Highly Social Insect, MOLECULAR BIOLOGY AND EVOLUTION, Vol: 27, Pages: 497-500, ISSN: 0737-4038

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• Citations: 48

Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJP, Kitts P, Lynch JA, Murphy T, Oliveira DCSG, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MMG, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi J-H, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Grunder S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FMF, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu L-L, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson IHM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schluens H, Schmitt T, Schneider M, Schueler A, Schurko AM, Shuker DM, Simoes ZLP, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RAet al., 2010, Functional and Evolutionary Insights from the Genomes of Three Parasitoid <i>Nasonia</i> Species, SCIENCE, Vol: 327, Pages: 343-348, ISSN: 0036-8075

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• Citations: 653

Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, Zdobnov EM, Robertson HM, Robinson GE, Werren JH, Sinha Set al., 2010, Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances, PLOS COMPUTATIONAL BIOLOGY, Vol: 6, ISSN: 1553-734X

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• Citations: 24

Yerly S, Junier T, Gayet-Ageron A, El Amari EB, von Wyl V, Guenthard HF, Hirschel B, Zdobnov E, Kaiser Let al., 2009, The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection, AIDS, Vol: 23, Pages: 1415-1423, ISSN: 0269-9370

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• Citations: 92

Gatfield D, Le Martelot G, Vejnar CE, Gerlach D, Schaad O, Fleury-Olela F, Ruskeepaa A-L, Oresic M, Esau CC, Zdobnov EM, Schibler Uet al., 2009, Integration of microRNA miR-122 in hepatic circadian gene expression, GENES & DEVELOPMENT, Vol: 23, Pages: 1313-1326, ISSN: 0890-9369

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• Citations: 298

Tapparel C, Junier T, Gerlach D, Van Belle S, Turin L, Cordey S, Muehlemann K, Regamey N, Aubert J-D, Soccal PM, Eigenmann P, Zdobnov E, Kaiser Let al., 2009, New Respiratory Enterovirus and Recombinant Rhinoviruses among Circulating Picornaviruses, EMERGING INFECTIOUS DISEASES, Vol: 15, Pages: 719-726, ISSN: 1080-6040

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• Citations: 113

Elsik CG, Tellam RL, Worley KC, Gibbs RA, Abatepaulo ARR, Abbey CA, Adelson DL, Aerts J, Ahola V, Alexander L, Alioto T, Almeida IG, Amadio AF, Anatriello E, Antonarakis SE, Anzola JM, Astashyn A, Bahadue SM, Baldwin CL, Barris W, Baxter R, Bell SN, Bennett AK, Bennett GL, Biase FH, Boldt CR, Bradley DG, Brinkman FSL, Brinkmeyer-Langford CL, Brown WC, Brownstein MJ, Buhay C, Caetano AR, Camara F, Carroll JA, Carvalho WA, Casey T, Cervelatti EP, Chack J, Chacko E, Chandrabose MM, Chapin JE, Chapple CE, Chen H-C, Chen L, Cheng Y, Cheng Z, Childers CP, Chitko-McKown CG, Chiu R, Choi J, Chrast J, Colley AJ, Connelley T, Cree A, Curry S, Dalrymple B, Diep Dao M, Davis C, de Oliveira CJF, de Miranda Santos IKF, de Campos TA, Deobald H, Devinoy E, Dickins CM, Yan D, Dinh HH, De Donato M, Donohue KE, Donthu R, Dovc P, Dugan-Rocha S, Durbin KJ, Eberlein A, Edgar RC, Egan A, Eggen A, Eichler EE, Elhaik E, Ellis SA, Elnitski L, Ermolaeva O, Eyras E, Fitzsimmons CJ, Fowler GR, Franzin AM, Fritz K, Gabisi RA, Garcia GR, Garcia JF, Genini S, Gerlach D, German JB, Gilbert JGR, Gill CA, Gladney CJ, Glass EJ, Goodell J, Grant JR, Graur D, Greaser ML, Green JA, Green RD, Guan L, Guigo R, Hadsell DL, Hagen DE, Hakimov HA, Halgren R, Hamernik DL, Hamilton C, Harhay GP, Harrow JL, Hart EA, Hastings N, Havlak P, Henrichsen CN, Hernandez J, Hernandez M, Herzig CTA, Hiendleder SG, Hines S, Hitchens ME, Hlavina W, Hobbs M, Holder M, Holt RA, Hu Z-L, Hume J, Iivanainen A, Ingham A, Iso-Touru T, Jamis C, Jann O, Jensen K, Jhangiani SN, Jiang H, Johnson AJ, Jones SJM, Joshi V, Junier T, Kapetis D, Kappes SM, Kapustin Y, Keele JW, Kent MP, Kerr T, Khalil SS, Khatib H, Kiryutin B, Kitts P, Kokocinski F, Kolbehdari D, Kovar CL, Kriventseva EV, Kumar CG, Kumar D, Lahmers KK, Landrum M, Larkin DM, Lau LPL, Leach R, Lee JCM, Lee S, Lemay DG, Lewin HA, Lewis LR, Li C, Lien S, Liu GE, Liu Y-S, Liu Y, Logan KM, Lopez J, Lozado RJ, Lutzow YS, Lynn DJ, MacNeil MD, Maglott D, Malinverni R, Maqbool NJ, Maret al., 2009, The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution, SCIENCE, Vol: 324, Pages: 522-528, ISSN: 0036-8075

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• Citations: 885

Papaioannou MD, Pitetti J-L, Ro S, Park C, Aubry F, Schaad O, Vejnar CE, Kuehne F, Descombes P, Zdobnov EM, McManus MT, Guillou F, Harfe BD, Yan W, Jegou B, Nef Set al., 2009, Sertoli cell Dicer is essential for spermatogenesis in mice, DEVELOPMENTAL BIOLOGY, Vol: 326, Pages: 250-259, ISSN: 0012-1606

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• Citations: 148

Matsui T, Yamamoto T, Wyder S, Zdobnov EM, Kadowaki Tet al., 2009, Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates, BMC GENOMICS, Vol: 10, ISSN: 1471-2164

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• Citations: 4

Gerlach D, Kriventseva EV, Rahman N, Vejnar CE, Zdobnov EMet al., 2009, miROrtho: computational survey of microRNA genes, NUCLEIC ACIDS RESEARCH, Vol: 37, Pages: D111-D117, ISSN: 0305-1048

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• Citations: 56

Lemay DG, Lynn DJ, Martin WF, Neville MC, Casey TM, Rincon G, Kriventseva EV, Barris WC, Hinrichs AS, Molenaar AJ, Pollard KS, Maqbool NJ, Singh K, Murney R, Zdobnov EM, Tellam RL, Medrano JF, German JB, Rijnkels Met al., 2009, The bovine lactation genome: insights into the evolution of mammalian milk, GENOME BIOLOGY, Vol: 10, ISSN: 1474-760X

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• Citations: 149

Yerly S, Junier T, Gayet-Ageron A, El Amari EB, von Wyl V, Guenthard HF, Hirschel B, Klimkait T, Zdobnov E, Kaiser Let al., 2009, Impact of newly HIV diagnosed individuals on the transmission of drug resistance, 18th International HIV Drug Resistance Workshop, Publisher: INT MEDICAL PRESS LTD, Pages: A40-A40, ISSN: 1359-6535

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