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AGeS: a software system for microbial genome sequence annotation

pipeline programs

Grover D, Kumar K.
GSID: Ad4mn9YyNzIJ
K Kumar, V Desai, L Cheng, M Khitrov, D Grover… - PLoS …, 2011 - journals.plos.org

Background The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput, and fully integrated and automated. Although a few Web-based …

Search for gravitational waves associated with γ-ray bursts detected by the interplanetary network.

Physical review letters

Aasi J, Abbott BP, Abbott R, Abbott T, Abernathy MR, Acernese F, Ackley K, Adams C, Adams T, Addesso P, Adhikari RX, Affeldt C, Agathos M, Aggarwal N, Aguiar OD, Ajith P, Alemic A, Allen B, Allocca A, Amariutei D, Andersen M, Anderson RA, Anderson SB, Anderson WG, Arai K, Araya MC, Arceneaux C, Areeda JS, Ast S, Aston SM, Astone P, Aufmuth P, Augustus H, Aulbert C, Aylott BE, Babak S, Baker PT, Ballardin G, Ballmer SW, Barayoga JC, Barbet M, Barish BC, Barker D, Barone F, Barr B, Barsotti L, Barsuglia M, Barton MA, Bartos I, Bassiri R, Basti A, Batch JC, Bauchrowitz J, Bauer TS, Baune C, Bavigadda V, Behnke B, Bejger M, Beker MG, Belczynski C, Bell AS, Bell C, Bergmann G, Bersanetti D, Bertolini A, Betzwieser J, Bilenko IA, Billingsley G, Birch J, Biscans S, Bitossi M, Biwer C, Bizouard MA, Black E, Blackburn JK, Blackburn L, Blair D, Bloemen S, Bock O, Bodiya TP, Boer M, Bogaert G, Bogan C, Bond C, Bondu F, Bonelli L, Bonnand R, Bork R, Born M, Boschi V, Bose S, Bosi L, Bradaschia C, Brady PR, Braginsky VB, Branchesi M, Brau JE, Briant T, Bridges DO, Brillet A, Brinkmann M, Brisson V, Brooks AF, Brown DA, Brown DD, Brückner F, Buchman S, Buikema A, Bulik T, Bulten HJ, Buonanno A, Burman R, Buskulic D, Buy C, Cadonati L, Cagnoli G, Calderón Bustillo J, Calloni E, Camp JB, Campsie P, Cannon KC, Canuel B, Cao J, Capano CD, Carbognani F, Carbone L, Caride S, Castaldi G, Caudill S, Cavaglià M, Cavalier F, Cavalieri R, Celerier C, Cella G, Cepeda C, Cesarini E, Chakraborty R, Chalermsongsak T, Chamberlin SJ, Chao S, Charlton P, Chassande-Mottin E, Chen X, Chen Y, Chincarini A, Chiummo A, Cho HS, Cho M, Chow JH, Christensen N, Chu Q, Chua SS, Chung S, Ciani G, Clara F, Clark DE, Clark JA, Clayton JH, Cleva F, Coccia E, Cohadon PF, Colla A, Collette C, Colombini M, Cominsky L, Constancio M, Conte A, Cook D, Corbitt TR, Cornish N, Corsi A, Costa CA, Coughlin MW, Coulon JP, Countryman S, Couvares P, Coward DM, Cowart MJ, Coyne DC, Coyne R, Craig K, Creighton JD, Croce RP, Crowder SG, Cumming A, Cunningham L, Cuoco E, Cutler C, Dahl K, Dal Canton T, Damjanic M, Danilishin SL, D'Antonio S, Danzmann K, Dattilo V, Daveloza H, Davier M, Davies GS, Daw EJ, Day R, Dayanga T, DeBra D, Debreczeni G, Degallaix J, Deléglise S, Del Pozzo W, Denker T, Dent T, Dereli H, Dergachev V, De Rosa R, DeRosa RT, DeSalvo R, Dhurandhar S, Díaz M, Dickson J, Di Fiore L, Di Lieto A, Di Palma I, Di Virgilio A, Dolique V, Dominguez E, Donovan F, Dooley KL, Doravari S, Douglas R, Downes TP, Drago M, Drever RW, Driggers JC, Du Z, Ducrot M, Dwyer S, Eberle T, Edo T, Edwards M, Effler A, Eggenstein HB, Ehrens P, Eichholz J, Eikenberry SS, Endrőczi G, Essick R, Etzel T, Evans M, Evans T, Factourovich M, Fafone V, Fairhurst S, Fan X, Fang Q, Farinon S, Farr B, Farr WM, Favata M, Fazi D, Fehrmann H, Fejer MM, Feldbaum D, Feroz F, Ferrante I, Ferreira EC, Ferrini F, Fidecaro F, Finn LS, Fiori I, Fisher RP, Flaminio R, Fournier JD, Franco S, Frasca S, Frasconi F, Frede M, Frei Z, Freise A, Frey R, Fricke TT, Fritschel P, Frolov VV, Fulda P, Fyffe M, Gair JR, Gammaitoni L, Gaonkar S, Garufi F, Gehrels N, Gemme G, Gendre B, Genin E, Gennai A, Ghosh S, Giaime JA, Giardina KD, Giazotto A, Gleason J, Goetz E, Goetz R, Gondan L, González G, Gordon N, Gorodetsky ML, Gossan S, Goßler S, Gouaty R, Gräf C, Graff PB, Granata M, Grant A, Gras S, Gray C, Greenhalgh RJ, Gretarsson AM, Groot P, Grote H, Grover K, Grunewald S, Guidi GM, Guido CJ, Gushwa K, Gustafson EK, Gustafson R, Ha J, Hall ED, Hamilton W, Hammer D, Hammond G, Hanke M, Hanks J, Hanna C, Hannam MD, Hanson J, Harms J, Harry GM, Harry IW, Harstad ED, Hart M, Hartman MT, Haster CJ, Haughian K, Heidmann A, Heintze M, Heitmann H, Hello P, Hemming G, Hendry M, Heng IS, Heptonstall AW, Heurs M, Hewitson M, Hild S, Hoak D, Hodge KA, Hofman D, Holt K, Hopkins P, Horrom T, Hoske D, Hosken DJ, Hough J, Howell EJ, Hu Y, Huerta E, Hughey B, Husa S, Huttner SH, Huynh M, Huynh-Dinh T, Idrisy A, Ingram DR, Inta R, Islas G, Isogai T, Ivanov A, Iyer BR, Izumi K, Jacobson M, Jang H, Jaranowski P, Ji Y, Jiménez-Forteza F, Johnson WW, Jones DI, Jones R, Jonker RJ, Ju L, Haris K, Kalmus P, Kalogera V, Kandhasamy S, Kang G, Kanner JB, Karlen J, Kasprzack M, Katsavounidis E, Katzman W, Kaufer H, Kaufer S, Kaur T, Kawabe K, Kawazoe F, Kéfélian F, Keiser GM, Keitel D, Kelley DB, Kells W, Keppel DG, Khalaidovski A, Khalili FY, Khazanov EA, Kim C, Kim K, Kim NG, Kim N, Kim S, Kim YM, King EJ, King PJ, Kinzel DL, Kissel JS, Klimenko S, Kline J, Koehlenbeck S, Kokeyama K, Kondrashov V, Koranda S, Korth WZ, Kowalska I, Kozak DB, Kringel V, Krishnan B, Królak A, Kuehn G, Kumar A, Kumar DN, Kumar P, Kumar R, Kuo L, Kutynia A, Lam PK, Landry M, Lantz B, Larson S, Lasky PD, Lazzarini A, Lazzaro C, Leaci P, Leavey S, Lebigot EO, Lee CH, Lee HK, Lee HM, Lee J, Lee PJ, Leonardi M, Leong JR, Leonor I, Le Roux A, Leroy N, Letendre N, Levin Y, Levine B, Lewis J, Li TG, Libbrecht K, Libson A, Lin AC, Littenberg TB, Lockerbie NA, Lockett V, Lodhia D, Loew K, Logue J, Lombardi AL, Lopez E, Lorenzini M, Loriette V, Lormand M, Losurdo G, Lough J, Lubinski MJ, Lück H, Lundgren AP, Ma Y, Macdonald EP, MacDonald T, Machenschalk B, MacInnis M, Macleod DM, Magaña-Sandoval F, Magee R, Mageswaran M, Maglione C, Mailand K, Majorana E, Maksimovic I, Malvezzi V, Man N, Manca GM, Mandel I, Mandic V, Mangano V, Mangini NM, Mansell G, Mantovani M, Marchesoni F, Marion F, Márka S, Márka Z, Markosyan A, Maros E, Marque J, Martelli F, Martin IW, Martin RM, Martinelli L, Martynov D, Marx JN, Mason K, Masserot A, Massinger TJ, Matichard F, Matone L, Mavalvala N, May G, Mazumder N, Mazzolo G, McCarthy R, McClelland DE, McGuire SC, McIntyre G, McIver J, McLin K, Meacher D, Meadors GD, Mehmet M, Meidam J, Meinders M, Melatos A, Mendell G, Mercer RA, Meshkov S, Messenger C, Meyer MS, Meyers PM, Mezzani F, Miao H, Michel C, Mikhailov EE, Milano L, Miller J, Minenkov Y, Mingarelli CM, Mishra C, Mitra S, Mitrofanov VP, Mitselmakher G, Mittleman R, Moe B, Moggi A, Mohan M, Mohapatra SR, Moraru D, Moreno G, Morgado N, Morriss SR, Mossavi K, Mours B, Mow-Lowry CM, Mueller CL, Mueller G, Mukherjee S, Mullavey A, Munch J, Murphy D, Murray PG, Mytidis A, Nagy MF, Nardecchia I, Naticchioni L, Nayak RK, Necula V, Nelemans G, Neri I, Neri M, Newton G, Nguyen T, Nielsen AB, Nissanke S, Nitz AH, Nocera F, Nolting D, Normandin ME, Nuttall LK, Ochsner E, O'Dell J, Oelker E, Oh JJ, Oh SH, Ohme F, Omar S, Oppermann P, Oram R, O'Reilly B, Ortega W, O'Shaughnessy R, Osthelder C, Ottaway DJ, Ottens RS, Overmier H, Owen BJ, Padilla C, Pai A, Palashov O, Palomba C, Pan H, Pan Y, Pankow C, Paoletti F, Papa MA, Paris H, Pasqualetti A, Passaquieti R, Passuello D, Pedraza M, Pele A, Penn S, Perreca A, Phelps M, Pichot M, Pickenpack M, Piergiovanni F, Pierro V, Pinard L, Pinto IM, Pitkin M, Poeld J, Poggiani R, Poteomkin A, Powell J, Prasad J, Predoi V, Premachandra S, Prestegard T, Price LR, Prijatelj M, Privitera S, Prodi GA, Prokhorov L, Puncken O, Punturo M, Puppo P, Pürrer M, Qin J, Quetschke V, Quintero E, Quitzow-James R, Raab FJ, Rabeling DS, Rácz I, Radkins H, Raffai P, Raja S, Rajalakshmi G, Rakhmanov M, Ramet C, Ramirez K, Rapagnani P, Raymond V, Razzano M, Re V, Recchia S, Reed CM, Regimbau T, Reid S, Reitze DH, Reula O, Rhoades E, Ricci F, Riesen R, Riles K, Robertson NA, Robinet F, Rocchi A, Roddy SB, Rolland L, Rollins JG, Romano R, Romanov G, Romie JH, Rosińska D, Rowan S, Rüdiger A, Ruggi P, Ryan K, Salemi F, Sammut L, Sandberg V, Sanders JR, Sankar S, Sannibale V, Santiago-Prieto I, Saracco E, Sassolas B, Sathyaprakash BS, Saulson PR, Savage R, Scheuer J, Schilling R, Schilman M, Schmidt P, Schnabel R, Schofield RM, Schreiber E, Schuette D, Schutz BF, Scott J, Scott SM, Sellers D, Sengupta AS, Sentenac D, Sequino V, Sergeev A, Shaddock DA, Shah S, Shahriar MS, Shaltev M, Shao Z, Shapiro B, Shawhan P, Shoemaker DH, Sidery TL, Siellez K, Siemens X, Sigg D, Simakov D, Singer A, Singer L, Singh R, Sintes AM, Slagmolen BJ, Slutsky J, Smith JR, Smith MR, Smith RJ, Smith-Lefebvre ND, Son EJ, Sorazu B, Souradeep T, Staley A, Stebbins J, Steinke M, Steinlechner J, Steinlechner S, Stephens BC, Steplewski S, Stevenson S, Stone R, Stops D, Strain KA, Straniero N, Strigin S, Sturani R, Stuver AL, Summerscales TZ, Susmithan S, Sutton PJ, Swinkels B, Tacca M, Talukder D, Tanner DB, Tao J, Tarabrin SP, Taylor R, Tellez G, Thirugnanasambandam MP, Thomas M, Thomas P, Thorne KA, Thorne KS, Thrane E, Tiwari V, Tokmakov KV, Tomlinson C, Tonelli M, Torres CV, Torrie CI, Travasso F, Traylor G, Tse M, Tshilumba D, Tuennermann H, Ugolini D, Unnikrishnan CS, Urban AL, Usman SA, Vahlbruch H, Vajente G, Valdes G, Vallisneri M, van Beuzekom M, van den Brand JF, Van Den Broeck C, van der Sluys MV, van Heijningen J, van Veggel AA, Vass S, Vasúth M, Vaulin R, Vecchio A, Vedovato G, Veitch J, Veitch PJ, Venkateswara K, Verkindt D, Vetrano F, Viceré A, Vincent-Finley R, Vinet JY, Vitale S, Vo T, Vocca H, Vorvick C, Vousden WD, Vyachanin SP, Wade AR, Wade L, Wade M, Walker M, Wallace L, Walsh S, Wang M, Wang X, Ward RL, Was M, Weaver B, Wei LW, Weinert M, Weinstein AJ, Weiss R, Welborn T, Wen L, Wessels P, West M, Westphal T, Wette K, Whelan JT, White DJ, Whiting BF, Wiesner K, Wilkinson C, Williams K, Williams L, Williams R, Williams TD, Williamson AR, Willis JL, Willke B, Wimmer M, Winkler W, Wipf CC, Wiseman AG, Wittel H, Woan G, Wolovick N, Worden J, Wu Y, Yablon J, Yakushin I, Yam W, Yamamoto H, Yancey CC, Yang H, Yoshida S, Yvert M, Zadrożny A, Zanolin M, Zendri JP, Zhang F, Zhang L, Zhao C, Zhu H, Zhu XJ, Zucker ME, Zuraw S, Zweizig J, Aptekar RL, Atteia JL, Cline T, Connaughton V, Frederiks DD, Golenetskii SV, Hurley K, Krimm HA, Marisaldi M, Pal'shin VD, Palmer D, Svinkin DS, Terada Y, von Kienlin A.
PMID: 25032916
Phys Rev Lett. 2014 Jul 04;113(1):011102. doi: 10.1103/PhysRevLett.113.011102. Epub 2014 Jun 30.

We present the results of a search for gravitational waves associated with 223 γ-ray bursts (GRBs) detected by the InterPlanetary Network (IPN) in 2005-2010 during LIGO's fifth and sixth science runs and Virgo's first, second, and third science runs....

Perceptions of Behavioral Norms Related to HIV Transmission by People with HIV and by Residents of Their Communities.

Social influence

Miller CT, Bunn JY, Grover KW, Solomon SE.
PMID: 26167138
Soc Influ. 2014 Jan 01;9(1):1-19. doi: 10.1080/15534510.2012.712548.

We examined how people with HIV are both part of and apart from the communities in which they live. We compared perceptions of behavioral norms of 203 people with HIV living in 33 different communities with community-level normative perceptions...

Malate-Induced Hysteresis of Phosphoenolpyruvate Carboxylase from Crassula argentea.

Plant physiology

Ngam-Ek A, Seery TA, Amis EJ, Grover SD.
PMID: 16667161
Plant Physiol. 1989 Nov;91(3):954-60. doi: 10.1104/pp.91.3.954.

The hysteretic behavior of phosphoenolpyruvate (PEP) carboxylase from Crassula argentea has been investigated. Incubation of the purified enzyme with the inhibitor malate prior to starting the reaction by the addition of PEP resulted in a kinetic lag of several...

Disulfiram inhibition of the alternative respiratory pathway in plant mitochondria.

Plant physiology

Grover SD, Laties GG.
PMID: 16661923
Plant Physiol. 1981 Aug;68(2):393-400. doi: 10.1104/pp.68.2.393.

Disulfiram (tetraethylthiuram disulfide) was found to be a potent and selective inhibitor of the alternative respiratory path of plant mitochondria. The onset of inhibition by disulfiram takes several minutes and the inhibition is not readily reversed by washing, nor...

Echinocandins: A ray of hope in antifungal drug therapy.

Indian journal of pharmacology

Grover ND.
PMID: 20606829
Indian J Pharmacol. 2010 Feb;42(1):9-11. doi: 10.4103/0253-7613.62396.

Invasive fungal infections are on the rise. Amphotericin B and azole antifungals have been the mainstay of antifungal therapy so far. The high incidence of infusion related toxicity and nephrotoxicity with amphotericin B and the emergence of fluconazole resistant...

Constraints on Oscillation Parameters from ν_{e} Appearance and ν_{μ} Disappearance in NOvA.

Physical review letters

Adamson P, Aliaga L, Ambrose D, Anfimov N, Antoshkin A, Arrieta-Diaz E, Augsten K, Aurisano A, Backhouse C, Baird M, Bambah BA, Bays K, Behera B, Bending S, Bernstein R, Bhatnagar V, Bhuyan B, Bian J, Blackburn T, Bolshakova A, Bromberg C, Brown J, Brunetti G, Buchanan N, Butkevich A, Bychkov V, Campbell M, Catano-Mur E, Childress S, Choudhary BC, Chowdhury B, Coan TE, Coelho JAB, Colo M, Cooper J, Corwin L, Cremonesi L, Cronin-Hennessy D, Davies GS, Davies JP, Derwent PF, Dharmapalan R, Ding P, Djurcic Z, Dukes EC, Duyang H, Edayath S, Ehrlich R, Feldman GJ, Frank MJ, Gabrielyan M, Gallagher HR, Germani S, Ghosh T, Giri A, Gomes RA, Goodman MC, Grichine V, Group R, Grover D, Guo B, Habig A, Hartnell J, Hatcher R, Hatzikoutelis A, Heller K, Himmel A, Holin A, Hylen J, Jediny F, Judah M, Kafka GK, Kalra D, Kasahara SMS, Kasetti S, Keloth R, Kolupaeva L, Kotelnikov S, Kourbanis I, Kreymer A, Kumar A, Kurbanov S, Lang K, Lee WM, Lin S, Liu J, Lokajicek M, Lozier J, Luchuk S, Maan K, Magill S, Mann WA, Marshak ML, Matera K, Matveev V, Méndez DP, Messier MD, Meyer H, Miao T, Miller WH, Mishra SR, Mohanta R, Moren A, Mualem L, Muether M, Mufson S, Murphy R, Musser J, Nelson JK, Nichol R, Niner E, Norman A, Nosek T, Oksuzian Y, Olshevskiy A, Olson T, Paley J, Pandey P, Patterson RB, Pawloski G, Pershey D, Petrova O, Petti R, Phan-Budd S, Plunkett RK, Poling R, Potukuchi B, Principato C, Psihas F, Radovic A, Rameika RA, Rebel B, Reed B, Rocco D, Rojas P, Ryabov V, Sachdev K, Sail P, Samoylov O, Sanchez MC, Schroeter R, Sepulveda-Quiroz J, Shanahan P, Sheshukov A, Singh J, Singh J, Singh P, Singh V, Smolik J, Solomey N, Song E, Sousa A, Soustruznik K, Strait M, Suter L, Talaga RL, Tamsett MC, Tas P, Thayyullathil RB, Thomas J, Tian X, Tognini SC, Tripathi J, Tsaris A, Urheim J, Vahle P, Vasel J, Vinton L, Vold A, Vrba T, Wang B, Wetstein M, Whittington D, Wojcicki SG, Wolcott J, Yadav N, Yang S, Zalesak J, Zamorano B, Zwaska R.
PMID: 28644674
Phys Rev Lett. 2017 Jun 09;118(23):231801. doi: 10.1103/PhysRevLett.118.231801. Epub 2017 Jun 05.

Results are reported from an improved measurement of ν_{μ}→ν_{e} transitions by the NOvA experiment. Using an exposure equivalent to 6.05×10^{20} protons on target, 33 ν_{e} candidates are observed with a background of 8.2±0.8 (syst.). Combined with the latest NOvA...

New evolution of cone-beam computed tomography in dentistry: Combining digital technologies.

Imaging science in dentistry

Jain S, Choudhary K, Nagi R, Shukla S, Kaur N, Grover D.
PMID: 31583200
Imaging Sci Dent. 2019 Sep;49(3):179-190. doi: 10.5624/isd.2019.49.3.179. Epub 2019 Sep 24.

Panoramic radiographs and computed tomography (CT) play a paramount role in the accurate diagnosis, treatment planning, and prognostic evaluation of various complex dental pathologies. The advent of cone-beam computed tomography (CBCT) has revolutionized the practice of dentistry, and this...

Outcomes of a text message, Fitbit, and coaching intervention on physical activity maintenance among cancer survivors: a randomized control pilot trial.

Journal of cancer survivorship : research and practice

Gell NM, Grover KW, Savard L, Dittus K.
PMID: 31776849
J Cancer Surviv. 2020 Feb;14(1):80-88. doi: 10.1007/s11764-019-00831-4. Epub 2019 Nov 27.

PURPOSE: We aimed to determine the effect of a health coach, text message, and Fitbit intervention on moderate-to-vigorous physical activity (MVPA) maintenance in cancer survivors following a supervised exercise program compared to provision of a Fitbit alone.METHODS: Participants were...

Patient preferences pertaining to treatment options for drug-resistant focal epilepsy.

Epilepsy & behavior : E&B

Sinha SR, Yang JC, Wallace MJ, Grover K, Johnson FR, Reed SD.
PMID: 35016055
Epilepsy Behav. 2022 Jan 08;127:108529. doi: 10.1016/j.yebeh.2021.108529. Epub 2022 Jan 08.

OBJECTIVE: To determine patient acceptability of benefit-risk trade-offs in selecting treatment options for drug-resistant mesial temporal lobe epilepsy, including open brain surgery, laser ablation (laser interstitial thermal therapy [LITT]), and continued medications.METHODS: A discrete-choice experiment survey was developed, consisting...

Tales of a department: how the COVID-19 pandemic transformed Detroit's Henry Ford Hospital, Department of Neurology-part I: the surge.

BMJ neurology open

Ramadan AR, Alsrouji OK, Cerghet M, Chopp M, Danoun O, Grover KM, Ismail M, Katramados AM, Mohamed GA, Mehta CB, Newman DS, Osman G, Reuther J, Sallowm Y, Zaman IF, Barkley GL.
PMID: 33665616
BMJ Neurol Open. 2020 Jul 12;2(1):e000070. doi: 10.1136/bmjno-2020-000070. eCollection 2020.

The COVID-19 pandemic has reshaped the way healthcare systems operate around the world. The major hurdles faced have been availability of personal protective equipment, intensive care unit beds, ventilators, treatments and medical personnel. Detroit, Michigan has been an epidemic...

What is your diagnosis? Subcutaneous mass in a cat.

Veterinary clinical pathology

Whitman R, Sandoval K, Miller B, Groover J, Craft S, Beatty SSK.
PMID: 34374117
Vet Clin Pathol. 2021 Dec;50(4):621-623. doi: 10.1111/vcp.12931. Epub 2021 Aug 09.

No abstract available.

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